Microbial Communities

Microbial Communities Cristiana Callieri, Ester M Eckert, and Andrea Di Cesare, National Research Council, Verbania, Italy Filippo Bertoni, ASCA—University of Amsterdam, Amsterdam, The Netherlands r 2019 Elsevier B.V. All rights reserved. Introduction Aquatic microbial communities encompass all the organisms living in (marine, fresh, and brackish) water habitats that are not visible to the naked eye (conventionally, less than 1 mm), thus including representatives from all three domains of life—Archaea, Bacteria, and Eukarya. Viruses, together with viroids, plasmids and other non-cellular life forms, are excluded from the three domains system, but, given their impact on microbial populations, are usually included in microbial community studies. Unlike a population—which includes only individuals of the same “species”—or a guild—which groups metabolically related populations—a community is not defined by phylogeny or functional traits but by its habitat. Thus, an aquatic microbial community can be defined as an assemblage of co-occurring, and potentially interacting, microscopic “species,” present in a defined habitat in space and time. Despite the small size of these organisms—and the related challenges in studying them—microorganisms are key to the ecological dynamics of the biosphere. As it reaches even the most extreme environments, microbial life's sheer biomass is consequential to the entire planet: in the oceans alone, microbes contribute to as much as 90% of the total biomass. And while oceans cover over 70% of the World's surface (1.3  109 km3), meaning that most water on Earth (B97%) is seawater, inland waters—including lakes, ponds, rivers, streams, wetlands, and groundwater—and ice confined in polar caps and glaciers only account for B1% and B2% of the hydrosphere respectively, but have a similarly crucial role for life in the biosphere. All these aquatic environments are dominated by microbial communities. But microorganisms are not only the most diffused life form; they are also characterized by an incredible functional and genetic diversity, contributing to most, if not all, biogeochemical processes on Earth. As such, microbial communities represent a crucial component of global dynamics, and an important repository of genetic diversity. In aquatic environments their abundance is significant, with concentrations—even excluding microbial eukaryotes—around approximately 106 cells per milliliter of marine or fresh water. They are responsible for the ongoing production and recycling of organic matter and are involved in fundamental energy flows, exhibiting the ability to perform a range of biogeochemical transformations. The planetary impact of microbial communities and of their diversity (Fig. 1)—all the more evident when considering the crucial contributions they offered to the history of life on this planet, like the Great Oxygenation Event—depends on the accumulation of smaller causes into effects at a larger scale. But, given the vast nature of the environments the microbes inhabit, microbial life is most commonly approached at a large scale and through its cumulative effects. This is why, in this overview, we will focus especially on planktonic communities and on large-scale interactions and dynamics. In the conclusions we will get back to the importance of microscale dynamics and their interactions with macrobiota, to briefly consider the possibilities they open for novel research. Microbial Lifestyles in Aquatic Habitats In aquatic habitats there is a major distinction in lifestyles that structures research on microbial communities: this is the division between microbial organisms living suspended in the water column and therefore drifting with water currents, known as plankton (from the Greek term for vagabond), and those living attached to a substrate and in the sediment deposited at the bottom of water bodies, known as benthos (Greek for depth). Planktonic microorganisms are transported by water currents or simply by the turbulence created by water layers at different temperatures (i.e., density). Their growth is therefore strongly driven by physical forces that can transport them in layers enriched with nutrients or, conversely, can segregate them to deep waters (called hypolimnetic, in lakes and bathypelagic, in oceans). Despite this general dependence on water dynamics, some planktonic organisms possess locomotion appendages like flagella or cilia, or internal gas vacuoles by which the cells can regulate their buoyancy. Therefore, even at slow velocity and in calm water conditions, the motile cells can regulate their position. Usually considered as free-living cells, these organisms can also form aggregates of various