The Web of Life – Microbes


The little things are infinitely the most important. ~ Irish-Scottish physician and writer Arthur Conan Doyle

Dutch tradesman and amateur scientist Antonie van Leeuwenhoek (1632–1723) handcrafted microscopes as a hobby, raising the power of their magnification to a new level. This afforded him a vista of the miniature as never before. His curiosity had him peering at all sorts of organic samples; leading to his discovery of a diverse variety of microorganisms; what Leeuwenhoek termed animalcules, which made “pleasing and nimble” movements.

Among all the marvels that I have discovered in Nature, these little animals are the most marvelous of all. ~ Antonie van Leeuwenhoek

Leeuwenhoek wrote no books but starting in 1673 he began writing letters to the newly formed Royal Society of London, describing what he had seen with his microscopes. His first letter relayed his observations of bee stings. He kept writing for 50 years.

A microbe is an organism too tiny to be seen without a microscope: a microorganism. Microbes comprise a diverse variety of unicellular organisms, including virus, bacteria, archaea, fungi, protists, microscope plants (green algae), and animals such as plankton, planarian, and mites. While most microbes are prokaryotes, many are eukaryotes, including amoeba, which are generally considered unicellular.

The essential simplicity of microbes is largely an illusion. ~ English biologist Brian Ford


We live in a microbial world. ~ American microbiologist Carolyn Bohach

Whereas large life merely inhabits Earth, microbes collectively rule. Plants and animals would not exist without them.

Critical portions of the genomes employed by macroscopic life were contributed by microbes. The genetic unity of life owes to viruses, the busybodies of the microbial world.

A tiny minority of microbes are marauders. While vexatious, even lethal, these microscopic felons have been a formidable force in evolution. Immune systems, which are integral to health, developed to their consummate degree from wars with microbes.

Only microbes make their own food. Plants feed themselves by exploiting microbes as intracellular slaves.

Microbes manage the nitrogen cycle. Only they can fix nitrogen, and so sustain the life of plants.

Microbes degrade cellulose, providing the critical means for recycling dead plant tissue. Fields and forests thrive courtesy of microbes.

All animals rely upon microbes for sustenance. Gut flora eat first and feed their hosts leftovers. They even tell the host what they want to eat, and, being a good host, it obliges.


Microbes are everywhere; by far the most abundant and diverse life on the planet; at least 25 times the total biomass of all animal life. There are a trillion species of microbe, of which only a miniscule fraction is known.

Microbes are in the soil, the water, the air; practically everywhere. Their reach far exceeds all other life.

Microbes are plentiful 10 kilometers up in the air. Some make it to 32 km.

Frigid temperatures do not deter the littlest ones. Microbes thrive over 1/2 kilometer below Antarctic ice.

The abundance of microbes owes to their unceasing dedication to making more of the themselves. While macroscopic life spends much of its time and energy on other entertainments besides reproduction, most of the metabolic energy of microbes is spent making more microbes.

And they do so terribly quickly. A fresh little one pops out of a mommy microbe in a matter of minutes (on average, ~15 minutes; though some are significantly swifter).

Marine Microbes

Subseafloor microbes are some of the most common organisms on earth. There are more of them than there are stars or sand grains. ~ American microbiologist Karen Lloyd

Prokaryotes, especially archaea, are particularly plentiful in marine waters, posing as plankton. There are at least a million bacteria in a milliliter of seawater. They are most abundant in estuaries, such as the mouth of the Mississippi, where they break down organic matter to be recycled. By contrast, in coastal waters, viruses greatly outnumber bacteria (100 million per milliliter), with even higher concentration in the oceans (4×1030 per milliliter).

Moving through water is highly problematic when your size is measured in molecules. But in numbers there is power. So, like shoaling fish, marine microbes flock together to swim.

Flocks can move in a synchronised way over long length scales and several times faster than a single bacterium. ~ Swedish physical chemist Joakim Stenhammar

Marine microbes live all through the water column, flourishing in the deep trenches of the Pacific Ocean, at least as far as 11 km down.

On the seafloor, archaea and bacteria scavenge the marine snow proteins that descend from the deceased above. That is but the top layer of communities stratified through time. 90% of marine microbes are not in the water, but instead in the muck. Even 750 meters beneath the ocean live sediment microbes.

Benthic sediment slowly accumulates. It is seldom stirred, and so remains unaerated and unreplenished, becoming a nutrient and oxygen desert with the passage of millennia. Yet deep under the surface populations of microbes get by.

Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. ~ Danish aquatic microbiologist Hans Røy

The trick is to sip oxygen. The microbes in 1 cubic meter of sea floor sediment take 10 years to consume the amount of oxygen taken by an average person in a single breath. This parsimony allows microbes to live in marine mire deposited over 80 million years ago.

Some microorganisms can exist for millennia. They are metabolically active but in stasis, with less energy than we thought possible of supporting life. ~ Karen Lloyd

In the Soil

Each tonne of soil has 1016 microbes, give or take a billion. These down-and-dirty hordes keep busy breaking down organic material to generate essential nutrients for plants. Every year, nitrogen-fixing bacteria recycle some 130 million tonnes of atmospheric nitrogen back into the soil.

Damaged soil damages the larger environment. The intricate interlace of ecology cannot be over-esteemed.

Microbes remain abundant within the planetary crust over 5 kilometers down. Oil-bearing formations are home to microbes that deep, and specialists live even deeper.

Microbial communities have been found in hot water 3 kilometers beneath the North Sea bed. The current record for heat-tolerant bacteria comes from a South African gold mine: 3.5 kilometers down, at 115º C.


It’s a small world. Global wind circulation can move Earth’s smallest types of life to just about anywhere. ~ American biologist David Smith

The skies teem with microbial life. This is how microbes make a worldwide community.

6.4 million tonnes of aerosols cross the Pacific each year. Besides the dust and pollutants, over a tonne of microbes make the journey.

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The amount of ice in clouds affects their formation, rainfall, and lifetime. Ice in clouds originates with airborne ice-nucleating particles.

Salts thrown up from ocean spray and mineral dust from desert winds might do the trick. These inorganic bits are abundant in the skies. But they can’t seed ice crystals above –15 °C, which is the temperature inside half of the clouds that form over land. While airborne minerals and dust can create nuclei, organic aerosols are the common seed for aerial condensation.

Microbes in clouds are the nuclei around which water droplets, snow, and hail form. At least 30% of global precipitation stems from microbes. High concentrations of bacteria are at the core of hailstones. Hence, atmospheric microbial flows directly influence weather and climate.

Sea spray is one of the major sources of atmospheric particles, including those needed to form the ice for clouds. The ice-nucleating material is biogenic: loaded with diatoms, a common marine alga. Global cloud formation and precipitation patterns are greatly affected by microscopic populations of phytoplankton, which produce sea spray particles when they die. That process is accelerated by bacteria which eat living phytoplankton, releasing plankton body parts that affect cloud formation.

There is a connection between microbes in seawater and atmospheric sea spray. Chemical changes affect the reflectivity of marine clouds and have profound impacts on climate over a large portion of the planet. ~ American biochemist Kimberly Prather

Evaporation and condensation can be lickety-split on low-viscosity particles: less than a second. Conversely, condensation on high-viscosity aerosols can be quite slow, taking many hours for a particle to grow in size.

The rate of water condensation on organic aerosols can vary tremendously. Cloud droplet growth depends on the composition of the seed aerosol, especially viscosity.

Clouds produce precipitation when their droplets grow big enough to overcome atmospheric updrafts. Most of the time, falling involves freezing. Ice crystals can grow faster than liquid droplets, which means that ice stands a better chance of reaching critical mass before vanishing via evaporation.

Common bacteria can produce proteins that facilitate snowflake formation at a significantly warmer temperature than ice crystals can otherwise form. The task is not as simple as it might seem. Pure water in the atmosphere can stay liquid down to –40º C. Yet with will there is a way.

High-flying daredevils, microbes move through the atmosphere and prompt precipitation to recycle themselves to the surface. Scraggly salt and dust are no precipitation precipitators; no, indeed. Microbes make it rain.

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Rain or no, ~800 million viruses fall from the sky onto each square meter of Earth every day. The daily downing of airborne prokaryotes is comparable.

The upper troposphere is not just a travel route. It is a microbial habitat. While most bacteria form spores to hibernate at high altitude, some hardy microbial species enjoy the ride.

Microbes are more than high fliers. They are also down to earth, and getting about swimmingly well, by hitching rides on anything that moves. The global microbial community is further knit together with the able assistance of animals, which act as porters for miniscule stowaways. It’s nice to know that the oversized brutes are good for something.


Microbes indulge in a variety of social behaviors involving complex systems of cooperation, communication, and synchronization. ~ English microbiologist Stuart West et al

There are biological constants to behaviors. The struggle to survive is shouldered with similar strategies and evasions across the domains of life. Microbial sociality echoes through evolution to the organisms that arose from them. The complexities and contradictions that characterize the sociality of the most intelligent macrobes are apparent in microbes.


Exchange between microbes is a crucial process driving the development of microbial ecosystems. ~ American microbiologist Michael Mee et al

Like macroorganisms, microbes participate in various cooperative social behaviors, though the intimacy of their cooperative endeavors far exceeds those of their larger successors.

Specific environmental cues may elicit cross-species coordination of gene expression among diverse microbial groups, potentially enabling multispecies coupling of metabolic activity. ~ Elizabeth Ottesen

Microbial group or colonial cooperation involves communications and willful exchanges that radically transform the lives of community members. Distinct microbe populations share nutrients and genes to keep microbial society as healthy and robust as possible.

The fitness of microorganisms can depend on cooperation between cells. ~ English microbiologist Ben Raymond et al

Microbes cooperate to better exploit resources, resist stressful environments, protect themselves and their territory against other microbes, and to wage war.

Microbes evolved multiple mechanisms for enforcing cooperation, by performing differential actions to others (i.e., rewarding cooperators and/or penalizing cheaters) according to kinship (i.e., genome-wide relatedness) or kind (i.e., phenotypic similarity caused by genetic relatedness at certain loci). Much discrimination in microbes appears to be based on kind rather than kin. ~ American plant pathologist Louise Glass et al


Multicellular communities of single-celled organisms attached to a surface are the predominant form of life on Earth. Development of these biofilms involves distinct stages of self-organization, starting with a single cell that senses and approaches a surface. ~ Swedish microbiologist Ute Römling

Microbes have been living together in biofilms for billions of years. This is how they have founded almost all of Earth’s ecosystems: as colonies, creating stable communities that share nutrients and other essentials.

Biofilms are often cooperative associations among several groups: bacteria, fungi, algae, protozoa, as well as their oversized descendants: plants and animals. Such colonies are capable of collated perception, distributed information processing, and collective gene regulation – essentially, transforming into a superorganism.

A quorum for biofilm creation begins with a chemical effusion among a population that signals congressional intent. Many bacteria have 2 or more quorum-sensing systems. This lets them know the nature of the engagement, which helps optimize group integration.

Chemical communication among bacteria involves complex interconnected regulatory networks that serve to fine-tune the expression of diverse group behaviors. ~ American microbiologist Michiko Taga & American molecular biologist Bonnie Bassler

The first step to colonization is adhering to a suitable surface. This is initially done via reversible van der Waals forces.

A firmer anchor is had by cell adhesion structures, such as pili: tiny fibrous appendages on bacteria that get a grip. A different type of pili – conjugative pili – is used by bacteria during conjugation, now better known as horizontal gene transfer (HGT).

HGT was identified in 1946, when American molecular biologist Josua Lederberg and American geneticist Edward Tatum found that the intestinal bacterium E. coli engaged in a process resembling sex to exchange circular gene-bearing plasmids – whence the term conjugation.

The decision to form a biofilm changes genetic expression among those involved, invoking a network of protein interactions different from those of solitary life.

As a biofilm evolves, it builds and adapts to its surroundings. The earliest colonists create microhabitats and contribute food, serving as a welcoming matrix for other microbes to attach and grow into a gleaming film, forming cosmopolitan communities.

The most successful colonies are thick microbial mats with dozens of dynamic interactive layers. Life is good.

Biofilms are highly resilient. They produce protective enzymes that coat the outer surface.

This has an element of altruism, as fitter bacteria help protect their weaker fellows. This fortifies the colony, which is much tougher than any individual ever could be.

Biofilms comprise members optimally juxtaposed. Individuals are invariably at different stages of their life cycle.

Many colonists may be killed by an antibacterial agent, such as penicillin, which attacks replicating cells. They become nutrition for those that survive by virtue of being inactive during the onslaught.

