Microbial cooperation

Microorganisms engage in a wide variety of social interactions, including cooperation. A cooperative behavior is one that benefits an individual (the recipient) other than the one performing the behavior (the actor).[1] This article outlines the various forms of cooperative interactions (mutualism and altruism) seen in microbial systems, as well as the benefits that might have driven the evolution of these complex behaviors.

Introduction

Microorganisms, or microbes, span all three domains of life, including bacteria, archaea, viruses, and many unicellular eukaryotes (e.g., some fungi and protists). Typically defined as unicellular life forms that can only be observed with a microscope, microorganisms were the first cellular life forms, and were critical for creating the conditions for the evolution of more complex multicellular forms.

Although microbes are too small to see with the naked eye, they represent the overwhelming majority of biological diversity, and thus serve as an excellent system to study evolutionary questions. One such topic that scientists have examined in microbes is the evolution of social behaviors, including cooperation. A cooperative interaction benefits a recipient, and is selected for on that basis. In microbial systems, cells belonging to the same taxa have been documented partaking in cooperative interactions to perform a wide range of complex multicellular behaviors such as dispersal, foraging, construction of biofilms, reproduction, chemical warfare, and signaling. This article will outline the various forms of cooperative interactions seen in microbial systems, as well as the benefits that might have driven the evolution of these complex behaviors.

History

Table 1: Hamilton's classification of the four types of social behaviors.[1]
Effect on recipient
+
Effect on actor + Mutual benefit Selfishness
Altruism Spite

From an evolutionary point of view, a behavior is social if it has fitness consequences for both the individual that performs that behavior (the actor) and another individual (the recipient). Hamilton first categorized social behaviors according to whether the consequences they entail for the actor and recipient are beneficial (increase direct fitness) or costly (decrease direct fitness).[2] Based on Hamilton's definition, there are four unique types of social interactions: mutualism (+/+), selfishness (+/−), altruism (−/+), and spite (−/−) (Table 1). Mutualism and altruism are considered cooperative interactions because they are beneficial to the recipient, and will be the focus of this article.

Explaining cooperation remains one of the greatest challenges for evolutionary biology, regardless of whether the behavior is considered mutually beneficial or altruistic. According to classical evolutionary theory, an organism will only behave in ways that maximize its own fitness. Therefore, the origin of cooperative interactions, or actions by individuals that result in other individuals receiving fitness benefits, seems counterintuitive.

Theoretical explanations for the evolution of cooperation can be broadly classified into two categories: direct fitness benefits or indirect fitness benefits. This follows from Hamilton's 1964 insight that individuals gain inclusive fitness directly through their impact on their own reproduction (direct fitness effects), as well as through their impact on the reproduction of individuals with related genes (indirect fitness effects).[2]

Types of cooperation

Mutualism

Perhaps the most common cooperative interactions seen in microbial systems are mutually beneficial (+/+). Mutually beneficial social interactions provide a direct fitness benefit to both individuals involved, while outweighing any cost of performing the behaviour.[3] In an environment with individual microbes, mutualism is most often performed in order to increase individual fitness benefit. However, in a community, microorganisms will interact on a large scale to allow for the persistence of the population, which will thereby increase their own fitness.[4]

The majority of the time, organisms partaking in these behaviours have a shared interest in cooperation. In microbial systems, this is often seen in the production of metabolically expensive molecules, known as public goods. Many microbes, especially bacteria, produce numerous public goods that are released into the extracellular environment. The diffusion that occurs allows for them to be used by neighbouring organisms, despite being produced for the individual.

One very popular example of mutually beneficial microbial interactions involves the production of siderophores. Siderophores are iron-scavenging molecules produced by many microbial taxa, including bacteria and fungi. These molecules are known as chelating agents and play an important role in facilitating the uptake and metabolism of iron in the environment, as it normally exists in an insoluble form.[5] In order for bacteria to access this limiting factor, cells will manufacture these molecules, and then secrete them into the extracellular space.[6] Once released, the siderophores will sequester the iron, and form a complex, which is recognized by bacterial cell receptors. It can then be transported into the cell and reduced, making the iron metabolically accessible for the bacteria. The production of siderophores is often used as an example of mutualism as the compounds are not constricted to individual usage. As long as the organism possesses a receptor for the siderophore-Fe (III) complex, they can be taken up and utilized.[7]