kinds in different environmental conditions. Benthonic microorganisms live attached to a fixed substrate or at the interface between water and sediment. Collecting organic material settling from above, the benthos takes part in the sedimentation processes and is usually more concentrated than the plankton. These organisms usually form aggregates embedded in an extracellular matrix composed of extracellular polymeric substances (EPS), called biofilms, which facilitate transport and exchange of chemicals, nutrients, and signaling compounds, while helping in protecting against predation. Early mats of similar biofilms are thought to have had an important role in the evolution of life (see Box 1). Within these aggregates, bacterial community composition varies based on the substrate, the broader habitat, and the species included. For example, the Cytophaga-Flavobacteria-Bacteroidetes (CFB) group mostly dominate the biofilm on This is an update of J. Passarge and J. Huisman, Microbial Communities, In Encyclopedia of Ecology, edited by Sven Erik Jørgensen and Brian D. Fath, Academic Press, Oxford, 2008, pp. 2328–2334. 126 Encyclopedia of Ecology, 2nd edition, Volume 1 doi:10.1016/B978-0-12-409548-9.11222-9 Aquatic Ecology: Microbial Communities 127 Fig. 1 Maps of predicted global marine bacterial diversity (modified from Ladau, J., et al. (2013). Global marine bacterial diversity peaks at high latitudes in winter. ISME Journal 7, 1669–1677). Color scale shows relative richness of marine surface waters as predicted by Species Distribution Modeling (SDM). In December, the Operational Taxonomic Unit (OTU) richness peaks in temperate and higher latitudes in the Boreal Hemisphere. In June, OTU richness peaks in temperate latitudes in the Austral Hemisphere. Predicted richness during the spring and fall is intermediate. Box 1 Living at the interface: the phycosphereFar from capturing the complexity of microbial lifestyles, this foundational division sometimes gets in the way of studying more detailed, micro-scale interactions and habitats. Indeed, as it is often true in ecology, even at the microscale the interface between two different environments tends to be more productive and rich in interactions. Microhabitats like marine snow particles, or the phycosphere of algae—the halo of organic compounds excreted by phytoplanktonic cells—are crucial to microbial communities, especially in environments otherwise characterized by low nutrient concentrations. In the phycosphere, bacteria or other microorganisms can be found as free-living single cells near algal cells or directly attached on their surface, in biofilms (Fig. 2). The study of the phycosphere at single-cell level has shown how this microenvironment is a hotspot of bacteria–phytoplankton interactions, where the exchange of infochemicals and metabolites is very high. One of these substances is dimethylsulfoniopropionate (DMSP), a source of sulfur and carbon for heterotrophic bacteria, which is actively exudated by algae and produced during cell lysis. The lifestyle of bacteria in aggregates has the advantage to protect them against small flagellate predation (hetero- and mixotrophic nano flagellates), to increase the sedimentation rate and to offer a nutrient richer microenvironment. While challenging our categorizations of microbial life, microenvironments and their microdynamics remind us of the importance of paying attention to life at any scale—as even the smallest niche might reveal key to the history of life on Earth. macrophytes, followed by alpha- and betaproteobacteria. The presence of Planctomycetes on plant biofilms depends strongly on the nutrient content and plant age, as these bacteria can be affected by organic compounds produced by plants. Microbial Diversity of Planktonic Communities Prokaryotes Prokaryotes are defined by their cell structure, which lacks membrane-bound organelles and nucleus. They include the whole domains Bacteria and Archaea and can perform autotrophic and heterotrophic metabolisms. An important subdivision in this group is that between Gram-positive bacteria, bounded by a single-unit lipid membrane and a thick layer of peptidoglycan, and Gram-negative bacteria, with an outer membrane, a lipopolysaccharide layer, but a thin peptidoglycan layer. This rough classification, based on the result of a staining procedure, remains still valid, despite the changes brought about by molecular biology in the classification of microorganisms. This is because the composition of the outer part of the cells, which is identified by the Gram 128 Aquatic Ecology: Microbial Communities Fig. 2 An example of phycosphere: a microenvironment where bacteria, cyanobacteria and eukaryotes meet. Left: DAPI colored