Bacteria within communities interact to organize their behavior. ~ Chinese microbiologist Jintao Liu et al

Diverse species of microbes communicate with each other and even feed each other. Interdependence and symbiosis take various forms.

Chlorobium aggregatum is a consortium of 2 bacteria species that feed each other. Peripheral bacteria oxidize sulfide into sulfate via a photosynthetic process. A central anaerobic heterotroph reduces the sulfate to sulfide. Consortium life is economical because it reduces reliance on the environment for crucial nutrients.

When a biofilm reaches a threshold size, it suddenly begins to oscillate in its growth pattern. These oscillations resolve inherent group conflict.

Bacteria on the outside of the biofilm are most vulnerable to chemical and antibiotic attacks. At the same time, they provide protection for interior community members. But outer bacteria are closest to the nutrients needed for growth. If outer cells grow unchecked, they will consume all the food, and starve the sheltered interior cells.

To gain equity, interior colony members produce a metabolite necessary for growth of the outside bacteria. This lets the inner cells periodically brake consumption by the outer members. By creating a rhythm of sharing throughout the colony, biofilms stay robust.

Cells that reside within a community cooperate and compete with each other for resources. This conflict between protection and starvation is resolved through emergence of long-range metabolic co-dependence between peripheral and interior cells. Collective oscillation in biofilm growth benefits the community. Oscillations support population-level conflict resolution by coordinating competing metabolic demands in space and time. ~ American microbiologist Gürol Süel et al

Coordination becomes especially important when facing food shortages. When bacteria populations discern that nutrient supply is dwindling, they cooperatively respond to optimize consumption. Rather than trying to hog what is left, as humans would be prone to do, bacterial communities take turns.

Time-sharing enables biofilms to counterintuitively increase growth under reduced nutrient supply. Distant biofilms coordinate their behavior to resolve nutrient competition through time-sharing. ~ Jintao Liu et al

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Dental plaque is a biofilm. The plaque comprises bacteria embedded in an amorphous matrix secreted and shared by the colony. The matrix sticks to the teeth, hewing to its homestead to survive.

Such aggregation is a common technique for hanging together on a surface. Microbial communities reside on rocks, vegetation, and in the soil as adhesive aggregates.

Biofilms are a profoundly important force in the development of ecosystems, both aquatic and terrestrial. In sediment and bedrock, biofilms are essential in recycling elements and forming soils.

A microbe in water is a different creature than when in a biofilm. A biofilm becomes its own habitat, with different gradients of oxygen, pH, nutrient concentration, and other aspects. Biofilms have a wide variety of structures, some quite complex.


Quorum-sensing (QS) is the term for decision-making in decentralized groups to coordinate behavior.

Microbial quorum-sensing occurs at the molecular level via chemical signal exchanges. Using a common language, different species of bacteria employ quorum-sensing to synchronize their activities. Further, bacteria coordinate their gene expression via QS. In effect, via quorum-sensing, single-cell microbes behave as a multicellular organism.

Bacteria commonly live in high-density populations, making them prone to viral predation. Using QS, they coordinate their responses to infection. Like highly evolved eukaryotes, bacteria have adaptive immune systems.

The language that invokes biofilms, and subsequent quorum-sensing, is common to more than bacteria. Eukaryotic cells respond to QS signaling. Human white blood cells can be induced to change their behavior by receiving QS signals.

QS is used to coordinate the switching on of social behaviors at high densities, when such behaviors are more efficient, and will provide the greatest benefit. ~ English molecular biologist Sophie Darch et al

For microbes, the density of group populations must be high enough for QS to be effective in coordinating activities. Until population density reaches a recognized threshold, QS is a monitoring mechanism. Biofilms facilitate productive quorum-sensing.

Quorum-sensing is genetically conserved throughout life. Viruses employ quorum-sensing to strategically infect. Social insects use quorum-sensing to make collective decisions, such as where to forage or nest, as do schools of fish when feeding or evading predators.


In evolutionary terms, selfishness got an early start. Cheating is common in ostensibly cooperative microbe colonies.

Prymnesium parvum are a golden algae species that live in the oceans and in freshwater. When nutrients are abundant, they merrily photosynthesize.

But when enough nitrogen and phosphorus are not available, P. parvum get ugly. They hunt by producing a toxin – prymnesin – that kills aquatic organisms, including fish. They carnivorously feast on other algae.

To produce sufficient effect, P. parvum cooperate in their poisonous predation; at least most do. There are invariably cheaters which benefit from the toxic exertions of others without troubling themselves to produce venom.

The level of cheating depends upon how related the participating population is. The less related, the more cheating.

Quorum-sensing is used by colonial bacteria to coordinate and monitor public goods production, and to discover and check cheaters in the population. Cooperative members sometimes solve this public goods dilemma by the producers confining their work products to themselves, thereby denying access to cheats.


Coordination confers considerable advantages at the molecular level. Bacteria often get their nutrients from complex polymers which must be broken down.

The necessary enzymatic action can only be achieved by concerted secretion of enzymes, which requires coordination. Microbe survival is often interdependence in action.

Pathogenic behavior, affording prey cell adhesion or invasion, is expressed by virulence factors: proteins or other synthesized molecules secreted via enzymatic activity. These proteins are coded by genes which may come from DNA in the cell, bacteriophage DNA, or plasmids acquired from others.

If only a few pathogenic cells secreted a certain virulence factor, such small concentrations would be unlikely to achieve the intended effect, but may well alert the host, who would dispose the impudent few.

Quorum-sensing allows pathogens to succeed. Biofilms are less susceptible to host defense systems than less clustered microbes.


Cellulomonas and Azotobacter are 2 bacteria with a synergistic relationship. Cellulomonas breaks down the cellulose left by dead plants, releasing glucose. The glucose feeds Azotobacter, which fixes atmospheric nitrogen into ammonium, which helps fill the metabolic needs of Cellulomonas.

Not all synergisms are so innocent. Dental caries, gum disease, and gas gangrene are infections caused by bacteria interacting synergistically.

Real estate is a cutthroat business. Microbes contend for the best patch of habitat by secreting substances that kill or inhibit competitors. Producing antibiotics as an inhibitor – antibiosis – is a form of antagonism practiced by many bacteria and fungi. Penicillin is exemplary.


Microbial populations wage war against each other, even a population of the same species. Microbes use a myriad of antibiotics to defend their territory or invade established communities.

There is considerable genetic diversity among individuals, even in communities of the same species. One study found that a bacterial population averaged only 72% similarity in genetic makeup.

The reason for this is the ease with which microbes can pick up and incorporate new genetic material. (The genes for antibiotic resistance are a popular product with bacteria under duress, and often readily available.) Microbes individually decide what they need, and what they are willing to share.

Coexistence is maintained by cooperation. Above a certain threshold of genetic dissimilarity, antagonistic interactions increase sharply. Microbes are tribal.

Biofilms illustrate bacterial clannishness. Bacteria create biofilms when stressed. Sometimes that stress comes from microbial competitors chewing through the food supply. Related bacteria congregate into a biofilm and produce antibiotics to rout their rivals.


Despite tribal antagonisms, microbes are generally gregarious, and broad-minded about it. Their cooperation commonly extends to mutualist associations with many other species.

 Teamwork in the Rhizosphere

Both bacteria and microscopic fungi need to be mobile to survive and thrive, including ones that live in the rhizosphere: the narrow area of soil that is directly influenced by plant root secretions. The 2 team up to get around. Fungal spores attach themselves to bacteria to hitch a ride, or bacteria entrap spores and wrap them in their flagella, then carry them along. (Soil outside the rhizosphere is called bulk soil.)

Paenibacillus vortex is exemplary. These bacteria will even recover fungal spores from a life-threatening locale, moving them to a new home where they can germinate and start new colonies.

The payback comes when a bacterium hits an air pocket canyon too large to cross. The bacterium releases its spores, allowing the fungi to germinate into a colony that spans the gap. The bacterium then strolls over the bridge made by the fungi’s mycelia (the branch-like weave that grows from the spores).


Plants interact with a multitude of beneficial bacteria who call their rooted host home. When pathogens threaten, homebody microbes pitch in to protect the plant, producing phytohormones that help keep plant tissue healthy.

A phytohormone is a plant hormone. Hormones in plants and animals are signaling molecules that regulate physiology and behavior.

Symbiosis among microbial species evolved to optimize the special skills that each species can contribute. Housing in larger hosts means a decent living, the company of fellows, and an upscale long-term residence.

Microbial associations may be beneficial, commensal, or pathogenic. Relationships vary between a microbe and its host by species, or even by population. Normally genteel microbes can turn nasty if their environment deteriorates.

Sometimes residence is a means to an end. Some microbes use plants as a way station on their way to infecting insects and other animals that visit or prey upon the plants. The easiest way to consumer is through producers.

Biofilms associated with plant roots promote a mutual exchange of nutrients. Biofilms form the microbiome of all animals, assisting in almost all facets of living.


The distribution of microorganisms in and on the human body reflects adaptations to life on land which were made about 400 million years ago. Terrestrial vertebrates developed skin, lungs, internal fertilization, and protective membranes around the embryo. The skin became relatively impermeable, and mucous membranes were confined to protected sites. Because microorganisms generally thrive only in moist environments, these adaptations to a mostly dry environment have shaped the abundance, location and phenotypes of human-associated microorganisms and have limited the exchange of microorganisms between individuals. ~ American microbiologist David Relman

The microbiome is the microbial ecological community that comprises every multicellular eukaryote. A wide variety of bacteria, archaea, and fungi make their living in and on a larger host.

Most of the cells in a human body are microbiota. Microbes inhabit every part of a plant, including flowers.

(Guesses about the ratio of microbial to human body cells has varied from 10 times as many to rough equivalence between the two. “The story of the 10-to-1 ratio has all the characteristics of an academic urban legend,” said Norwegian sociologist Ole Rekdal. Most estimates grant microbes numerical superiority. Further, almost all appraisals try to account only for bacteria, failing to consider fungi, protists, and viruses (which likely sizably outnumber bacteria). The “resident alien” to host cell ratio is simply not known, even approximately.)

Microbiota play critical roles in the lives of every plant and animal. Microbiotic bacteria are known to keep the biorhythmic clock for bioluminescent squid. The daily internal clocks of mammals may as well be set by microbiota.

Circadian clocks are so important that they evolved early on. Single-celled cyanobacteria keep a 10-nanometer diameter protein that acts as a pocket watch. This protein maintains time of day in a noisy environment and remains accurate regardless of temperature.

For diverse animals, including iguanas, squids, and many insects, behavior plays a central role in the establishment and regulation of microbial associations. Once host-microbe associations are established, microbes can influence host behavior in ways that have far-reaching implications for host ecology and evolution. ~ American ethologist Vanessa Ezenwa

The quality of the microbiome is a major factor in the quality of life for its host. From the earliest stage of life, microbiota provide genetic guidance to proper development in animals. Some animals, such as the green iguana, tailor their microbiome at different stages of their lives.

A sponge is about as simple as an animal can be. Yet sponges have complex microbiomes.

Coral polyps are teeming with microbes that symbiotically scavenge for nutrients, remove wastes, and perform other tasks necessary for coral to survive.

Early in an animal’s life, microbes prime the immune system against their nefarious cousins. Symbionts continually regulate their host’s immune system, and they fight for their host when infected.

When microbiota are not transferred to offspring, innate behaviors direct younglings to acquire their own. Bees and other social creatures get their microbes from their nest mates: often by direct contact, but sometimes by feeding on feces.

The kudzu bug is born without symbionts. It acquires its microbiome from capsules left by its mother, instinctively searching for them if they are not apparent.

Microbiota not only affect physical health, they influence mental sense of well-being. This effect cannot be explained purely physiologically: some field energy must be involved.

The microbiome influences behavior in many ways. A female fruit fly strongly prefers mating with a male reared on the same diet, and so with similar microbial symbionts.

 Gut Flora

Most people just focus on bacteria, but there are also viruses and even fungi. It’s the interaction between all of these things and the host gut that is really important. ~ Dutch virologist Bas Dutilh

On their own, animals are only able to digest simple sugars. Gut microbes predigest practically everything an animal eats, providing their host with absorbable sustenance via fermentation.

Besides digestion, gut flora have an ongoing cooperative relationship with host cells. Gut microbes communicate with host cells, influencing their activity and food choice.

The intestine has to allow for digestion and absorption of dietary nutrients while also carefully harboring and managing the teeming microbial community within. Access to genes is determined by the host, but usage of particular genes is regulated by the microbes. ~ American molecular geneticist John Rawls


Ruminants, such as cows, house a vast fermentation chamber in the foregut: the rumen. Horses, elephants, and rabbits divert the roughage into the hindgut (cecum) for the same purpose.