There are many explanations in place that justify the evolution of mutually beneficial interactions. Most importantly, in order for the production of public goods to be evolutionarily beneficial, the behaviour must provide a direct benefit to the reproductive performance of the actor that outweighs the cost of performing the behaviour.[5] This is most often seen in the case of direct fitness benefit. As bacteria are most often found in colonies, neighbouring bacteria are likely to express genetic commonality. Therefore, by increasing the chances for a nearby bacterium to grow and divide, the host is increasing their own passage of genetic material. In the case of siderophores, a positive correlation was found between relatedness among bacterial lineages and siderophore production.[6]

Microbial communities are not only interested in the survival and productivity of their own species, however. In a mixed community, different bacterial species have been found to adapt to different food sources, including the waste products of other species, in order to stave off unnecessary competition.[8] This allows heightened efficiency for the community as a whole.

Having a balanced community is very important for microbial success. In the case of siderophore production, there must be equilibrium between the microbes that spend their energy to produce the chelating agents, and those that can utilize xenosiderophores. Otherwise, the exploitative microbes would eventually out-compete the producers, leaving a community with no organisms able to produce siderophores, and thus, unable to survive in low iron conditions. This ability to balance between the two populations is currently being researched. It is thought to be due to the presence of low-affinity receptors on the non-producers, or producers generating a toxin-mediated interference mechanism.[9]

Figure 1: The Prisoner Dilemma in a bacterial community. GASP mutants initially reach a high population density and subsequently decrease population viability.(a) Colony forming units (CFU) measured at day 1 (blue bars) and day 4 (red bars) of pure WT and GASP cultures and co-cultures with starting fractions of 90% WT and 10% GASP, 50% WT and 50% GASP, and 10% WT and 90% GASP. Error bars indicate the standard error of the mean of three replicate cultures. The inset shows that the change in the number of CFUs between day 4 and day 1 depends on the initial GASP fraction of a culture. (b) Growth curves, measured as optical density (OD) at 600 nm, of well-mixed batch cultures. A pure WT culture (black) sustains its population density for days, whereas a pure GASP culture (red) initially reaches a higher population density which later declines and drops below the level of the pure WT culture. WT-GASP co-cultures (dashed lines) show the frequency dependence of the overshooting and subsequent decline of population density.

While the production of public goods aims to benefit all individuals, it also leads to the evolution of cheaters, or individuals that do not pay the cost of producing a good, but still receive benefits (Figure 1). In order to minimize fitness costs, natural selection will favor individuals that do not to secrete while taking advantage of the secretions of their neighbors. In a population of siderophore secreting cells, non-secreting mutant cells do not pay the cost of secretion, but still gain the same benefit as the wild-type neighbors. Recently, Griffin et al. (2004) investigated the social nature of the production of siderophores in Pseudomonas aeruginosa.[10] When cells were grown in pure culture were placed in an iron-limiting environment, populations of cells that secreted siderophores (wild-type) outcompeted a population of mutant non-secretors. Therefore, siderophore production is beneficial when iron is limiting. However, when the same populations were placed in an iron-rich environment, the mutant population outcompeted wild-type population, demonstrating that siderophore production is metabolically costly. Finally, when both wild type and mutant bacteria were placed in the same mixed population, the mutants can gain the benefit of siderophore production without paying the cost, and hence increase in frequency. This concept is commonly referred to the tragedy of the commons.

The prisoner's dilemma game is another way that evolutionary biologists explain the presence of cheating in cooperative microbial systems. Originally framed by Merrill Flood and Melvin Dresher in 1950, the Prisoner's Dilemma is a fundamental problem in game theory, and demonstrates that two individuals might not cooperate even if it is in both their best interests to do so. In the dilemma, two individuals each choose whether to cooperate with the other individual or to cheat. Cooperation by both individuals gives the greatest average advantage. However, if one individual decides to cheat, they will obtain a greater individual advantage. If the game is played only once cheating is the superior strategy since it is the superior strategy. However, in biologically realistic situations, with repeated interactions (games), mutations, and heterogeneous environments, there is often no single stable solution and the success of individual strategies can vary in endless periodic or chaotic cycles. The specific solution to the game will depend critically on the way iterations are implemented and how pay-offs are translated to population and community dynamics.