and visualized at epifluorescence; Right: the same field without DAPI where only autofluorescence is visible (1250  ). Box 2 Estimating Microbial DiversityThe definition of species for Prokaryotes is hampered by various traits, including their poorly developed morphology and the fact that the vast majority of these organisms remains uncultured, and thus little is known about their physiology and behaviour. The main source of information on bacterial and archaeal diversity derives from environmental surveys of DNA sequences. Species are often defined through similarity thresholds of marker sequences, such as the small-subunit rRNA (16S and 18S rRNA gene for prokaryotes and eukaryotes, respectively). Taxonomic grouping of the sequences is considered operational, meaning that it is based on the dataset of a specific study, and the term species is replaced by Operational Taxonomic Unit (OTU). However, even such molecular microbial diversity is far from being fully explored, and recent estimates of the global number of OTUs of Archaea and Bacteria differ as much as between millions and billions. This is because many taxa are very low in abundance, as in many sequencing campaigns a large part of the sequences is presented only once in the whole dataset (Fig. 3). Such sequences can be related to active species that are very low in number, to dormant or dead cells, to free DNA or simply due to sequencing errors. Thus, the actual richness of this so-called rare-biosphere is difficult to estimate. The upper pelagic zone of the ocean alone is estimated to harbor more than 35  103 prokaryotic species, whereas richness in the deep sea is around an order of magnitude poorer. In general, temperature seems to be a driving factor of richness in the oceans. Estimates of freshwater diversity are also in the range of tens of thousands and terrestrial ecosystems are an important source of diversity of freshwater ecosystems. Therein sediments are particularly rich in OTUs. Molecular richness of microbial eukaryotes found in aquatic environments is predicted to be more than 100  103 with similar numbers of OTUs in the sea and in freshwaters. These numbers far exceed the numbers of species determined morphologically (morpho species). This is, on the one hand, due to the fact that some species look the same but are genetically different (many fungi, e.g., but also diatoms), in which case morphological identification underestimates species diversity. On the other hand, some species have more than one copy of the 18S rRNA gene in their genome, which can be very polymorph (e.g., in some Ciliate species over 40 polymorphic sites of the 18S rRNA gene were found) and thus diversity is vastly overestimated by molecular technics. stain, strongly determines the capacity of cells to resist to stressing environmental conditions or to communicate with other microorganisms, making it a key for cell taxonomy (see Box 2). The marine bacterium Pelagibacter ubique, belonging to the SAR11-cluster of Alphaproteobacteria, is the most abundant microorganism on earth. Actinobacteria, Alphaproteobacteria and Betaproteobacteria, Flavo- and Sphingobacteriales numerically dominate the freshwater bacterioplankton. The acI clade of Actinobacteria and the Beta I and II clades of Betaproteobacteria comprise 30%–50% of the total bacterial cells in the water column. Similarly, the ultramicrobacteria of freshwater LD12 lineage, sister group of the marine SAR11, previously considered rare in lacustrine ecosystems, have been recently found to reach abundances comparable with those of the oceans. This discovery has opened a new view on the dispersal of microorganisms between marine and freshwater habitats. Another important phylum of photosynthetic bacteria is composed by Cyanobacteria. These microorganisms come in a variety of forms (including both coccoid and filamentous forms) and lifestyles (from single free-living cells to colonial aggregates) and are ubiquitous in aquatic environments. This is because, thanks to their long evolutionary history, they possess a variety of metabolic pathways that give them competitive advantage and facilitate their adaptation to diverse environmental conditions, from the most eutrophic to pristine oligotrophic waters. Because of this adaptability and plasticity, they are particularly successful in changing, adverse conditions: hence the current increase in occurrence of toxic cyanobacterial harmful algal blooms (CHABs), facilitated by anthropogenic climate disruptions on a planetary scale—which associated cyanobacteria to environmental distress. One of the most enigmatic microbial groups in the oceans is the Marine Group I (MGI.1a) of Archaea: the Thaumarchaeota (formerly 1.1a Crenarchaeota). These