A variety of microbes dine in a rumen, which is the 1st chamber in the 4-chamber complex stomach of cud-chewing herbivores. The animals themselves produce no enzymes to break down the cellulose in the grasses that are the mainstay of their diet.

But the microbial population does. Roughage is broken down in stages, during which the animal regurgitates and chews partially digested food (cud), periodically burping methane produced by the hard-working microbes within.

Rumen microbes feed their host via fermentation. After initially hydrolyzing cellulose to glucose, they ferment the glucose into organic acids that serve as their host’s primary nutrient.


A major portion of animal stool comprises the last meal that microbes shared with their host. While handling the host meal satisfyingly consumed the lives of many gut flora, others are headed out on a group vacation.

Flatworms See the Light

Symsagittifera roscoffensis is a small marine flatworm. During its early development, a certain green alga – Tetraselmis convolutae – invades the worm’s tissues, stimulating a dramatic physiological conversion: losing the ability to feed independently.

The algae embed themselves near the surface of the worm’s transparent body, finding optimal spots to catch sunlight. Via photosynthesis, alga feed the worm oxygen and sugar while the worm provides nitrogen and a comfortable home. The worm’s behavior is altered by such intimate integration, as it prefers sunny locations on the beach to optimize photosynthetic opportunities for its cohort.


The optimum temperature for cell growth is related to the temperature stability of critical macromolecules, such as nucleic acids and proteins, and to how temperature variations affect enzymatic actions necessary to synthesize new cells. Most cell types and organisms are mesophiles: suited to 25–45 °C.

Multicellular animals and plants cannot tolerate an ambient temperature exceeding 50 °C. Above that, only microbes can thrive.

A number of bacteria are happy in hot water, at 85 °C, and some even grow in boiling water, as hot as 100 °C. These high-temperature-tolerant microbes are thermophiles. The distinctive feature of thermophiles is that their enzymes remain stable at high temperatures.

Enzymes commonly become sluggish when it gets cold. But psychrophilic microbes like the chill. (Psychros is the Greek word for “cold.”)

Microbes are alive and well at the poles, in regions permanently frozen, and at near-freezing ocean depths: 0–2 °C. The algae Phormidium frigidum call the bottom of ice-covered lakes in Antarctica home.

Lousy cellular osmotic pressure is a killer. To stay alive, cell walls exchange gases and fluids for energy intake and waste disposal.

If the internal pressure inside a cell is too low, water will seep in, causing swelling, until the cell bloats to death by bursting. Conversely, dehydration results if water can’t get in because osmotic pressure is too high.

Because of this, most microbes make a living in locations with low concentrations of salts and nutrient molecules. Whence the practice of preserving foods by salting or adding copious amounts of sugar.

Some microbes can take the pressure: osmophiles. There are microbial communities at the bottom of the Mariana Trench: 11 kilometers down; the deepest seafloor on Earth. The pressure there is 1,000 times that of sea level.

Some microbes like salt. Halophiles (halos is Greek for salt) require a salty home, needing at least at a 10% salt concentration, with some archaea tolerating up to 37%. There are both archaea and bacterial halophiles.

The Dead Sea in Israel is too salty for fish, and long thought devoid of all life, but haloarchaea love it there. If one finds itself in a liquid less than 10% salt, it disintegrates, as its cell wall falls apart.

Deep Lake in Antarctica is so salty that it stays liquid at minus 20 °C, remaining ice-free throughout the year. In the frigid salt sludge thrive 4 dominant genera of archaea that maintain their distinctiveness while sharing genes among themselves. These 4 comprise 72% of the population in this low-diversity lake ecosystem.

Liberating hydrogen atoms in solution can be a serious problem. Few life forms tolerate the acidic environment that results. Most microbes prefer a pH of 6 to 8 and cannot stand pH as low as 3 or 4. Acidification is the basis for pickling food to preserve it.

Acidophiles can easily take 1.5 pH. The archaeon Picrophilus oshimae grows best at 0.7 pH. Acidophiles maintain an internal pH of 6–7 by constantly pumping out hydrogen ions from their cell envelopes.

Thermoacidophiles prosper at scorching temperature and low pH. The archaeon Thermoplasma acidophilum lives in self-heating coal refuse piles and other such nasty places.

At the other end of the pH scale, some microbes keep the best life sign when the situation is highly alkaline. Alkaliphilic photosynthetic bacteria inhabit alkaline soda lakes in East Africa that have a pH of 11.

 Hot Clams

Hydrothermal sea vents are literally a hot spot for life. Giant clams and tube worms live there, as do methane-eating microbes (methanotrophs), as well as bacteria that subsist on carbon dioxide (CO2), and get energy by respiring hydrogen sulfide (H2S).

Food service for the worms and clams is slim to none. So how does a giant clam become a giant? Endosymbiotic bacteria live inside the animal’s tissue cells let the clam live large. CO2, H2S, and O2 are absorbed by the animals and transported to the tissues where the endosymbiotic bacteria flourish and furnish needed organic compounds to its host’s cells.

Another oddity is that H2S is typically toxic to tissues, as it interferes with bioenergetic metabolism. The bacteria also must be immune to sulfide poisoning. These adaptations are not yet fully understood.


Microbes live everywhere that life can exist: the poles, deserts, geysers, rocks, at the bottom of the ocean, and at least as deep as 7 kilometers below the Earth’s surface. Extremophiles can survive in a vacuum and are highly resistant to radiation. Microbes may even be space travelers.

The various mechanisms and adaptations that allowed life to thrive at every extreme on this planet, almost beyond the imagination, indicate that a vast diversity of life throughout the universe is likely the norm, and quite like the microbes on Earth.


Archaea were long thought kissing cousins to bacteria, as they look like them, though weirdly so. Both are “primitive” prokaryotes, with selfsame structure and function. Many have similar lifestyles.

Looks are deceiving. RNA analysis revealed archaea more closely related to eukaryotes and only a distant relation to bacteria. That makes sense because eukaryotes arose from archaeal origin: archaea incorporated bacteria that begat eukaryotic cells. Such evolutionary endosymbiosis transpired numerous times, begetting a variety of eukaryotic life.

Archaeans exist everywhere that life can survive. They are an extremely robust and versatile life form, with both extremophiles and ubiquity in their favor.

Archaea are so prevalent as to play roles in the carbon and nitrogen cycles. All told, archaea account for 10–20% of Earth’s biomass. That’s particularly impressive when considering that the average archaean is 1 micrometer (µm; one-millionth of a meter) tiny, and the largest is 15 µm. A human hair is 100 µm thick.

Archaea may be autotrophic, heterotrophic, or saprotrophic. Autotrophic archaea eat photons: phototrophs. Photosynthesis is a more evolved process.

Some archaea are lithotrophs: consuming inorganic substrates, such as ammonia, hydrogen sulfide, and sulfur. Many lithotrophs are extremophiles. Nothing beats a hot sulfur Sunday to a Sulfolobus, a thermoacidophile which lives in hot springs and hydrothermal vents, where the water is as acidic as stomach acid (pH = 2–3) and near boiling.

Other archaea gas themselves up with methane (methanotrophs), nitrogen (nitrifiers), or carbon dioxide. Some archaea outgas what others eat. Methanogens – methane makers – are carbon dioxide consumers that exude methane waste.

Archaean saprovores play an essential role in decomposition and recycling organic nutrients. This is an analogous role to the stone eaters that convert inorganic materials into energy. Lithotrophs introduce new material into the food web, while saprotrophs reintroduce.

The diversity of archaeal lifestyles highlights that they represent a catchall empire of wildly successful organisms. Their classification remains controversial because they defy the typical methods of categorization, such as by reproduction style, as all archaeans are asexual.

While bacteria can be classified to some degree by shape, archaea tend to be pleomorphic: able to alter shape in response to environmental conditions. There are also shape-shifting bacteria.

Deinococcus is an extremophilic bacterium that is pleomorphic. It is also one of the most radioresistant (radiation-resistant) organisms known, as well as being able to survive dehydration, cold, vacuum, and acid. Its extreme reluctance to die earned it a listing in The Guinness Book Of World Records as the world’s toughest bacterium.

Categorizing by differences in genomes is thwarted by archaeal facility with horizontal gene transfer: otherwise similar archaea creating genomes that are not closely related. In many ways, archaeal versatility defies their easy classification.

More than any other domain, archaeal ubiquity and adaptive fluidity emphasize that the potentiality of life’s manifestations is nearly unlimited. Archaea exclaim that life is bound to arise whenever and wherever inorganic resources and environmental stability exceed a minimal threshold.

Social to a fault, archaea are commonly mutualists or commensals. No archaeal pathogens or parasites are known. Archaea are the most moral organisms.


Really, they’re just stripped-down versions of us. ~ Bonnie Bassler

Along with archaea, bacteria have been on Earth 3.5 billion years. In that time, members of these 2 domains adapted to every place where life could possibly survive.

In the late 1970s, bacteriologists estimated 10,000 to 20,000 species of bacteria. Greater awareness has upped the species count to somewhere between 10 million and 1 billion. Even the latter may be an underestimate, depending on how you’d like to splice speciation.

By weight, 80–90% of Earth’s biomass is bacterial. Bacteria make up nearly 2/3rds of all biodiversity on Earth. Their enduring success owes to numerous facets, beginning with the fact that they reproduce with an efficiency as close to the limits of physics as practically possible.

One can only underestimate the little ones once derided as “germs.” New discoveries continue to enlighten as to the sophistication of bacteria.

Despite their small size and relative simplicity, bacterial cells appear to possess a robust and complex level of subcellular organization, both spatially and temporally, that was once thought to only exist in more complex organisms. ~ American microbiologist and physicist Nathan Kuwada


Bacteria are often exposed to harsh environmental conditions; so they wear a coat. Glycocalyx is a polysaccharide matrix, sometimes interlaced with various proteins and lipids, that forms a coating on the surface of bacteria, right outside the cell wall.

This coat can alternately act as a slime or an adherent. As a slime layer, glycocalyx protects from dehydration and nutrient loss. In a biofilm, glycocalyx can act as a formidable glue. How bacteria control their glycocalyx characteristics is not known.

Glycocalyx also appears on epithelia and other eukaryotic cells; a bacterial innovation that has worn well through evolutionary time.

In multicellular organisms, glycocalyx acts as an ID badge that the body uses to distinguish between its own healthy cells and unwelcome tissue, including invaders. Only identical twins have chemically identical glycocalices. The glycocalyx of everyone else is unique.


Most bacteria are 1–4 µm long; their details visible only by an electron microscope. Beyond the norm, the size range of bacteria is considerable.

Prochlorococcus is a tiny thing: 0.6 µm, one of the smallest photosynthetic bacteria, and one of the most numerous. There are 100,000 Prochlorococcus in a single drop of seawater. Prochlorococcus exhales at least 50% of the oxygen in Earth’s atmosphere.

The smallest bacterium, Mycoplasma, is 0.1 µm. (Mycoplasma bacteria are typically saprotrophic or parasitic. Because they lack a cell wall, these bacteria are immune to common antibiotics. Several species of Mycoplasma are human pathogens, including one that causes walking pneumonia.) At the other extreme, a bacterium in the mud of a seabed off the coast of Namibia measures up to 0.75 millimeters, and so not even a microbe, as it is visible to the naked eye.

Bacteria come in a variety of shapes. Bacteria may be a ball, a rod, a box, a corkscrew, or a star. Bacteria are classified in 1 of 2 ways: by shape, or by how they react to Gram staining.

Gram staining dyes bacteria to test the thickness of their cell wall. (A detailed explaining of Gram staining is in the glossary.) Ones with a thick cell wall are Gram-positive, while thin-walled bacteria are Gram-negative.

Bacteria are categorized by their 3 different shapes: cocci, bacilli, and spirilla. Cocci (singular: coccus) are spherical. Bacilli (singular: bacillus) are rod-shaped. Spirilla (singular: spirillum) have a curved or spirally twisted body.

Bacteria shape and mode of locomotion are related. Bacterial propulsion varies from body wiggles to flagella to ionic rotors.


In dealing with bacteria as pathogens, medical science has termed subspecies of bacteria by strain and type. A strain (variety) of bacteria is a culture from a single parent, but which differs from other bacterial cultures of the same species by structure or metabolism. A type of bacteria is a subspecies that varies in immunities (serotype), susceptibility to viruses (phage type), or pathogenic properties (pathotype).