In the bacteria Escherichia coli, a Prisoner Dilemma situation can be observed when mutants exhibiting a Grow Advantage in Stationary Phase (GASP) phenotype [11] compete with a wild type (WT) strain in batch culture.[12] In such batch culture settings, where the growth environment is homogenized by shaking the cultures, WT cells cooperate by arresting bacterial growth in order to prevent ecological collapse while the GASP mutants continue to grow by defecting to the wild type regulatory mechanism. As a consequence of such defection to the self-regulation of growth by the GASP cells, although higher cell densities are achieved in the short term, a population collapse is attained in the long run due to the tragedy of the commons (Figure 1). On the contrary, although WT cells do not achieve such high population densities, their populations are sustainable at the same density in the long term. As predicted by theory,[13] in a spatial setting such as those implemented experimentally by microfluidics chips, coexistence between the two strains is possible due to the localization of interactions and the spatial segregation of cheaters.[14] When provided with such a spatial environment, bacteria can self-organize into dynamic patterns of cell aggregation, desegregation which ensure that cooperator WT cells can reap the benefits of cooperation (Figure 2).

Figure 2: Spatial Prisoner Dilemma and the coexistence of cheaters and cooperators in an E. Coli community. WT and GASP E. coli coexist in a single-patch habitat. (a) Microscopy pictures showing a section of a habitat consisting of a single patch (8500×100×15${\displaystyle \mu m}$) at three time-points, the white bar indicates 50 m. WT (green) and GASP (red) cells develop into a structured community. Initially (1 hour) planktonic cells colonize the habitat, a day later many multi-cellular aggregates have formed. The composition of these aggregates (indicated by their color) changes over time. (b) GASP fraction through time of microhabitats consisting of a single patch with a volume equal to the total volume of an 85-patch microhabitat. Mean of experiments (red solid line), black dashed lines indicate the mean the standard deviation.

Greig & Travisano (2004) addressed these ideas with an experimental study on yeast Saccharomyces cerevisiae.[15] S. cerevisiae possesses multiple genes that each produce invertase, an enzyme that is secreted to digest sucrose outside of the cell. As discussed above, this public good production creates the potential for individual cells to cheat by stealing the sugar digested by their neighbors without contributing the enzyme themselves. Greig & Travisano (2004) measured the fitness of a cheater type (who possessed a reduced number of invertase genes) relative to a cooperator (who contained all possible invertase genes).[15] By manipulating the level of social interaction within the community by varying the population density, they found that the cheater is less fit than the cooperator at low levels of sociality, but more fit in dense communities. Therefore, they propose that selection for "cheating" causes natural variation in the amount of invertase genes an individual may possess, and that variation in invertase genes reflects constant adaptation to an ever-changing biotic environment that is a consequence of the instability of cooperative interactions.

Altruism

The second type of cooperative interactions is altruistic, or interactions that are beneficial to the recipient but costly to the actor (-/+). Justifying the evolutionary benefit of altruistic behavior is a highly debated topic. A common justification for the presence of altruistic behaviors is that they provide an indirect benefit because the behavior is directed towards other individuals who carry the cooperative gene.[2] The simplest and most common reason for two individuals to share genes in common is for them to be genealogical relatives (kin), and so this is often termed kin selection.[16] According to Hamilton, an altruistic act is evolutionarily beneficial if the relatedness of the individual that profits from the altruistic act is higher than the cost/benefit ratio this act imposes. This rationale is referred to as Hamilton's rule.

Natural selection normally favors a gene if it increases reproduction, because the offspring share copies of that gene. However, a gene can also be favored if it aids other relatives, who also share copies. Therefore, by helping a close relative reproduce, an individual is still passing on its own genes to the next generation, albeit indirectly. Hamilton pointed out that kin selection could occur via two mechanisms: (a) kin discrimination, when cooperation is preferentially directed toward relatives, and (b) limited dispersal (population viscosity), which keeps relatives in spatial proximity to one another, allowing cooperation to be directed indiscriminately toward all neighbors (who tend to be relatives).[2] In microbial systems, these two mechanisms are equally important. For example, most microbial populations often begin from a small number of colonizers. Because most microbes reproduce asexually, close genetic relatives will surround cells as the population grows. These clonal populations often result in an extremely high density, especially in terrestrial systems. Therefore, the probability that a cells altruistic behavior will benefit a close relative is extremely high.