Archaea are commonly found in oceanic and freshwater plankton, mainly in mesopelagic and hypolimnetic Aquatic Ecology: Microbial Communities 129 Fig. 3 Potential outcome of a meta-sequencing study of the 16S rDNA gene diversity clustered into Operational Taxonomic Units (OTUs). Most of the OTUs are very low in abundance in the dataset and therefore rare, only very few OTUs have high relative abundances and are considered abundant. waters, where they comprise up to about 40% of the microbial community. Members of the MGI.1a clade have also been found in high-altitude lakes during stratification, whereas the clade SAGMGC-1 was retrieved in high densities in surface water in winter. Microbial Eukaryotes Microbial eukaryotes, whose cells are recognized by the membrane-bound nuclei and organelles, are massively abundant; in the euphotic zones of the world's oceans alone, there are 102–104 protist cells per mL. The definition of eukaryotic microbes is usually arbitrarily based on size, including everything smaller than 3 mm. Thus, representatives of the whole domain Eukarya, except for vertebrates, are included in this category, like many unicellular algae (e.g., Chlorophyta, Diatoms, Dinoflagellates). Functional classification is mainly based on their metabolism, meaning whether they sequester carbon through primary production, heterotrophy or mixotrophy—in which the same cell can fix CO2, as well as assimilate it from dissolved or particulate organic carbon. Considering that many species are capable of this versatile metabolism, comparably little attention has been devoted to mixotrophy, mainly due to technical difficulties in identifying whether a pigmented cell is currently following a purely autotrophic lifestyle or not. The most common eukaryotic freshwater primary producers, referred to as phytoplankton, include members of Chlorophyta, Haptophyceae, Bacillariophyceae, Cryptophyta, Chrysophyceae and Dinoflagellata. In the euphotic zone of the open ocean Dinophyceae, Dictochophyceae, Bacillariophyceae, Pelagophyceae, Synurophyceae, and Chrysophyceae are particularly abundant. Unpigmented microbes include but are not limited to small aquatic fungi, choanoflagellates, cercozoans, ciliates, and Chrysophyceae. In addition to these widespread groups, a large portion of eukaryotic plankton diversity seems to reside in heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts. To date many eukaryotes remain uncultured, such as the abundant flagellated bacterial predators classified in the marine Stramenopiles groups 4 and 1 (MAST-4 and MAST-1C), which include Bacillariophyceae and Chrysophyceae. On marine snow (sinking organic particles) fungi and Labyrinthulomycetes seem to dominate the biomass of the community. Despite this, and their likely importance in aquatic environments, aquatic fungi are still poorly understood and deserve more attention, since they are highly diverse in terms of function and phylogenetic diversity. Virioplankton Despite their still controversial classification, viruses are abundant and crucial to ocean life. It has been estimated that ocean waters harbor about 4  1030 viruses, most of them infecting heterotrophic and autotrophic bacteria. The ratio between viruses and bacteria is comprised between 3 and 10. Through the water column, viruses mainly occupy the euphotic layers and their abundance drops as depth increases; contextually, virioplankton is more abundant near the coast and decreases in the open ocean. Although generally viruses are small acellular organisms, composed almost exclusively by a genome coding for few proteins, the diversity of the mechanisms employed in their replication and biochemistry is higher than that observed for cellular organisms. Moreover, viruses harbor high genetic and biological diversity, and seem to have played—and still play—a key role in the evolution of life. Microbial Functional Pathways in Aquatic Systems Aquatic microbial communities show a large variation of metabolic activities, ranging from primary production to the heterotrophic utilization of organic compounds. The conversion of inorganic carbon (or other electron acceptors) into organic living material—which characterizes both photoautotrophic (relying on the energy of light) and chemoautotrophic (dependent on chemical energy in minerals) microorganisms—is performed by the producers that are at the base of the trophic chain. Autotrophic picoplankton (microorganisms smaller than 2 mm, including picocyanobacteria and picoeukaryotes) contribute 130 Aquatic Ecology: Microbial Communities substantially to primary production, both in marine and freshwaters. In the oceans, Prochlorococcus and Synechococcus contribute around 75% to CO2 fixation, but