Bacteria possess highly developed sensory systems for the detection of nutrients, energy sources, and toxins, and the capacity to store and evaluate the manifold information provided by these diverse receptors. The final outcome of this sensory integration is the decision to continue swimming in the same direction or tumble into a different course. Thus, some of the most fundamental features of brains, such as sensory integration, memory, decision-making, and the control of behavior, can all be found in these simple organisms. ~ American neuroscientist John Morgan Allman

Bacteria are responsive to light (sight), have a sense of contact (touch), respond to chemicals through direct contact (taste) and through the air (smell).

Bacteria can sense up to some 50 different chemicals using proteins embedded in the outer membrane. A further network of some 12–14 proteins are involved in the interpretation and transduction of the signals to control swimming direction. ~ Anthony Trewavas

Meningococcus is the bacterium that causes meningitis. It uses 3 different temperature-sensing RNA molecules to watch for rising host temperature, which indicates an inflammation-activated immune response. This lets meningococcus anticipate and coordinate its processes to evade this immune system reaction.

Magnetospirillum, a freshwater and sediment dweller, has an uncommon fondness for ionic iron, which it ingests, enabling it to respond to magnetic fields. Magnetospirillum is but one of numerous magnetically sensitive bacteria.

 Magnetotactic Microbes

Magnetotactic microbes know their way around via Earth’s magnetic fields. Magnetotactic bacteria behave as bar magnets because they have magnetite in their cells, if there is enough iron in the water. With low iron levels, the bacteria still grow, but do not make magnetite particles, and so are not magnet microbes.

These bacteria are typically found in or near mud, such as bogs and marshes. Magnetotactic microbes use their innate compass to find their way to the best mud bath.

Magnetotactic bacteria are just the lowercase of the compass crowd. Honeybees, butterflies, birds, turtles, and dolphins are known to have magnetite in their brains for use as a navigational guide. Many other animals are sensitive to magnetic fields; how so is often not known.


Biological organisms use a myriad of signaling pathways to monitor the environment and adjust their genetic programs in accordance with environmental changes. ~ American microbiologist Terence Hwa et al

Bacteria pay close attention to what is going on in their environment, including listening to the communiqués of other microbial species. 2 gut microbes illustrate.

When under duress, E. coli secrete indole: a signaling molecule that renders them more tolerant of antibiotics. Salmonella, which is source of food poisoning, cannot produce indole, but they understand its context.

Once forewarned, Salmonella prepare themselves for hard times. One stratagem Salmonella use is to hide inside gut tissue until the toxins wane.

More virulent strains of Salmonella appear more adept at cheating death at the hands of antibiotics. These battle-hardened bacteria are then able repopulate and wreck even more havoc. Salmonella constantly monitor their surroundings and adjust their lifestyle accordingly.

This bug is clever in adapting to its environment. During infection, it lives in hostile environments, and can use multiple approaches to adjust its functions. ~ American molecular biologist Joshua Adkins

The infection process involves hundreds of genes and proteins, both for an infectious bacterium and the host. Pathogens sense their host and adeptly tailor their gene expression to exploit their situation.

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Many pathogenic bacteria enter their animal host by being eaten. Once inside, what the bacteria encounter is a brutal environment. These microbes must avoid detection by the immune system and successfully compete with resident bacteria who will fight to protect their turf.

The invaders evolved technological tools to get the job done. On their exterior is a syringe with which a bacterium anchors itself to a host cell. The pathogen then injects its target with clever proteins that dampen the cell’s immune response.

Once pacified, the host cell is primed for victimhood. The pathogen inserts a tiny straw that it adroitly uses to selectively suck nutritious molecules out of the cell without inflicting collateral damage. After all, the goal is to make a living and keep the fuel supply in good working order.

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Bacteria remember their viral invaders by sampling short DNA sequences. ~ Israeli microbiologists Ido Yosef & Udi Qimron

Bacteria are themselves subject to infection by viruses (bacteriophages). Those that survive a viral attack remember the encounter by taking genic sequences from the virus which can reliably serve as a viral identifier. These sequences are then integrated into a bacterium’s own DNA. These analyzed genetic bits act as the physical correlate for immune system memory which is energetically based in a bacterium’s mind.

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Bacteria can slow their metabolism when facing starvation or other stress. In this phase, bacteria are resistant to external disruptions, such as antimicrobial agents. They may also engage in experimental self-evolution via genetic manipulations.

Spores obtain a stable memory of the growth and gene expression history of their progenitor cells, which influences their future. ~ German bacteriologist Ilka Bischofs

When bacteria sporulate they instill a memory which tells the spores when they should revive. In going dormant, bacteria try to foretell the future. They can either make many spores that resuscitate only in a nutrient-rich environment, or fewer but more robust spores that can revive in leaner environments. Spore memory provides the means to improve adaptation to ecological niches.

Bacteria can build shelters in which to hibernate until conditions improve. When facing desiccation in saltwater, E. coli bacteria manipulate salt crystallization to create a complex 3d shelter in which they can hibernate. They revive with rehydration, which happens when their salt cave melts.

Bacteria possess self-identification and can recognize their own kind. Sense of self is essential for boundary formation in a colony, such as a biofilm.

Boundaries form between colonies of different strains, but not between colonies of a single strain. A fundamental requirement for boundary formation is the ability to discriminate between self and nonself. ~ American microbiologist Karine Gibbs et al

Individually and as a colony, bacteria make rational investment decisions regarding growth and migration given available resources and stresses found in the local environment. Bacteria exhibit intelligence in their choices.

Using cell-to-cell communication, colonies of billions or trillions of bacteria can literally reach a consensus on actions. Bacteria that previously existed harmlessly on the skin, for instance, may exchange chemical signals and reach a consensus that their numbers are large enough to start an infection. ~ biological physicist José Onuchic

Benevolent bacteria and their evil twins face diametric challenges, both of which tax their cunning, but to which both rise to the occasion.

Mutualist bacteria must negotiate relationships with numerous other species to peaceably abide. Those that live inside a microbiome must cooperatively accommodate themselves amid a community of microbes and bring something to the party so that the host does not regard a bacterium as an unwelcome gate crasher.

In contrast, gate crashers must run a gauntlet of host defenses. While many attack vectors and counter-defenses are genetically baked into infectious agents, there frequently arises the need for innovation to meet the unexpected, as environments differ greatly among individuals.

To penetrate diverse organs and tissues and to survive and thrive in our bodies, bacteria become skilled subversives, hijacking cells and cellular communication systems, forcing them to behave in ways that serve the bugs’ own purposes. Many microbes take control by wielding specialized tools to inject proteins that reprogram the cellular machinery to do the bugs’ bidding. A few are also known to employ tactics that rid the body of benign or beneficial bacteria, to better commandeer the environment for themselves. ~ American microbiologist Brett Finlay

Some pathogenic bacteria directly cause pain to its host by tickling nerve cells with toxins. This seems counterintuitive to its cause, in alerting the body to bacterial presence.

Causing pain is instead a knowing subterfuge. Nerve cell bustling from pain impairs recruitment and activation of innate immune cells.

 Work Uniform

Blue light is most prevalent in the open oceans, as it penetrates into deep waters — whereas in warm equatorial and coastal waters there is more green light, and in estuaries the light is often red. ~ David Scanlan

Cyanobacteria live off the light: converting sunshine into usable energy. These primary producers are the base of the ocean’s food web – upon their productive fecundity life in the ocean depends.

Synechococcus is one such photosynthesizer, widely found in well-lit waters of the tropical to temperate oceans. These picoplankton don’t just sit around sunning themselves. Synechococcus get into uniform to work: changing their pigmentation to match light frequency, to soak up as much energy as possible.

Synechococcus are planktonic ‘chameleons’: dynamically changing their pigment with the ambient light colour. ~ David Scanlan

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A bacterial cell that’s growing is also constantly shedding parts of its cell wall, similar to how a snake sheds its skin every so often. ~ Chinese American bioengineer Casey Huang

Sometimes losing the work uniform is the only way to survive. Infectious bacteria are subject to attack by host cells, which recognize the invaders by their coat: recognizable portions of the bacterial cell wall. To dodge detection, these bacteria rid themselves of their recognizable cell walls, thereby going undercover as dormant shapeless blobs. Once the coast looks clear, a shape-shifting bacterium rebuilds its cell wall in a process termed reversion.

Many antibiotics, including penicillin, target the cell wall. Having got a sample of an antibiotic, which is ineffective when the cell wall is down (as the chemical has nothing to latch onto), a bacterium analyzes the antibiotic compound to figure a way to thwart it if it reappears. This is one way that antibiotic resistance develops.

Genetic Uptake

Bacteria are genetic packrats. They scavenge genic snippets from the environment, including long-dead organisms. DNA fragments several hundreds of thousands of years old may provide valuable adaptive information.

Bacteria use their pili to snag DNA. The process of incorporating retrieved DNA is termed natural transformation.

Bacteria are DNA connoisseurs. They are choosy about the genic bits they acquire. This involves intelligent analysis for content quality.

Bacteria commonly swap genes among themselves. Many selectively shed and uptake plasmids, which are independent DNA molecules separate from genophoric DNA.

Like a genetic copying machine, plasmids divide independently. Plasmids provide extra survival information that is both useful to a bacterium and transferable.

These transfers enable bacteria to adapt to novel environmental conditions, access new food sources, or evade destruction by antibiotics and toxic compounds: sometimes by alchemic genes that can transform mercury or other heavy metals into less noxious forms.

When antibiotics hit the dirt, resident soil bacteria tweak themselves to resistance. Bacteria may at times refuse to share such defensive knowledge, but some transfer does take place to itinerant pathogens on their way to the next host.

With its dry patches and air pockets presenting insurmountable obstacles, the soil is difficult terrain for bacteria. To get around they need a liquid film in which to swim. Fungal filaments (hyphae) provide the perfect motorway. Even better, soil fungi create wide-ranging networks, termed mycelia – a wondrous cosmopolitan infrastructure for bacteria. In such comfortable environs, bacteria are especially generous with their genetic exchanges.

It’s possible that over the course of the Earth’s history, bacterial diversity increased massively with the development of mycelium-forming fungi. ~ Swiss environmental microbiologist Lukas Wick

Generally, horizontal gene transfer is common, and occurs between distantly related organisms: microbes, fungi, plants, and animals. Plants extensively employ genic exchange to foster their mutualistic relationships with bacteria and fungi.


Bacteria have developed intricate communication capabilities (e.g. quorum-sensing, chemotactic signaling and plasmid exchange) to cooperatively self-organize into highly structured colonies with elevated environmental adaptability. Communication permits colonial identity, intentional behavior, purposeful alteration of colony structure, decision-making and the recognition and identification of other colonies. ~ Israeli physicist Eshel Ben-Jacob et al

Many bacteria live as single cells. Others are more communal. Regardless of lifestyle, bacteria are sociable: communicating among themselves and operating as a community.

Bacteria interact by releasing biocompounds to help them adapt to their environment. Colonial populations coordinate actions, such as mass secretions, by first releasing signaling molecules.

When conditions become too stressful, bacteria can transform themselves into enduring inert spores. (Bacterial sporulation is an exemplary existence proof of energyism: that physical bodies are artifacts of vital life energy. If life was merely made of matter, revival from sporulation would not be possible, as spores are utterly inert: dehydrated, and materially dead. But then, material science cannot explain life at all.) Sporulation is a collective process which begins only after consultation and assessment by colony members. Starving bacteria emit chemical messages conveying their distress. With such communiqués about, each bacterium makes its own interpretation of the state of the colony relative to itself. Sporulation is put off until a majority rule in its favor. Colonial bacteria are democratic in their decisions.

Bacterial colonies are invariably diversified. Individuals within possess a spectrum of distinct characteristics and talents. This diversity increases the probability of population survival in unpredictable environments.

Bacteria face a social problem which humans are well acquainted with: cheaters. To single out microbial miscreants, cooperators first generate a new communication dialect which defectors have trouble imitating. They can then collectively alter their own identity into a new genetic state, leaving the cheaters out of further cooperative endeavors. These periodic intelligence operations benefit the group by improving cooperative social skills.

Neisseria, a commensal bacterium that colonizes the mucous membranes of many animals, pair up to be more effective. Streptococcus, another commensal genus, though with some pathogenic species, grow in chains. Staphylococcus, a cocci genus, form clusters that resemble grapes. Most are harmless residents of the skin and mucosal surfaces, as well as a worldwide presence in soil.

Some bacteria elongate, forming filaments that contain numerous cells, like mycelium (a threaded fungal mass). This is what actinobacteria do. They are one of the dominant bacterial phyla, common in soil, freshwater and seawater, and a major player in the carbon cycle, thanks to their saprotrophic lifestyle of breaking down organic matter.


The soil is a cosmopolitan environment, rich with microscopic life. For a microbe predator, living in the soil can be pay dirt.