While altruistic behaviors are most common between individuals with high genetic relatedness, it is not completely necessary. Altruistic behaviors can also be evolutionarily beneficial if the cooperation is directed towards individuals who share the gene of interest, regardless of whether this is due to coancestry or some other mechanism.[17] An example of this is known as the "green beard" mechanism, and requires a single gene (or a number of tightly linked genes) that both causes the cooperative behavior and can be recognized by other individuals due to a distinctive phenotypic marker, such as a green beard.[2]

The most studied slime mold from this perspective is Dictyostelium discoideum, a predator of bacteria that is common in the soil. When starving, the usually solitary single-celled amoebae aggregate and form a multicellullar slug that can contain 104–106 cells. This slug migrates to the soil surface, where it transforms into a fruiting body composed of a spherical tip of spores and a stalk consisting of nonviable stalk cells that hold the spores aloft (Figure 2). Roughly 20% of the cells develop into the non-reproductive stalk, elevating the spores and aiding their dispersal.[18]

Programmed cell death (PCD) is another suggested form of microbial altruistic behavior. Although programmed cell death (also known as apoptosis or autolysis) clearly provides no direct fitness benefit, it can be evolutionary adaptive if it provides indirect benefits to individuals with high genetic relatedness (kin selection). Several altruistic possibilities have been suggested for PCD, such as providing resources that could be used by other cells for growth and survival in Saccharomyces cerevisiae.[19][20] While using kin selection to explain the evolutionary benefits of PCD is common, the reasoning contains some inherent problems. Charlesworth (1978) noted that it is extremely hard for a gene causing suicide to spread because only relatives that do NOT share the gene would ultimately benefit.[21] Therefore, the possible solution to this problem in microbes is that selection could favor a low probability of PCD among a large population of cells, possibly depending upon individual condition, environmental conditions, or signaling.

Other microbial interactions

Quorum sensing

Figure 3: Diagram of quorum sensing. (left) In low density, the concentration of the autoinducer (blue dots) is relatively low and the substance production is restricted. (right) In high density, the concentration of the autoinducer is high and the bacterial substances (red dots) are produced.

The integration of cooperative and communicative interactions appear to be extremely important to microbes; for example, 6–10% of all genes in the bacterium Pseudomonas aeruginosa are controlled by cell-cell signaling systems.[22] One way that microbes communicate and organize with each other in order to partake in more advanced cooperative interactions is through quorum sensing. Quorum sensing describes the phenomenon in which the accumulation of signaling molecules in the surrounding environment enables a single cell to assess the number of individuals (cell density) so that the population as a whole can make a coordinated response. This interaction is fairly common among bacterial taxa, and involves the secretion by individual cells of 'signaling' molecules, called autoinducers or pheromones.These bacteria also have a receptor that can specifically detect the signaling molecule. When the inducer binds the receptor, it activates transcription of certain genes, including those for inducer synthesis. There is a low likelihood of a bacterium detecting its own secreted inducer. Thus, in order for gene transcription to be activated, the cell must encounter signaling molecules secreted by other cells in its environment. When only a few other bacteria of the same kind are in the vicinity, diffusion reduces the concentration of the inducer in the surrounding medium to almost zero, so the bacteria produce little inducer. However, as the population grows the concentration of the inducer passes a threshold, causing more inducer to be synthesized. This forms a positive feedback loop, and the receptor becomes fully activated. Activation of the receptor induces the up regulation of other specific genes, causing all of the cells to begin transcription at approximately the same time. In other words, when the local concentration of these molecules has reached a threshold, the cells respond by switching on particular genes. In this way individual cells can sense the local density of bacteria, so that the population as a whole can make a coordinated response.[23]

In many situations, the cost bacterial cells pay in order to coordinate behaviors outweighs the benefits unless there is a sufficient number of collaborators. For instance, the bioluminescent luciferase produced by Vibrio fischeri would not be visible if it was produced by a single cell. By using quorum sensing to limit the production of luciferase to situations when cell populations are large, V. fischeri cells are able to avoid wasting energy on the production of useless product. In many situations bacterial activities, such as the production of the mentioned public goods, are only worthwhile as a joint activity by a sufficient number of collaborators. Regulation by quorum sensing would allow the cells to express appropriate behavior only when it is effective, thus saving resources under low density conditions. Therefore, quorum sensing has been interpreted as a bacterial communication system to coordinate behaviors at the population level.

The opportunistic bacteria Pseudomonas aeruginosa also uses quorum sensing to coordinate the formation of biofilms, swarming motility, exopolysaccharide production, and cell aggregation.[24] These bacteria can grow within a host without harming it, until they reach a certain concentration. Then they become aggressive, their numbers sufficient to overcome the host's immune system, and form a biofilm, leading to disease within the host. Another form of gene regulation that allows the bacteria to rapidly adapt to surrounding changes is through environmental signaling. Recent studies have discovered that anaerobiosis can significantly impact the major regulatory circuit of quorum sensing. This important link between quorum sensing and anaerobiosis has a significant impact on production of virulence factors of this organism.[25] It is hoped that the therapeutic enzymatic degradation of the signaling molecules will prevent the formation of such biofilms and possibly weaken established biofilms. Disrupting the signalling process in this way is called quorum inhibition.