in lakes the contribution of Synechococcus ranges from 5% to 65% of total phytoplankton production (Lake Constance, Germany), with higher contribution measured in ultra-oligotrophic lakes (80% in Lake Baikal). These estimates have been obtained by the use of radioactive compounds that are good tracers even when measuring low activities. With the diffusion of molecular biology techniques functional pathways became easier to study, as it is now possible to quantify the presence of specific functional genes, and to better characterize the transcription products, thus demonstrating the functionality of genes. Alternative heterotrophic metabolisms performed by Bacteria and Archaea in addition to the well-known glycolysis (crucial to sugar metabolism), have been studied in details. Important among them is the pentose phosphate pathway to generate NADPH and pentose, studied through the presence of genes codifying for different enzymes in the pathway. Another important metabolic pathway in aquatic systems is nitrification, the two-step metabolism, which oxidizes the ammonium to nitrate and then to nitrite. The microorganisms involved in the first step are nitrifying bacteria that include ammonia-oxidizing bacteria (AOB) like Nitrosomonas and Nitrosoccoccus and ammonia-oxidizing archaea (AOA) like Thaumarchaeota. The amoA gene, encoding for the alfa-subunit of the ammonia monooxygenase enzyme, which catalyzes an important step of bacteria nitrification, is associated with an archaeal metagenomic fragment. This discovery underlines the ecological importance of Archaea in aquatic ecosystems, by emphasizing their role in the first step of nitrification and their possible competitions and relations with nitrifying Bacteria. Another pathway that recently received more attention is the dark inorganic carbon assimilation that can be performed by chemoautotrophs affiliated with Bacteria and Archaea. Chemolithoautotrophic bacteria fix CO2 in the dark through a variety of carboxylation reactions to satisfy metabolic requirements such as the synthesis of fatty acids, nucleotides and amino acids or anaplerotic demands. Thaumarchaeota too can perform dark assimilation, but they use the hydroxypropionate–hydroxybutyrate carbon assimilation pathway. The dichotomy between autotrophic and heterotrophic organisms—also thanks to molecular biology—became increasingly insufficient to describe the scaffold of microbial functional pathways. Like for macrobial eukaryotes, also the microbial world is rich in cells combining different metabolic strategies. Despite this richness, the combination of autotrophic and heterotrophic metabolisms to sustain growth and maintainance can be an energetic cost for the cell. For example, the light-harvesting apparatus needs a high investment in energy terms, but can be a resource in case of organic matter limitation in some oligotrophic systems. Even the opposite strategy can prove successful, as in the case of Synechococcus, a picocyanobacteria abundant in marine and freshwaters, that consumes organic sulfur compounds, playing an important role in the cycle of dimethylsulfopropionate and methanethiol. The ability of Synechococcus and Prochlorococcus to take up amino acids and urea has been demonstrated in axenic cultures, showing how these cyanobacteria can occupy different trophic levels, also contributing to the secondary production in aquatic environments. Some bacteria can use chromophores like proteorhodopsin, which works as a light-driven proton pump, therefore allowing these organisms to act as a photo-organoheterotrophic bacteria. Important groups like SAR11 (Pelagibacter ubique) and some Flavobacteria are among the bacterial group containing proteorhodopsin. Another illustration of the metabolic complexity of microbial communities is the discovery of a group of anoxygenic photosynthetic bacteria that use bacteriochlorophyll a (Bchl-a) for photosynthesis in the absence of oxygen, thus being able to also survive in aerobic conditions. The unexpected abundance of new metabolic pathways in microbial communities we briefly described here is allowing microbiologists to revise our understanding of nutrient and energy flows in aquatic ecosystems. Extrinsic and Intrinsic Drivers Structuring the Microbial Community Assembly When considering microbial community assembly in aquatic habitats, the Baas-Becking hypothesis (“everything is everywhere, but the environment selects”) is a useful heuristic selection on the part of the environment—and its variables and (micro) dynamics— that can help understanding how communities form and are organized. In addition, microbial dispersal is a passive process but not an entirely stochastic one, so that microbial biogeographical