Myxobacteria are eusocial soil bacteria whose survival depend upon communication, coordination, and specialization for constructing a complex structure that affords foraging, feeding, and reproductive dispersal in ways that no individual could achieve. M. xanthus is exemplary.

Myxococcus xanthus

Myxococcus xanthus are a very social bacteria. Their three-dimensional structures contain hundreds of thousands of bacteria, plus extra cellular material that holds the bacteria together like glue. ~ Russian biologist Oleg Igoshin

Myxococcus xanthus is a ubiquitous soil bacterium. M. xanthus are predatory. They hunt, kill, and consume fungi and other bacteria; though not alone.

M. xanthus are inveterate joiners. Whether prey is plentiful or scarce, their first impulse is to get together.

A problem that cooperatively inclined bacteria face is how to recognize and avert freeloaders. M. xanthus solve this by first getting acquainted.

Close relatives are readily accepted as abettors. If relations are scarce, the bacteria may tentatively decide to cooperate so that a multicellular structure can be built.

When facing a feast, M. xanthus come together into a dense and highly motile swarm. Then they hunt.

M. xanthus self-organize into high-density waves that move them along in a decided direction. They surround prey and close in.

A swarm of M. xanthus produces powerful antibiotics that kill prey, along with the enzymes needed to chew prey proteins into digestible bits. Single cells are unable to produce sufficient quantities of antibiotics or enzymes to effectively feast. Besides, dining with friends is more fun.

The sophistication of M. xanthus swarms is marvelous. They recognize each other and sense how neighbors are faring. Cells with deficiencies are taken care of by comrades.

M. xanthus create a chemical communication network that coordinates their activities. They swap vesicle packages containing information and supplements that keep them together as a coordinated unit. They share the spoils of the hunt.

Scarcity also gets M. xanthus together, but instead for the consolation of living through hard times. When food is scarce, M. xanthus take a different form of swarm. They create a fruiting body: a mound of spores that can survive for a long time, even years, until conditions improve. A single spore could not survive; togetherness is a necessity.

M. xanthus fruiting bodies self-organize to the scale that gives them the greatest chance of survival. Fruiting bodies are arranged to optimize the odds.

Most of the cells that participate in forming myxobacterial fruiting bodies sacrifice themselves to ensure that others will form spores and survive to reproduce. ~ American biologists Richard Losick & Dale Kaiser

When the prospect of decent food is sensed, spores reinvigorate into the next generation.


Haemophilus influenzae – a bacterium in the respiratory tract that can cause ear infections – needs dietary iron like everything else alive. Some manage to collect more than they need, while neighbors may run short. In this instance, the iron-rich readily share to help their brethren.

Bacteria under attack by antibiotics signal their kin, increasing the chances of some surviving, as the informed ramp their resistance to fend off the assault.

Typically, only a small number of bacteria in a colony are drug resistant. These hardy souls help their more vulnerable comrades survive, even at a cost to themselves.

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Bacteria selectively pick up genetic material in the environment in a process termed transformation. The death of bacteria, or simply loose plasmids, make free DNA available.

Free DNA stabilizes in the soil by combining with soil components. These are taken up by living cells. Biofilms attached to river stones happily practice what is called epilithon: aquatic transformation.

Single-celled bacteria and archaea have an immune response to viruses that infect them. As a physical memory, these prokaryotes retain strands of nucleic acids that convey information about the incursion. When a bacterium recognizes that it has been invaded, it splices and copies signature genetic material from the pathogen, then distributes that for others to pick up. By doing this, a bacterium transfers information vital to conferring immunity to that pathogen.


Microbiomes demonstrate that the sociality of bacteria is not limited to strain, species, or kind. Bacteria are just naturally sociable.


Bioluminescent creatures, including fish, squid, jellyfish, clams, and worms, harbor bacteria that perform the reverse of photosynthesis: turning chemical compounds into light energy.

The bacteria produce a pigment, luciferin, which reacts with oxygen to create light, abetted by the enzyme luciferase, which catalyzes the reaction. Different bacterial strains product their own distinct colors, from yellow to blue.

This symbiotic partnership gives the bacterial employer various advantages: lighting for communication to others of the same species; assistance in predation, either as a lure or a hunting light; or camouflage, by matching the overhead environmental light seen from below.

In an astonishing feat of counter-illumination, animals that employ bioluminescence as camouflage have photoreceptive vesicles to sense light levels, and thereby control the contrast of their symbiotic illumination to create optimal optical matching. These vesicles are often separate, but the Hawaiian bobtail squid integrates the whole light works.

The bioluminescent bacteria Vibrio fischeri lives in a light organ in the squid’s mantle. Fed a sugar and amino acid diet by the squid, the bacteria hide the squid’s silhouette when viewed from below by matching the amount of light hitting the top of the mantle.

There is no purely physiological (matterist) explanation for how these precise, coordinated counter-illumination displays are possible.

 Eating with the Enemy

Breviates are a group of unicellular protists that arose a billion years ago, when oxygen was scarce in the deep ocean. Breviates adapted to anoxic conditions by having a rather simple metabolism: fermentation. This process yields significantly less energy than bacteria can muster with nitrate respiration but requires scant oxygen.

Bacterial symbiosis would do breviates a world of good. The problem is that bacteria are breviates favorite prey.

Fortunately for breviates, some bacteria are fearless. Arcobacter are badass bacteria: they colonize animal intestinal tracts, causing painful infections.

Arcobacter fearlessly flock to the surface of breviates (which do not have intestines to colonize). Both benefit.

When both organisms meet each other, they sort of hot-wire their metabolisms. ~ German marine microbiologist Emmo Hamann

During their metabolism, breviates exude hydrogen. Arcobacter happily suck this down and respire nitrate, which feeds its host breviate.

Breviates have enzymes that help them reap the bounty provided by Arcobacter. These enzymes are produced only when Arcobacter are present.

To profitably colonize a host, many bacteria use specific proteins, known as virulence factors. The virulence factors that Arcobacter use are precisely the ones that stimulate host breviates to produce the enzymes that aid their mutualism. Sometimes virulence is a virtue.


The bacterial diet is literally elemental. Nitrogen is popular, plucked from the air, water, or soil.

Nitrogen-fixing bacteria are essential to the survival of many plants. Nitrogen-fixers have welcome homes in these plants.

Soil-based Pseudomonas carboxydovorans are on a carbon monoxide diet. Thermophilic Thiobacillus suck sulfur. Gallionella eat iron, add oxygen, and expel rust (iron oxide), staining their habitat brown.

Many of the ancients who arose when oxygen was scarce are literally stick-in-the-muds. Heliobacteria, who shun O2, are exemplary. They can be found flourishing in flooded rice paddies, where oxygen levels are low.

Many bacteria share food with others. Some do so directly, building flexible straws (nanotubules) that let them exchange munchies.

 Power Grid

Consortia of archaea and bacteria are abundant in Nature. ~ German marine biologist Antje Boetius

The remains of marine life make their way to the ocean floor as dissolved organic matter (DOM), the deposit of marine snow. The dead biomass decays in subsurface sediments, producing methane which rises to the seafloor.

Before reaching the water column, the methane is consumed by consortia of methanogenic archaea and bacteria which may form voluminous mats on the ocean floor. These microbes work together to make a meal.

Archaea intake methane (CH4) and oxidize it to carbonate (H2CO3). The reaction continues as the archaea pass energy to partner bacteria through pili, which are connective tubes that the bacteria provide. Using readily-available sulfate (SO42–), the bacteria reduce the carbonate and respire hydrogen sulfide (H2S).

 Energetic Drinker

Rhodopseudomonas palustris is a common, waterborne, purple bacterium with expansive tastes. It can alternate between phototropic and chemical intake, depending upon where the bacterium happens to be.

Fond of high-energy drinks, R. palustris suckle electricity from electron-rich minerals in sediments. Or, if floating near the surface, they drink in light. Either way, the electrons are metabolically consumed as pure energy.

When in the mud, R. palustris soak up electrons through naturally occurring conductive minerals. As they pull electrons away from iron, they create iron oxide crystals which precipitate into the soil around them. These crystals can become conductive, acting as feeding circuits that allow a purple bacterium to oxidize minerals it could not otherwise reach. R. palustris knows how to go with the flow.


When life is good, bacteria multiply by binary fission. After splitting in 2, each daughter clone eats its way back up to size.

The reproductive cycle can be amazingly swift: a bacterial population can double in less than 10 minutes. 1 bacterium can produce a million in 5 hours.

Rapid reproduction affords rapid evolution. Besides genetic inheritance, bacterial evolution is vectored by the experiences of the mother cell via epigenetic processes, as well as gene transfers.


The spore exists in an inert, resting condition that is capable of high resistance and very long-term survival. ~ American biologists Kathleen Park Talaro & Barry Chess

Bacterial growth patterns reflect intricate knowledge of surrounding conditions. When food becomes unavailable or water scarce, some bacteria become dry motes: folding themselves into little, tight balls, entering a state of suspended animation.

These endospores wait out the hard times, until awakening with the advent of nourishment. This time travel can last centuries, possibly longer.

A microbiologist cultured bacteria from the gut of a mastodon entombed in a bog some 10,000 years ago. The bog became a water hazard on a golf course where the mastodon’s remains were found. Though having a largely selfsame metabolic capability, the ancient bacteria could digest maltose sugar which today’s bacteria cannot.

Viable endospores found in a 25 million-year-old fossilized bee have been found. A 250-million-year-old salt crystal was discovered that had a viable endospore, of a bacterium genetically different from known species.


No phone, no pool, no pets… king of the road. ~ American musician Roger Miller in the song “King of the Road” (1964)

Viruses travel light. While hardy enough to survive the elements, they enjoy the comfort of being indoors.

Viruses evolved from ancient cells, losing inessentials to slim down to fighting trim and vivacious virulence.

Loss is nothing else but change and change is Nature’s delight. ~ Roman Emperor Marcus Aurelius

Each type of virus has its own distinctive size, shape, chemical composition, and host requirements.

Viruses are not even complete single cells. They come in a light coat but little underneath: no nucleus, no mitochondria, no ribosomes.

The vitals of a virus are its virion, comprising the virus’ genome packaged within larger molecules. Some viruses carry other equipment, notably enzymes, to accelerate production once a virus is activated.

A virion is encapsulated within a capsid: a protein protective coat put on when leaving lodgings in a host cell. Despite comprising few building blocks, capsids are intricately complex structures, sometimes with enormous conformational diversity.

Viral capsids are marvels of biological engineering. They are sturdy enough to withstand pressure exerted by the tightly packed genomes inside yet can come apart or loosen easily to release the viral genome once the virus penetrates the cell. They are also great examples of genetic economy. Because of the limited coding capacity of viruses, capsids are built by using a few proteins over and over. ~ microbiologist Ekaterina Heldwein

To make it easy on themselves, many viruses evolved capsids that self-assemble.

Capsids became more and more sophisticated with time, allowing viruses to become infectious to cells that had previously resisted them. This is the hallmark of parasitism. ~ Pakistani virologist Arshan Nasir

Some viruses, mostly those that infect animals, also sport an overcoat: a lipid envelope derived from the host cell membrane. It helps them travel incognito, evading a host immune system.

Some enveloped viruses have spikes (peplomers): a glycoprotein protrusion out of the envelope but connected to the capsid. These spikes are sensors, essential for host specificity and viral infectivity. A peplomer will only bind to certain receptors on a host cell.

A virus assembles itself within its host’s cell. Hence, all viruses are obligate intracellular parasites.

Viruses are everywhere. Viruses inflict themselves on all life, including their own kind. Every organism is constantly interacting with viruses.

Viruses exist wherever life is found. They are a major cause of mortality, a driver of global geochemical cycles, and a reservoir of the greatest genetic diversity on Earth. ~ American biochemist Curtis Suttle

Certain avian and pig viruses get by with just 2 genes. HIV, a relatively large, enveloped RNA virus, has only 9 genes; the herpes virus a few hundred. Then there is a vast diversity of viruses – dubbed pandoraviruses – that have over 2,500 genes.

It is clear that the paradigm that viruses have small genomes and are relatively simple in comparison to cellular life has been overturned. ~ Curtis Suttle

By contrast, an E. coli bacterium has nearly 4,400 genes. A human cell has ~25,000 genes.

Viruses need only a genome large enough to invade host cells and redirect their activity to producing viral copies. Meanwhile, cells must carry on complex metabolic processes and maintain a communal existence.

Having minimal needs is why a virus may be only 20–300 nm in diameter, up to an order of magnitude smaller than a prokaryote. Small size facilitates infiltration. But it only works if one can rely upon one’s wiles.