Implications

While the evolution of cooperative interactions allowed microbial taxa to increase their fitness, it is hypothesized that cooperation provided a proximate cause to other major evolutionary transitions, including the evolution of multicellularity.[26] This idea, often referred to as the Colonial Theory, was first proposed by Haeckel in 1874, and claims that the symbiosis of many organisms of the same species (unlike the symbiotic theory, which suggests the symbiosis of different species) led to a multicellular organism. In a few instances, multicellularity occurs by cells separating and then rejoining (e.g., cellular slime molds) whereas for the majority of multicellular types, multicellularity occurs as a consequence of cells failing to separate following division.[27] The mechanism of this latter colony formation can be as simple as incomplete cytokinesis, though multicellularity is also typically considered to involve cellular differentiation.[28]

The advantage of the Colonial Theory hypothesis is that it has been seen to occur independently numerous times (in 16 different protoctistan phyla). For instance, during food shortages Dictyostelium discoideum cells group together in a colony that moves as one to a new location. Some of these cells then slightly differentiate from each other. Other examples of colonial organisation in protozoa are Volvocaceae, such as Eudorina and Volvox. However, it can often be hard to separate colonial protists from true multicellular organisms, as the two concepts are not distinct. This problem plagues most hypotheses of how multicellularisation could have occurred. However, most scientists accept that multicellular organisms, from all phyla, evolved by the colonial mechanism.

References

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An ecological cascade effect is a series of secondary extinctions that is triggered by the primary extinction of a key species in an ecosystem. Secondary extinctions are likely to occur when the threatened species are: dependent on a few specific food sources, mutualistic (dependent on the key species in some way), or forced to coexist with an invasive species that is introduced to the ecosystem. Species introductions to a foreign ecosystem can often devastate entire communities, and even entire ecosystems. These exotic species monopolize the ecosystem's resources, and since they have no natural predators to decrease their growth, they are able to increase indefinitely. Olsen et al. showed that exotic species have caused lake and estuary ecosystems to go through cascade effects due to loss of algae, crayfish, mollusks, fish, amphibians, and birds. However, the principal cause of cascade effects is the loss of top predators as the key species. As a result of this loss, a dramatic increase (ecological release) of prey species occurs. The prey is then able to overexploit its own food resources, until the population numbers decrease in abundance, which can lead to extinction. When the prey's food resources disappear, they starve and may go extinct as well. If the prey species is herbivorous, then their initial release and exploitation of the plants may result in a loss of plant biodiversity in the area. If other organisms in the ecosystem also depend upon these plants as food resources, then these species may go extinct as well. An example of the cascade effect caused by the loss of a top predator is apparent in tropical forests. When hunters cause local extinctions of top predators, the predators' prey's population numbers increase, causing an overexploitation of a food resource and a cascade effect of species loss. Recent studies have been performed on approaches to mitigate extinction cascades in food-web networks.

Co-operation (evolution)

In evolution, co-operation is the process where groups of organisms work or act together for common or mutual benefits. It is commonly defined as any adaptation that has evolved, at least in part, to increase the reproductive success of the actor's social partners. For example, territorial choruses by male lions discourage intruders and are likely to benefit all contributors.This process contrasts with intragroup competition where individuals work against each other for selfish reasons. Cooperation exists not only in humans but in other animals as well. The diversity of taxa that exhibits cooperation is quite large, ranging from zebra herds to pied babblers to African elephants. Many animal and plant species cooperate with both members of their own species and with members of other species.

Energy flow (ecology)

In ecology, energy flow, also called the calorific flow, refers to the flow of energy through a food chain, and is the focus of study in ecological energetics. In an ecosystem, ecologists seek to quantify the relative importance of different component species and feeding relationships.

A general energy flow scenario follows:

Solar energy is fixed by the photoautotrophs, called primary producers, like green plants. Primary consumers absorb most of the stored energy in the plant through digestion, and transform it into the form of energy they need, such as adenosine triphosphate (ATP), through respiration. A part of the energy received by primary consumers, herbivores, is converted to body heat (an effect of respiration), which is radiated away and lost from the system. The loss of energy through body heat is far greater in warm-blooded animals, which must eat much more frequently than those that are cold-blooded. Energy loss also occurs in the expulsion of undigested food (egesta) by excretion or regurgitation.