patterns are affected by the organisms’ fitness to the environment (or specific niche) and by microbial life history traits. The forces that influence the structure and function of aquatic microbial communities can be extrinsic—meaning they act at a broader, regional scale—and intrinsic—such as food-web interactions that are more site-specific. The former ones impart a sort of synchronization to different populations in the community by the action of a local array of factors like temperature or meteorology. Intrinsic factors further affect the pattern of synchronized microbial population, resulting in fluctuations in the community that are harder to predict. Extrinsic Drivers The extrinsic drivers regulating microbial communities can be broadly grouped in physical ones, like temperature, and currents, and chemical ones, like salinity, dissolved oxygen, nutrients, metals, and antibiotics. Considering the current climatic changes brought about by CO2 and other greenhouse gases emissions, and the subsequent prediction of a global rise in ocean temperatures in the order of 2–41C, temperature as a physical extrinsic driver has been receiving much attention—especially considering its profound impact on biological processes. Recent studies directly linked temperatures to changes in richness and diversity of microbial communities. Moreover, temperature was also documented as one of the extrinsic driver associated with the increase of the relative abundance of Vibrio spp. (a genus comprising different pathogens for humans and animals) resulting in a possible threat for human and animal health. Aquatic Ecology: Microbial Communities 131 In addition to temperature, in aquatic environments currents are important drivers because of their effect on the geographic dispersal of bacterial communities, which can strongly affect their composition. In particular, planktonic microbial communities drifting in the ocean experience a temperature variability up to 101C greater than the estimated seasonal fluctuations, resulting in a selection of bacteria more tolerant to this thermal exposure. Among the chemical drivers affecting microbial communities, salinity is certainly one of the main factors responsible for community assemblage composition, sometimes even more important than temperature, informing the many differences between marine and freshwaters. In addition to salinity, dissolved oxygen (DO) also occupies a central role in community dynamics because of its influence on biotic interactions and on nutrient flows within aquatic ecosystem. In particular, it has been found that higher DO concentrations, positively correlates with Alphaproteobacteria biomass while negatively affecting bacterial diversity, that dramatically decreases in anoxic waters. Nutrient availability determines a “bottom-up” pressure in the regulation of aquatic microbial communities. It is generally considered that the availability of phosphorus is limiting the growth of planktonic communities in most freshwaters and nitrogen and iron in many marine systems. Additionally, a shift in nutrient availability will strongly impact community composition, especially when coupled with temperature. However, given the complexity and interlinked nature of these dynamics, it is not always easy to identify a direct effect of nutrients on the whole community examined; this might result in smaller effects, for example a change limited to the composition of variable taxa only. The challenges of understanding the dynamics of the aquatic nutrient pool are worsened by anthropogenic impacts on nutrients concentrations, and even by particular climatic events like strong winds (possibly associated with dust dispersion in water) and volcanic eruptions (characterized by the release of ash and pumice in water altering the carbon/phosphorous ratio). In addition to these extrinsic drivers, two other factors have a strong impact on microbial communities and are often linked to anthropogenic pollution: antibiotics and metals. Originally, antibiotics are natural compounds released by microorganisms to kill other microbial competitors, and that have an important role as signal molecules, affecting the structure of microbial communities. The artificial isolation, synthesis and overuse of antibiotics in human and animal medicine and aquaculture, constitutes a massive and growing source of pollution, as these compounds are released through excreta into aquatic environments and accumulate, with unpredictable outcomes on microbial life. This is because antibiotics, regardless of their concentration, can exert a selective pressure, altering the structure of microbial communities in terms of both phenotypic distribution and composition, and promoting the