The genetic stuffing of viruses has nothing to do with their ability to lead a furtive life. Viruses are an existence-proof that the intelligence of a mind does not have to be tied to a physical substrate.

Pandoraviruses are a family with some of the largest viruses, and the biggest genomes. They are very strange beasts, particularly in what they don’t pack into their genome. Pandoraviruses lack the gene for the capsid protein. They even lack genes for energy production and cannot produce a protein on their own. It rightfully makes one wonder what is so valuable in the genetic material they do carry.

The mimivirus is a giant virus that infects amoebae. It has more than 900 protein-coding genes in its genome; a bigger bunch than some bacteria.

The term mimivirus derived from “mimicking microbe.”

When first discovered in 2003, the mimivirus was thought to be a bacterium.

In contrast to the pandoravirus, the mimivirus encodes the entire transcription apparatus, so can replicate itself within a host cytoplasm.

This giant virus is endowed with the genetic abilities to repair DNA, correct errors during its replication, produce messenger RNA transcripts from genes and translate those mRNAs into proteins. Some mimiviruses even have their own immune system to thwart infection from virophages.

The informational genes that the mimivirus has are considered the hallmarks of life. No wonder that the mimivirus was mistaken for a bacterium.

The mimivirus is ancient. It evolved by selectively assembling useful genic bits from the environment and its hosts.


Viruses have either DNA or RNA, but not both. RNA is typically single-stranded, while DNA a double helix.

There are distinctive exceptions to these conventions. The tremendous diversity of viruses illustrates the intrinsic flexibility in genomic structure.

Parvoviruses contain a single strand of DNA. Reoviruses, which cause respiratory and intestinal tract infections, carry double-stranded RNA.

Proteins are manufactured by translating a single RNA strand into an amino acid sequence. A single-stranded RNA genome is therefore ready for immediate translation without intermediate steps. It is called positive-strand RNA. An RNA genome that must be converted into a single strand prior to translation is termed negative-strand RNA.

RNA genomes may be segmented: individual genes in separate RNA molecules. The influenza virus, an orthomyxovirus, is exemplary.

Retroviruses possess the crafty knack of converting their RNA package to DNA inside the host cell by duplication, via a reverse transcriptase enzyme. The DNA is then incorporated into the host cell genome via an integrase enzyme.

A retrovirus thusly replicates as part of the host cell’s DNA. Commensurate with their sophistication, retroviruses sport a shiny lipid outer coat.

Poxviruses, such as the agent for smallpox, infect animals, both invertebrates and vertebrates. Poxviruses have very large DNA virions. They lack a typical capsid; instead, covered by a dense layer of lipoproteins and coarse fibrils on their exterior.

Owing to their rapid mutability, every viral population is a genetic assortment. Diversity has several evolutionary advantages. In the instance of viruses, it helps them on the job. Viruses both acquire useful genetic material from the environment (typically the cells they infect) and enhance existing tools.

◊ ◊ ◊

Viruses are social: establishing networks of connections among compatriots. Cooperation during infection is common, as the infection process is seldom easy.

The advantage of viral cooperation comes in taking advantage of specialized skill sets. Some viruses are better at certain tasks than others.

Tactical decisions may need to be made. For example, to boost total viral production, viruses may want host cells to live longer. This requires not interfering too much with an infected cell’s self-maintenance.

If a virus is co-infecting with a stranger instead of friends, it may consider this competition. The virus will work its host cell to death as quickly as possible to thwart its rival.

◊ ◊ ◊

From a host perspective, there are 2 varieties of virus: acute and persistent. While acute come and go, spreading whatever they have on offer, persistent viruses take up residence and never leave. Persistent viruses tend to be gentler with their host than their rambunctious acute cousins. This accommodating style is a learned skill.

All told, the world virus population is estimated to be 100 quintillion (1031). They outnumber bacteria 10-to-1 in most places. Despite being so tiny, viruses amount to 5% of the world’s biomass.


In its most primitive form, life is no longer bound to the cell. No, in its primitive form life is like fire, like a flame borne by the living substance; like a flame which appears in endless diversity and yet has specificity within it; which can adopt the form of the organic world. ~ Martinus Beijerinck

Viruses were discovered in 1898 by Dutch microbiologist Martinus Beijerinck when he examined a puzzling illness that beset tobacco plants.

Beijerinck mashed up diseased leaves and rinsed them through fine porcelain filters that trapped microscopic fungi and bacteria. The resultant clear water could still sicken tobacco plants. Beijerinck dubbed the source of malady “a contagious living fluid,” which he dubbed a virus. The term derives from the Latin word viru (poison), with a squeeze of Old English wose on the end, which evolved into the word ooze.

In 1935, American biochemist and virologist Wendell Stanley crystalized the tobacco mosaic virus (TMV), and realized that the virus remained active even after being crystallized. He won the Nobel prize for this, even though he wrongly presumed that the crystals were self-assembled proteins (no one at the time knew any better). (The Nobel committee regularly hands out prizes for fictional discoveries and accomplishments. The most celebrated of his namesake prizes is for promoting peace between recalcitrant parties. Alfred Nobel made his fortune as an arms dealer. His obituary called him “the merchant of death.”)

In 1939 came visual proof of the tobacco mosaic virus, from German biologists Helmut Ruska, Gustav Kausche, and Edgar Pfankuch, via electron microscopy.

In 1955, German biochemist Heinz Fraenkel-Conrat and American virologist Robley Williams showed that purified TMV RNA and its capsid self-assemble into a functional virus; hence demonstrating that viral packaging is the most stable state – the one with the lowest free energy. No one understands how such self-assembly is possible.


Viruses are simpler than cells, so, the logic goes, viruses cannot be living organisms. This viewpoint seems best dismissed as the semantic dog wagging by the tails of dogma. ~ American evolutionary biologist Paul Ewald

Whether viruses qualify as a life form is a long-standing controversy. Viruses possess several recognized criteria of life. They have a genome. Viruses have enzymes which keep their genome in good working order via self-repair. They evolve. Viruses self-assemble, albeit within a host cell.

The cellular nature of viruses is restored when viruses (re)take control of the cellular machinery of cells or when they integrate into cellular genomes. ~ Argentinian biologist Gustavo Caetano-Anollés et al

The typical virus does not have its own metabolism, nor can it reproduce by itself. The mimivirus is a known exception, and there may be others.

The Klosneuvirus, which preys on protists, is quite cell-like: able to fabricate all 20 of amino acids needed to stitch together proteins. Most living cells are unable to do so.

Like viruses, the obligate bacterial parasites rickettsia and chlamydia require a host for replication. No one questions their status as alive.

Many organisms require other organisms to live, including bacteria that live inside cells, and fungi that engage in obligate parasitic relationships. They rely on their hosts to complete their life cycle. And this is what viruses do. ~ Gustavo Caetano-Anollés

As to metabolism, many emergent lives – such as spores – start in stasis or kill time in a dormant state. A virus comes most vibrantly alive when it finds a home. A giant virus, thawed out of Siberian permafrost after being frozen for 30,000 years, roared back to being on the hunt once again.

A virus employs its own genes as a guide for assembling viral proteins and reproducing its own genome. Though using hijacked equipment, viruses manage their replication.

A cell with its nuclear DNA destroyed is dead. A virus can inhabit a dead cell, turning it into a viral zombie by activating the cell’s cytoplasm machinery to replicate.

A virus can even bring a cell back to life. Photosynthetic cyanobacteria and algae are often killed by ultraviolet (UV) radiation, which decimates their nuclear DNA. Viruses have in their toolkit enzymes to repair various host molecules, reclaiming the host from the grim reaper.

A cyanobacteria has at its photosynthetic center an enzyme that can be disabled by UV overexposure. Unable to metabolize, the cell dies.

But cyanophage viruses encode their own version of the bacterial photosynthetic enzyme. The viral variant is much more resistant to UV radiation. If a cyanophage infects a recently deceased cell, its photosynthesizer can replace the host’s, and bring the cell back from the dead.

Too much UV can kill even a virally revived cell. But if a cell harbors more than 1 disabled virus, the viral genome sometimes coherently reconstructs from genetic pieces. This self-assembly process is termed multiplicity reactivation.

In complementation, individual genes act in concert to reestablish functionality without fully reforming into a complete virus. Only viruses possess this “phoenix phenotype”: able to bring back the dead or self-resurrect.

Life is nothing but not being stone dead. ~ Irish playwright George Bernard Shaw


There are a variety of viral agents that are not complete viruses but have viral properties. One example is a prion, which is a misfolded protein that pathogenically propagates.

A satellite virus depends upon another virus to infect a host cell or some other service. Some satellites are not much more than conscious, intelligent strands of nucleic acids.

Viroids are tiny RNA particles that exist without a protective capsid. Most commonly, viroids are plant pathogens. The human pathogen hepatitis D is a viroid in being subviral RNA. Viroids often hitch a ride on full-fledged viruses to enter a host cell.

Other satellites are more fulsome, though still stripped down to essentials. Alphasatellites are single-stranded DNA that rely upon another virus for transmission.

A virophage is a satellite virus that is a parasite of another virus. Virophages depend upon enzymes provided by their host virus rather than the host cell.

Virophages have an ancient lineage. They are genetically like transposons: DNA sequences able to independently move within a genome, often by jumping a copy somewhere.

Transposons are common in eukaryotes. 67% of the human genome comprises transposable elements. These jumping genes may have evolved from virophages (or maybe vice versa).

 Mama & Sputnik

Size-wise, the mimivirus is surpassed by the mamavirus, which is slightly larger. Mama is a variant strain of mimi. Like mimi, mama infects amoebae: using its large array of genes to build a virus factory within the host cell.

Mamaviruses are subject to infection by Sputnik: a tiny virophage with just 21 genes. Sputnik breaks into mama’s factory to replicate itself.

Cells co-infected with Sputnik produce 70% fewer mamavirus particles, and those are often deformed. Amoebas survive longer with Sputnik making mama sick.

 Cafeteria roenbergensis

Cafeteria roenbergensis is a tiny, kidney-shaped zooplankton that eats bacteria. It is found in all the oceans, but especially thrives in coastal waters that are microbially-rich. C. roenbergensis keeps bacteria populations in check.

C. roenbergensis is itself preyed upon by a giant virus called CroV; Cro referring to C. roenbergensis.

CroV has the largest known genome for marine viruses, and 2nd overall: only bested by the mimivirus. Its large genetic complement affords it greater ability to manipulate its host. CroV can even produce DNA repair proteins to patch up problems that its host may have.

CroV and similarly complex viruses encode genes to modify and regulate the host translation system to their own advantage, which results in a “lifestyle” that is less dependent on host cell components than that of smaller viruses. ~ Canadian microbiologist Matthias Fischer et al

Mavirus is a virophage that hijacks the transcription machinery that CroV has in place during the late stage of infection. Mavirus’ genetic similarity to Sputnik suggests that virophages are almost as ancient as viruses themselves.

Given the opportunity, mavirus integrates its DNA into Cafeteria roenbergensis, thereby providing an innate immune system to the zooplankton. If infected by CroV, embedded mavirus particles can suppress CroV replication, and thereby enhance host survival. Here we have an example of altruism by a virophage.

 Intrigue at Organic Lake

Viruses are ubiquitous members of microbial communities, and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. ~ microbiologist Sheree Yau et al

The Antarctic is a forbidding place. For those who do manage to live there, existence is made all the harder by being preyed upon.

Organic Lake is a shallow, salty, sulfuric body of water in East Antarctica. The salt was trapped from the ocean when the lake formed 6,000 years ago, when sea levels were higher. The lake would freeze over absent its high salt content.

The density of organic matter within gives the lake’s namesake. This owes to slow decay caused by the salt and cold.

Some very tough algae live in Organic Lake: soaking in the 2 months of summer light and spending the rest of the year as spores. They are plagued by phycodnaviruses: large double-stranded DNA viruses.

The Organic Lake Virophage (OLV) preys on the local phycodnaviruses. In doing so, OLV curtails the damage done by their viral cousins, giving the algae some welcome respite.


Satellite viruses are a compelling argument for considering viruses as alive. It is silly to say that something not alive can interfere with the reproduction of something not alive. Satellite viruses clarify that being alive is not about self-sufficient reproduction, but instead the cunning to reproduce.


Every single cellular species is infected by a great variety of viruses. ~ French molecular biologist Patrick Forterre

Pathogenic viruses have been a threat to other life for so long that every type of cell has an immune system.

One strategy that many microbes use is to close up shop when viruses are noticed in the neighborhood. Many archaea and bacteria go dormant when they sense a threat. Fear is the most primitive emotion.