Secondary consumers, carnivores, then consume the primary consumers, although omnivores also consume primary producers. Energy that had been used by the primary consumers for growth and storage is thus absorbed into the secondary consumers through the process of digestion. As with primary consumers, secondary consumers convert this energy into a more suitable form (ATP) during respiration. Again, some energy is lost from the system, since energy which the primary consumers had used for respiration and regulation of body temperature cannot be utilized by the secondary consumers.

Tertiary consumers, which may or may not be apex predators, then consume the secondary consumers, with some energy passed on and some lost, as with the lower levels of the food chain.

A final link in the food chain are decomposers which break down the organic matter of the tertiary consumers (or whichever consumer is at the top of the chain) and release nutrients into the soil. They also break down plants, herbivores and carnivores that were not eaten by organisms higher on the food chain, as well as the undigested food that is excreted by herbivores and carnivores. Saprotrophic bacteria and fungi are decomposers, and play a pivotal role in the nitrogen and carbon cycles.The energy is passed on from trophic level to trophic level and each time about 90% of the energy is lost, with some being lost as heat into the environment (an effect of respiration) and some being lost as incompletely digested food (egesta). Therefore, primary consumers get about 10% of the energy produced by autotrophs, while secondary consumers get 1% and tertiary consumers get 0.1%. This means the top consumer of a food chain receives the least energy, as a lot of the food chain's energy has been lost between trophic levels. This loss of energy at each level limits typical food chains to only four to six links.

Food web

A food web (or food cycle) is the natural interconnection of food chains and a graphical representation (usually an image) of what-eats-what in an ecological community. Another name for food web is consumer-resource system. Ecologists can broadly lump all life forms into one of two categories called trophic levels: 1) the autotrophs, and 2) the heterotrophs. To maintain their bodies, grow, develop, and to reproduce, autotrophs produce organic matter from inorganic substances, including both minerals and gases such as carbon dioxide. These chemical reactions require energy, which mainly comes from the Sun and largely by photosynthesis, although a very small amount comes from hydrothermal vents and hot springs. A gradient exists between trophic levels running from complete autotrophs that obtain their sole source of carbon from the atmosphere, to mixotrophs (such as carnivorous plants) that are autotrophic organisms that partially obtain organic matter from sources other than the atmosphere, and complete heterotrophs that must feed to obtain organic matter. The linkages in a food web illustrate the feeding pathways, such as where heterotrophs obtain organic matter by feeding on autotrophs and other heterotrophs. The food web is a simplified illustration of the various methods of feeding that links an ecosystem into a unified system of exchange. There are different kinds of feeding relations that can be roughly divided into herbivory, carnivory, scavenging and parasitism. Some of the organic matter eaten by heterotrophs, such as sugars, provides energy. Autotrophs and heterotrophs come in all sizes, from microscopic to many tonnes - from cyanobacteria to giant redwoods, and from viruses and bdellovibrio to blue whales.

Charles Elton pioneered the concept of food cycles, food chains, and food size in his classical 1927 book "Animal Ecology"; Elton's 'food cycle' was replaced by 'food web' in a subsequent ecological text. Elton organized species into functional groups, which was the basis for Raymond Lindeman's classic and landmark paper in 1942 on trophic dynamics. Lindeman emphasized the important role of decomposer organisms in a trophic system of classification. The notion of a food web has a historical foothold in the writings of Charles Darwin and his terminology, including an "entangled bank", "web of life", "web of complex relations", and in reference to the decomposition actions of earthworms he talked about "the continued movement of the particles of earth". Even earlier, in 1768 John Bruckner described nature as "one continued web of life".

Food webs are limited representations of real ecosystems as they necessarily aggregate many species into trophic species, which are functional groups of species that have the same predators and prey in a food web. Ecologists use these simplifications in quantitative (or mathematical representation) models of trophic or consumer-resource systems dynamics. Using these models they can measure and test for generalized patterns in the structure of real food web networks. Ecologists have identified non-random properties in the topographic structure of food webs. Published examples that are used in meta analysis are of variable quality with omissions. However, the number of empirical studies on community webs is on the rise and the mathematical treatment of food webs using network theory had identified patterns that are common to all. Scaling laws, for example, predict a relationship between the topology of food web predator-prey linkages and levels of species richness.

Invasive species

An invasive species is a species that is not native to a specific location (an introduced species), and that has a tendency to spread to a degree believed to cause damage to the environment, human economy or human health.The term as most often used applies to introduced species that adversely affect the habitats and bioregions they invade economically, environmentally, or ecologically. Such species may be either plants or animals and may disrupt by dominating a region, wilderness areas, particular habitats, or wildland–urban interface land from loss of natural controls (such as predators or herbivores). This includes plant species labeled as exotic pest plants and invasive exotics growing in native plant communities. The European Union defines "Invasive Alien Species" as those that are, firstly, outside their natural distribution area, and secondly, threaten biological diversity. The term is also used by land managers, botanists, researchers, horticulturalists, conservationists, and the public for noxious weeds.The term "invasive" is often poorly defined or very subjective and some broaden the term to include indigenous or "native" species, that have colonized natural areas - for example deer considered by some to be overpopulating their native zones and adjacent suburban gardens in the Northeastern and Pacific Coast regions of the United States.The definition of "native" is also sometimes controversial. For example, the ancestors of Equus ferus (modern horses) evolved in North America and radiated to Eurasia before becoming locally extinct. Upon returning to North America in 1493 during their hominid-assisted migration, it is debatable as to whether they were native or exotic to the continent of their evolutionary ancestors.Notable examples of invasive plant species include The kudzu vine, Andean pampas grass, and yellow starthistle. Animal examples include the New Zealand mud snail, feral pigs, European rabbits, grey squirrels, domestic cats, carp and ferrets.Invasion of long-established ecosystems by organisms from distant bio-regions is a natural phenomenon, but has been accelerated massively by humans, from their earliest migrations though to the age of discovery, and now international trade.

Mesopredator release hypothesis

The mesopredator release hypothesis is an ecological theory used to describe the interrelated population dynamics between apex predators and mesopredators within an ecosystem, such that a collapsing population of the former results in dramatically-increased populations of the latter. This hypothesis describes the phenomenon of trophic cascade in specific terrestrial communities.

A mesopredator is a medium-sized, middle trophic level predator, which both preys and is preyed upon. Examples are raccoons, skunks, snakes, cownose rays, and small sharks.

Microalgae

Microalgae or microphytes are microscopic algae, typically found in freshwater and marine systems, living in both the water column and sediment. They are unicellular species which exist individually, or in chains or groups. Depending on the species, their sizes can range from a few micrometers (µm) to a few hundred micrometers. Unlike higher plants, microalgae do not have roots, stems, or leaves. They are specially adapted to an environment dominated by viscous forces. Microalgae, capable of performing photosynthesis, are important for life on earth; they produce approximately half of the atmospheric oxygen and use simultaneously the greenhouse gas carbon dioxide to grow photoautotrophically. Microalgae, together with bacteria, form the base of the food web and provide energy for all the trophic levels above them. Microalgae biomass is often measured with chlorophyll a concentrations and can provide a useful index of potential production. The standing stock of microphytes is closely related to that of its predators. Without grazing pressures the standing stock of microphytes dramatically decreases.The biodiversity of microalgae is enormous and they represent an almost untapped resource. It has been estimated that about 200,000-800,000 species in many different genera exist of which about 50,000 species are described. Over 15,000 novel compounds originating from algal biomass have been chemically determined. Most of these microalgae species produce unique products like carotenoids, antioxidants, fatty acids, enzymes, polymers, peptides, toxins and sterols.

Microbial food web

The microbial food web refers to the combined trophic interactions among microbes in aquatic environments. These microbes include viruses, bacteria, algae, heterotrophic protists (such as ciliates and flagellates).

In aquatic environments, microbes constitute the base of the food web. Single celled photosynthetic organisms such as diatoms and cyanobacteria are generally the most important primary producers in the open ocean. Many of these cells, especially cyanobacteria, are too small to be captured and consumed by small crustaceans and planktonic larvae. Instead, these cells are consumed by phagotrophic protists which are readily consumed by larger organisms. Viruses can infect and break open bacterial cells and (to a lesser extent), planktonic algae (a.k.a. phytoplankton). Therefore, viruses in the microbial food web act to reduce the population of bacteria and, by lysing bacterial cells, release particulate and dissolved organic carbon (DOC). DOC may also be released into the environment by algal cells. One of the reasons phytoplankton release DOC termed "unbalanced growth" is when essential nutrients (e.g. nitrogen and phosphorus) are limiting. Therefore, carbon produced during photosynthesis is not used for the synthesis of proteins (and subsequent cell growth), but is limited due of a lack of the nutrients necessary for macromolecules. Excess photosynthate, or DOC is then released, or exuded.