Dormancy may not work. Some microbes can only cheat infection by faking their death for a limited time, else the pose becomes a corpse.

The microbe is hedging its bet. If it goes dormant it might die. ~ American microbiologist Rachel Whitaker

Viruses have a counterstrategy: patience. Viruses can commonly wait out microbial dormancies, and so they too hibernate: quietly lurking until they sense nearby prey on the prowl.

Viruses gain entry to animals through the skin and mucosal linings, such as the nose, mouth, lungs, or eye membranes. Some viruses can be passed from an infected host through gametes to offspring.

Having entered a host, a virus attaches to a specific target cell that can promote its activation and reproduction.

Viruses have a selective host range: preferred prey. A virus recognizes its host cell by signature protein markers, called receptors, on the cell surface. (The term receptor here is something of a misnomer, as viruses are most certainly uninvited and unwelcome.) Receptor recognition occurs via subtle molecular bonding.

Pathogen host shifts represent a major source of new infectious diseases. ~ Chinese entomologist Ji Lian Li et al

Some viruses specialize in a single cell type. Others, less persnickety, settle for several cell types that originate from the same embryonic germ tissue.

Once a target cell is found, the virus extends fibrous feelers that it normally keeps folded up. The virus roves about until it finds its favored surface receptor.

A virus may perform preparatory work for entry, including changing its structure. It ejects some of its proteins through the cell membrane, creating a path to slide in.

The virus then passes its genetic material in, along with its vitals. After entry, the protein path collapses, and the cell membrane seals.

Despite their delicate subterfuge, most viruses cannot help but leave telltale traces on the cell surface that an immune system may detect. These molecular marks are the makings of an evolutionary race between a virus and its host, to respectively hide and detect infection.

Once inside, a virus sheds its protective coating, freeing its virion to methodically take over the cell.

Some viruses use a host cell’s own mechanisms to gain entry to the cell nucleus. Adenoviruses latch on the gatekeeper molecule of a cell’s nuclear pore complex which controls passage in and out of a nucleus.

The motor protein kinesin regulates nucleus transport into the cell nucleus. Once active, the virus uses the energy of the motor protein to shed its shell and expose its viral DNA. This prepares it for transport into the nucleus.

Activated motor action also has another effect: making the nuclear pore larger, easing entry. The virus slips into the nucleus. The protein closes the pore without leaving a trace of viral entrance.

Most DNA viruses enter the chosen cell’s nucleus before activating. The poxvirus is a notable exception. It carries its own machinery for genome transcription. Thus, the poxvirus can ply its trade in the cytoplasm and thereby replicate quickly.

By contrast to DNA viruses, RNA viruses generally replicate and assemble in the cytoplasm, though there are exceptions.

Activation may not be immediate. Viruses may patiently await certain changes within and around a cell that signal an auspicious status.

Viruses make a ‘decision’ when they infect a cell as to whether or not this is a good time to lyse the cell and make more virus or whether it would be more propitious to integrate their chromosome into the infected cell’s chromosome, turn off their genes and sit there for generations. Then when things look good again they use a different but related pathway to excise their chromosome, in order to make more virus and kill the cell. ~ American molecular biologist Arthur Landy

To exercise patience, a virus assembles an ensemble of proteins to insert its own genetic code in a precise location in the DNA of the host, thus ensuring that its DNA will persist for many generations of host cells. When the virus decides to activate for replication, it creates another protein ensemble to extract the DNA.

The viral DNA-packing ensemble incorporates key proteins that the cell uses to regulate expression of its own genes. Hence, these proteins reflect the state of the cell.

It makes the system gratuitously dependent on the proteins of the cell which serve as reporters of how well the cell is doing and where it is in its life cycle. This makes it exquisitely sensitive to the physiology of the cell. ~ Arthur Landy

Each virus type exists with variants. One or more strains can become activated upon invading a cell, while other strains await more favorable conditions to activate. Activated viral nucleic acids combine with the necessary host-cell amino acids to replicate.

Enveloped viruses exude offspring through the host cell membrane (lysogeny). A viral nucleocapsid binds to the membrane, which encloses it in a pouch.

Pinching off the pouch sends the virus on its way. Budding of enveloped viruses results in gradual shedding, without immediate sudden cell destruction; nonetheless, accumulated damage from viral intervention hastens cell demise.

Nonenveloped and complex viruses release their batched brood when the host cell bursts open in its final death throw (lysis). Lysogeny and lysis are the 2 methods of viral offspring release.

Influenza viruses know the dangers of their occupation, so they produce offspring with a wide variety of shapes, maximizing the odds in their favor.

Antiviral measures target proteins on the surface of a viral cell. Knowing this, the flu virus can quickly swap out one set of proteins for another, making the virus notoriously difficult to track and destroy.

Viruses mimic the immune system in order to evade it. ~ Australian molecular biologist Richard Berry

Viruses understand their host at the molecular level. One influenza virus mimics a host-cell histone protein, inhibiting the cell’s production of antiviral proteins by repressing gene expression in the host that controls antiviral proteins. Via mimicry, the virus demonstrates its understanding of the epigenetic mechanism by which a host cell mounts its defense against the virus.

Other viruses cloak themselves by fabricating proteins and placing them on the surface of infected cells, deceptively telling the immune system that nothing is wrong. Measles goes further and eradicates host remembrance of infection, thereby robbing the host immune system of any knowledge it may have gained for fighting infection.

The measles virus preferentially infects cells in the immune system that carry the memory of previously experienced infections. ~ Dutch virologist Rik de Swart

Viruses drive evolution by putting cells on the defensive, prodding cells to tighten their operations.

In the molecular arms race between viruses and their host cells, each side employs multiple strategies to deal with the other. Whereas the host has sophisticated antiviral signaling programs to combat viral infection, viruses use their own proteins to subvert these host defenses. Viruses are often lauded for these clever evasion tactics. However, the host may also have its own brand of molecular chicanery. During infection, a host cell-derived antiviral molecule is packaged inside viral particles. As a stowaway, the antiviral factor is poised to trigger immune defense pathways upon infection of another host cell. ~ American virologist John Schoggins

 Viral Altruism

Bacteriophages are viruses that infect bacteria. It’s a tough business, as bacteria have sophisticated anti-phage defense systems which recognize and target invaders.

Phages counter with genes that encode proteins which stall the bacterial immune system. To implement these anti-defense viral genes, a phage must enter a bacterial host cell and thwart the immune response.

The virus cannot possibly survive this initial assault to reproduce itself. The virus knows this. The initial attack is a sacrifice gambit. The virus’ compeers will carry on to mount the bacteria’s protein-making machinery once its defenses are down.

This cooperation between genetically identical individuals of a viral population is altruism. ~ Israeli geneticists Rotem Sorek & Aude Bernheim


Overcoming viral infection offers inoculation. A host learns about the virus, which invariably leaves genetic material behind. By being able to spot an intruder early, this recognition memory is weaponry against reinfection.

A virus generally kills its host cell, but some cells escape destruction by harboring the virus, Trojan-horse style. Such persistent infections can last from a few weeks to years. The measles virus can remain hidden in brain cells for years, eventuating into progressive damage and disease.

Oncogenic viruses enter host cells and permanently change its genome (transformation), leading to cancer. Transformed cells take on a whole new life, which basically translates to becoming a different cellular beast and going on a rampage: chromosomal alterations, changes in cell surface molecules, increased growth rate, and the ability to divide for indefinite durations. Mammalian viruses capable of initiating tumors are termed oncoviruses.

Less malevolent viruses move in and take up residence, lasting the host’s lifetime without significantly degrading quality of life. Having learned accommodation in evolutionary time, these viruses are typically content with quiet title. Herpes is exemplary.


If you love something, set it free. Just don’t be surprised if it comes back with herpes. ~ American writer Chuck Palahniuk

Herpes simplex (Greek for “creep like a snake”) is an ancient DNA virus even by virus standards. Herpes’ archaic lineage explains its well-tailored adaptations and its relatively benign coexistence with its hosts as a lysogenic lurker. Via vast experience, herpes developed a successful viral business model.

Herpes infect everything from humans to coral, with each species having its own specific set of viruses. ~ English virologist Charlotte Houldcroft

Some variants of herpes are so well engineered that they move easily among animal species not evolutionarily closely related.

There are 2 types of human herpes simplex. Both infect mucosal surfaces of the body, typically the mouth or genitals.

Herpes establishes residence, or latency, in the nervous system, tucked inside nerve cells. The virus never leaves. Symptoms of viral activity are treatable, but the virus cannot be eliminated.

The primary difference between herpes 1 and 2 is residence location. Herpes 1 establishes latency within the trigeminal ganglion, which are nerve cells near the ears. Herpes 2 usually resides in the sacral ganglion, at the lower base of the spine.

Herpes 1 infected the first hominids 6 million years ago (mya), while herpes 2 jumped to hominids 3–1.4 mya.

The herpes virus infects 20% of the human population. Most people with herpes, particularly genital herpes, do not know they have the virus. Doctors fail to diagnose 90% of herpes cases.

The painful symptoms of active herpes are sores, typically on the lips, inside the mouth, or on the genitals, though sores can appear on the hands (fingers) or eyes.

The most devastating effects are when the virus is transmitted to a newborn, typically during birth. This can be fatal, cause mental retardation, or blindness, if sores occur in the eyes.

Herpes is typically active within the body for a year or so, causing symptomatic discomfort to its host, until settling down into latency. Bodily stress riles the virus.

During latency, the herpes virus is dormant, and is not known to replicate. For the disease to spread, the virus must roust itself, becoming active for transmission when the time is ripe.

Herpes viruses engage in a dialogue with the host cell. ~ American immunologist Alka Prasad

Though its nervous system connection, herpes monitors sexual activity and becomes operative when its carrier becomes sexually engaged. Herpes can be stealthy and mobilize without triggering noticeable symptoms.

Herpes symptoms are provoked by systemic stress. This is part of a generalized response by the immune system. The T cells responsible for keeping herpes under control are diverted to more pressing business.

The herpes virus works by indirectly controlling a nerve cell’s mitochondrion, altering cell calcium level and neuron activity. It commandeers the proteins that mitochondria use to move about a cell, allowing the virus to travel freely and spread to uninfected cells.

Herpes can move through the body quickly. It has a protein that switches on the cellular motor protein dynein. This lets herpes zip along the nervous system’s intercellular highways (microtubules).

Overtaking the cellular motor to invade the nervous system is a complicated accomplishment that most viruses are incapable of achieving. Yet the herpes virus uses one protein, no others required, to transport its genetic information over long distances without stopping. ~ American immunologist Gregory Smith

Herpes fully incorporates itself into the human system, using the body’s mechanisms not only for replication and transport, but also tapping into the body’s internal communication system, and responding to suit itself.

 Viral Assistance

Some viruses help their hosts, particularly persistent residents. They may serve active duty as a front-line defense against infection of animal mucosal surfaces. Some strains of mammalian herpes virus help their host against bacterial infection.

Viruses provide DNA that can be employed to fight off infection by bacteria or another virus. More generally, viruses help train the host immune system to be more responsive and effective.


Viruses exit a host by discharge: bodily secretions, or even in droplets of moisture exhaled by a host.

Viruses survive outside, passively (inactively) traveling by various means. They may be whisked on the wind or jitneyed by insects. They often attach to particles, organic or inorganic, in water or soil. Waterborne viruses are especially fond of polluted water, where they thrive on bacteria.

Although viruses are commonly portrayed as pathogenic, most are not harmful. Many are beneficial to their hosts: helping provide a better living for their host bacteria, fungi, plants, insects, and animals of most every species.

More than one virus can infect the same cell. Depending upon their social inclinations, different viruses that meet may decide to collaborate, fashioning a new type of virus by mutually contributing apt genetic material.

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Viruses are routinely pressured by host reactions to alter their genomes with host nucleic acids or leave parts of viral nucleic acids in the host genome. ~ American paleopathologist Ethne Barnes

Viruses evolve more than themselves. Viruses have been accelerating the evolutionary adaptivity of all other life since their origination, shortly after prokaryotes arose.

Viruses either invented DNA or appreciated the innovation when they encountered it. They then spread DNA, unifying all life into a compatible genetic regime, thereby providing the illusion of a universal common ancestor.

The most direct way that viruses vector evolution is by injecting genes into host cells. When a host cell manufactures a new virus, some host genes may be incorporated. The new virus carries this genetic material to a new host, effecting gene transfer between hosts.

Viral genes may be added that become a critical part of the host species genome. 8% of the human genome is viral in origin, including the ability of cells to grow into tissues and organs, and to reproduce sexually. Animals would have never evolved beyond blobs of cells without viral innovations.

Most eukaryotic genomes are essentially old battlegrounds between critters and their viruses. ~ American entomologist Joe Ballenger

Viral genic injection is only the beginning of an evolving story. These interlopers – retroviruses and transposable elements – provoke cellular genetic innovation to counter them, furthering host evolution.

Arenaviruses acquire genes from host ribosomes, the organelle used to synthesize protein chains. Retroviruses help themselves to host transfer RNA (tRNA) molecules, which act as an adapter for bridging the 4-letter genetic code in messenger RNA (mRNA) with the 20-letter code of amino acids. These are just 2 examples of how viruses intelligently add to their toolkits with infectious enthusiasm. There are several other ways that viruses acquire knowledge to further their lifestyle.


The global population of bacterial viruses (bacteriophages, or phages) has been estimated to be 1031, outnumbering their bacterial hosts by tenfold. Bacteria have developed a formidable arsenal of sophisticated strategies to neutralize viruses, but phages always seem to find a way to evolve, persist and abound. ~ French virologists Manuela Villion & Sylvain Moineau

Bacteriophages infect bacteria. Over 140 genera of bacteria are subject to phage infection.

Some phages benefit the macroscopic life which harbor them by preying upon pathogenic bacteria. Humans medicinally employ phages as a remedy for bacterial infection. The first such treatment – for dysentery – was discovered in 1917.

Besides their own defensive stratagems, bacteria may gain genic intelligence from their brethren and use it to repel infection by bacteriophages. In doing so, they fortify their own immune system.

Phages can thwart these defenses by manipulating the genes that provide the bacterial immune response, thereby providing a phage with an anti-immune system.

When infecting bacterial cells, phages face a range of antiviral mechanisms, and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in order to thrive in most environments. ~ Canadian microbiologist Simon Labrie

Some phages are persistent within the bacteria in which they reside. Their self-interest becomes protecting their home. So, rather than accelerating a bacterium’s demise, phages help their bacterial host survive. This behavior is consistent with how microbiomes behave in macrobial hosts, such as animals and plants.

Antibiotics can take a severe toll on a bacteria population. Helpful phages may deliver genes that let their host bacteria withstand the antibiotic assault. Not only does the phage’s gift provide an immediate remedy, it confers immunity to other types of antibiotics.

 Communal Decisions

After injecting their genome into a host cell, most phages have one of 2 life-cycle options. A phage can enter a lytic life, which rather quickly culminates with the bacterial host in its death throes, spewing a plague of phages into the environment.

Alternately, a phage may live in lysogeny. The bacterium lives out its life, reproducing normally. The genetic package of the phage, called a prophage, is transmitted to daughter cells. Lysogeny yields slow-but-steady viral proliferation.

Phages choose their lifestyle after consulting with the community at large. They make a strategic decision based upon probability.

Phages trumpet their cellular invasion success by synthesizing a small peptide which gets incorporated into the protein-based quorum-sensing communication system that bacteria use. Each phage has its own signature peptide, so it knows its siblings. The viral language phages use is not understood by their bacterial hosts. But phages do understand host cell chatter and eavesdrop to stay informed.

Phages listen molecularly, and sense how crowded the neighborhood is with bacteria infected by others of their kind. If there isn’t much news, it means there are a bunch of bacteria about that are not infected. In this case, better to bust a move and practice lysis. The host is worked to death and explodes with infant phages eager to make their mark on the world.

If instead a phage learns that there are a lot of compatriots about, patience is well advised. Baby phages are as likely to go homeless as not. In this instance, the prudent option of lysogeny is taken.

The system provides an elegant mechanism for a phage to estimate the amount of recent infections and decide whether to employ the lytic or lysogenic cycle. ~ Israeli geneticist Zohar Erez et al


13 virus families infect bacteria. 5 are enveloped.

Only 2 phages have RNA genomes. The other 11 are DNA viruses. 2 of those are single-stranded. The rest are double-stranded.

The ocean is particularly rich with bacteriophages. More than 70% of oceanic bacteria are infected.

Ocean Viruses

Marine viruses affect bacteria, archaea, and eukaryotic organisms, and are major components of the marine food web. Viruses have the ability to manipulate the life histories and evolution of their hosts in remarkable ways. From the global transfer of niche adaptation genes to modifications of the ontogeny and ecology of marine organisms, it has become clear that the marine virome is a master of manipulation. ~ American virologists Forest Rohwer & Rebecca Vega Thurber

Viruses outnumber all other ocean residents by at least 15 to 1. There are 1030 viruses in Earth’s oceans. Each milliliter of seawater may contain 1 billion viral particles.

Virus genetic diversity is unparalleled. Their genomes are often unlike any other organism. This diversity is most flamboyantly on display in the ocean.

In each liter of seawater may be found 25 distinct viruses. A kg2 of marine sediment may host a million kinds of virus. Viruses remain abundant at least 100 meters underneath the deep-ocean bottom.

One reason for such viral diversity is that there are so many different hosts to infect. Each virus lineage evolves innovative ways to get past its host’s defenses. Speciation via specialization is the way to optimize expertise.

Viruses help produce Earth’s oxygen. Synechococcus is a widespread marine cyanobacterium, responsible for 25% of the world’s photosynthesis. The proteins from free-floating viruses within the cyanobacteria are instrumental in harvesting light for bioenergy.

In being responsible for 70% of marine microbial mortality, viruses play a crucial role in marine geochemical cycles, and in global nutrient cycling. Viruses catalyze the transformation of nutrients from living organisms to a dissolved state, where they can be incorporated by microbial communities.

Viruses contribute to carbon cycling via lysis: by converting organic carbon into dissolution. Many other organic chemicals are similarly affected by viral creative destruction.

In the Muck


Marine sediments cover 2/3rds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. ~ German microbiologist Tim Engelhardt et al

Marine muck is nutrient-poor, yet it is abundantly alive.

Sea floor sediment is chock full of viruses: 225 times more viruses than other microbes. Viruses are the largest fraction of living biomass there, even as the volume of microbes within the sea floor equals the biomass of all life in the oceans above.

In controlling the composition and size of the microbial community, marine sediment viruses act as predators. The microbes upon which they feed produce new viruses that remain in the sediment for extended periods, as the relatively few microbes there do not produce enough enzymes to do the viruses in.

Archaeal Viruses

10 viral families infect archaea, in a wide variety of shapes. Only 1 infects both archaea and bacteria.

The unique cell structure of archaea plays a role in defense against viruses. Archaea have a rudimentary immune system that guards against repeated infection.

Some archaeal viruses enjoy a benign relationship with their host: replicating a small number of copies and not causing lysis.

Archaea can only be infected by double-stranded DNA viruses. Almost all (96%) are enveloped.

DNA is considerably less liable to damage than RNA: particularly being more resistant to breaking down at high temperature. That archaeal viruses are the most robust coincides with the fact that archaea are the hardiest of cellular life forms.

Given the extreme environments that archaea often live in, there is less gene transfer between archaeal viruses and those that infect other domains. Nevertheless, there are viruses that infect archaea carrying genes of bacterial origin. This is how eukaryotic cells, which are a combination of archaea and bacteria, evolved: via viral infection. It also illustrates how viruses made DNA the universal genetic currency.

Plant Viruses

In contrast to bacteriophages and archaea viruses, over 75% of plant viruses have RNA genomes; typically, less than a dozen genes. As such, they can be quite small; sometimes less than half the size of a bacteriophage. They need to be.

Unlike animals, the cell walls of plants are an effective barrier to viral infection. A virus cannot penetrate a plant’s outer defense, illustrating another aspect of the astonishing savvy behind the evolution of flora.

Plant viruses must rely on another invasive agent, often an insect, to open a path by eating away at a plant. Roundworms and soil-borne protozoa deliver viruses via plant roots.

Once inside, viruses sneak throughout a plant by passage through plasmodesmata: the microscopic channels between plant cells.

A plant virus depends entirely upon the invasive vector it associates with. Such a virus can only infect the plants that its insect agent feeds on.

As most plant viruses are RNA, plants evolved a defense using RNA interference (RNAi), which disables the plant virus by chopping it up. For DNA viruses, a plant employs RNAi to methylate the viral DNA, thereby gumming its works. Viruses can counteract RNA silencing by expressing potent RNAi suppressor proteins.

Some viruses cooperate with one another to infect a plant. The tomato spotted wilt virus and iris yellow spot virus help each other tackle a tomato by dramatically changing their genetic expressions.

Virtually all plants fall victim to a viral infection some time during their lives. Some are infected as seeds – a tough way to sprout into life, though common. 20% of plant virus transmissions are from one generation to the next.

To cope with plant defenses, the RNA viruses that infect plants have extremely high mutation rates. A jump to animals is not especially difficult for these versatile viruses, especially animals that come into regular contact with plants.

The tobacco ringspot virus managed the leap from the tobacco plant to the mites that pester pollinating honeybees, and then to honeybees themselves. Such species-jumping multiplies the ways that a virus can disperse.

Viral Zombies

Pathogens and parasites can induce changes in host or vector behavior that enhance their transmission. ~ American biologist Laura Ingwell

Numerous viruses practice mind control: altering host behavior to improve the probability of infecting others.

 The Wasp & Its Virus

Many parasites of insect hosts have evolved associations with bacteria and viruses that help them perform their often-deadly deeds. ~ American entomologist Nancy Beckage

Caterpillars are eating machines. The parasitoid wasp Cotesia congregata chucks a spanner in the machine by infecting tobacco hornworms. A compromised caterpillar slows down and loses much of its appetite. This is a profound change.

Cotesia wasps finesse their parasitism via a polydnavirus: a virus genetically integrated with its wasp in a mutualistic relationship. This symbiotic system independently evolved with different viruses at least 3 times.

The wasp provides a home base for the polydnavirus, which does not reproduce in the caterpillar. The virus is replicated in special cells – calyx – within a female wasp’s ovary. Male wasps carry the viral sequence but cannot produce it.

Infection begins with the wasp injecting her eggs into a caterpillar. The virus paves the way for a happy incubation for wasp larvae hatching within the hornworm.

The polydnavirus provides the smarts for the wasp’s parasitism: suppressing the caterpillar’s immune system and controlling the cytokines that alter the hornworm’s behavior.

Beside genomic integration, the polydnavirus has other oddities. It has double-stranded DNA packaged much like chromosomes in eukaryotes. Despite having few viral genes, polydnavirus’ genome is one of the largest, and largely composed of introns, which is rare for a virus. 70% of the DNA is noncoding; far from the genic efficiency typical of viruses; but then, human understanding of genetics is rudimentary.

The origin of polydnaviruses remains a mystery. Many of its protein products are inscrutable and have no known homologs (similar structures).

The polydnavirus defies placement in an evolutionary niche, lending support to the theory that it was assembled rather than evolved.


Healthy gypsy moth caterpillars climb out onto leaves to feed at night. At night, they crawl back onto branches or bark to hide from predators.

Contrastingly, caterpillars infected with a baculovirus disregard normal safety procedures and are readily found on leaves in broad daylight. For the virus, the caterpillar being picked off by an aerial predator is a free flight ticket.

Eventually an infected caterpillar climbs to the top of the tree it is on. There the caterpillar is converted into a sac of virus that liquefies and rains down on foliage below. The viral particles sprinkle leaves and await being eaten by the next caterpillar victim. Fast flight or slow fall: both tactics spread the virus.

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Some plant viruses get insects to do the heavy lifting for them. By altering feeding preferences, targeted herbivorous insects act as viral agents to spread infection through a plant population. Different viruses independently evolved this trickery.

Aphids not infected with Barley yellow dwarf virus (bydv) prefer grazing on barley plants that are infected, while infected aphids prefer uninfected plants. Hence, bydv promotes both its acquisition and transmission by its insect porter.

Aphids are similarly manipulated by the potato leafroll virus for potato plants. The tomato spotted wilt virus pulls the same trick with thrips that suck on tomato leaves.

The manipulative wiles of viruses are widespread. To engender transmission, an active herpes virus often makes its host lusty.

Cytomegalovirus – a cousin to herpes – can drive the offspring of its carriers crazy. Though this common virus invokes at most mild symptoms in adults, women infected with cytomegalovirus run an increased risk of bearing a child who will develop schizophrenia.

People vaccinated with flu viruses become more socially active shortly after being inoculated.

Viruses were early adopters in the parade of parasites that make their carriers do their bidding. Many other pathogens know how to manipulate their hosts minds, often rendering a host so insensible as to put its own life in peril for the parasite’s sake.

That viruses can influence the minds of other organisms in specific ways which advantage the pathogen is convincing evidence that Nature is an exhibition that cannot be explained by merely biomechanical means.