The microbial loop describes a pathway in the microbial food web where DOC is returned to higher trophic levels via the incorporation into bacterial biomass.

Microbial intelligence

Microbial intelligence (popularly known as bacterial intelligence) is the intelligence shown by microorganisms. The concept encompasses complex adaptive behaviour shown by single cells, and altruistic or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.

Complex cells, like protozoa or algae, show remarkable abilities to organise themselves in changing circumstances. Shell-building by amoebae reveals complex discrimination and manipulative skills that are ordinarily thought to occur only in multicellular organisms.

Even bacteria, which show primitive behavior as isolated cells, can display more sophisticated behavior as a population. These behaviors occur in single species populations, or mixed species populations. Examples are colonies of myxobacteria, quorum sensing, and biofilms.

It has been suggested that a bacterial colony loosely mimics a biological neural network. The bacteria can take inputs in form of chemical signals, process them and then produce output chemicals to signal other bacteria in the colony.

The mechanisms that enable single celled organisms to coordinate in populations presumably carried over in those lines that evolved multicellularity, and were co-opted as mechanisms to coordinate multicellular organisms.

Bacteria communication and self-organization in the context of network theory has been investigated by Eshel Ben-Jacob research group at Tel Aviv University which developed a fractal model of bacterial colony and identified linguistic and social patterns in colony lifecycle.

Microbial population biology

Microbial population biology is the application of the principles of population biology to microorganisms.

Microorganism

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.

Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.

They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

Productivity (ecology)

In ecology, productivity refers to the rate of generation of biomass in an ecosystem. It is usually expressed in units of mass per unit surface (or volume) per unit time, for instance grams per square metre per day (g m−2 d−1). The mass unit may relate to dry matter or to the mass of carbon generated. Productivity of autotrophs such as plants is called primary productivity, while that of heterotrophs such as animals is called secondary productivity.

Pyoverdine

Pyoverdines (alternatively, and less commonly, spelled as pyoverdins) are fluorescent siderophores produced by certain pseudomonads. Pyoverdines are important virulence factors, and are required for pathogenesis in many biological models of infection. Their contributions to bacterial pathogenesis include providing a crucial nutrient (i.e., iron), regulation of other virulence factors (including exotoxin A and the protease PrpL), supporting the formation of biofilms, and are increasingly recognized for having toxicity themselves.Pyoverdines have also been investigated as "Trojan Horse" molecules for the delivery of antimicrobials to otherwise resistant bacterial strains, as chelators that can be used for bioremediation of heavy metals, and as fluorescent reporters used to assay for the presence of iron and potentially other metals.Due to their bridging the gaps between pathogenicity, iron metabolism, and fluorescence, pyoverdines have piqued the curiosity of scientists around the world for over 100 years.

Sustainable gardening

Sustainable gardening includes the more specific sustainable landscapes, sustainable landscape design, sustainable landscaping, sustainable landscape architecture, resulting in sustainable sites. It comprises a disparate group of horticultural interests that can share the aims and objectives associated with the international post-1980s sustainable development and sustainability programs developed to address the fact that humans are now using natural biophysical resources faster than they can be replenished by nature.Included within this compass are those home gardeners, and members of the landscape and nursery industries, and municipal authorities, that integrate environmental, social, and economic factors to create a more sustainable future.

Organic gardening and the use of native plants are integral to sustainable gardening.

The Evolution of Cooperation

The Evolution of Cooperation is a 1984 book by political scientist Robert Axelrod that expanded a highly influential paper of the same name, and popularized the study upon which the original paper had been based.

"The Evolution of Cooperation" is a 1981 paper by Axelrod and evolutionary biologist W. D. Hamilton in the scientific literature, which became the most cited publication in the field of political science.Evolution of cooperation is a general term for investigation into how cooperation can emerge and persist (also known as cooperation theory) as elucidated by the application of game theory. Traditional game theory did not explain some forms of cooperation well. The academic literature concerned with those forms of cooperation not easily handled in traditional game theory, with special consideration of evolutionary biology, largely took it's modern form as a result of Axelrod's and Hamilton's influential 1981 paper and the book that followed.

A revised edition of the 1984 book was published in 2006.

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