spread of antibiotic resistance genes, thus constituting a major threat for human health. While some metals (i.e., copper, zinc, nickel, lead, cadmium, mercury, silver, gold, and chromium) are necessary in small concentrations to microbial metabolisms for several cellular functions, in high concentrations they can be toxic for microbial life. Other metals, like uranium and antimony, are always toxic for microorganisms. Given their importance in contemporary human industries (mercury in electronics, dental and health care industry; copper and zinc as growth promoters in husbandry), metals are released and eventually accumulated in aquatic environment at an alarming rate. This anthropogenic contamination shapes microbial communities, engendering a strong reduction of microbial diversity, affecting metabolic pathways, and negatively influencing the expression of enzymes. Intrinsic Drivers The intrinsic (site-specific and biotic) drivers that structure microbial communities are those related to the interactions between species within the same environment. Interactions between microorganisms can be categorized in five broad groups: (1) predation, when one organism feeds on another one; (2) commensalism, when one organism benefits from another one without affecting it; (3) mutualism, when both organisms benefit each other; (4) parasitism, when the parasite benefits and the host is harmed; and (5) competition, when the organisms do not directly interact with each other but compete for the same resources. Some of these interactions can act directly on species composition, as for example predation, or indirectly by the production of allelopathic substances with beneficial or detrimental effects. The classical, and highly simplified, food chain would comprise primary producers that are eaten by primary consumers, which in turn are eaten by secondary consumers and so on up to the top predators. However, the photosynthesis performed by phytoplankton is not 100% efficient in terms of carbon fixation into biomass, and an estimated 13% of dissolved organic carbon is directly released into the water. These high quality substrates, such as sugars, are readily taken up by aquatic bacteria, which then themselves are consumed by primary consumers. These organisms are in turn eaten by zooplankton species and thereby the organic carbon is channeled back into the classical food chain, reaching higher organisms. Since this pathway is like a loop attached to the simplified food chain, it has been termed “the microbial loop” (Fig. 4A). This concept was established for marine bacterioplankton in the early 1980s and easily applies to freshwater ecosystems too. Given the privileged role that macroscopic life has been granted for most of the history of science, the microbial loop is generally considered an attachment to the classical food-chain. Nevertheless, it has been argued that, given the impressive biomass and energy turnover in the microbial loop, its diffusion, and its importance to the biosphere and its evolution, the classical food chain should be seen as an appendage to microbial trophic interactions. The two main pathways of the microbial loop (DOC —Dissolved Organic Carbon uptake, and predation) highlight the two most important factors defining the niche space of aquatic microbes: availability of organic and inorganic nutrients (bottom-up control) and agents of mortality such as viruses and HNF (top-down). 132 Aquatic Ecology: Microbial Communities Fig. 4 (A) Simplified scheme of an aquatic food web including the microbial loop and the viral shunt; (B) examples of potential successions of microorganisms observed in aquatic habitats. Consequently aquatic bacteria are often classified in two main guilds: fast-growing and grazing-resistant bacteria. Some of the fast- or opportunistically-growing bacteria are free-living, while others attach to particles, where organic carbon concentrations and turnover are typically higher. These bacteria are known for their efficient substrate uptake machinery, as well as their high vulnerability to protistan grazing. Typical members of this guild are Alteromonas and Flavobacteria, and Limnohabitans-affiliated bacteria, in marine and freshwaters respectively. A different survival-strategy is the investment in protection against protistan grazing, which is characteristic of the so-called grazing-resistant bacteria. Such protection can be due to morphological and structural features, as very small cells (ultramicrobacteria) with rigid cell walls, and long filamentous cells, are less commonly ingested by predators. Ultramicrobacteria are highly abundant in aquatic systems and include the ac1 group of Actinobacteria in freshwaters and Pelagibacter ubique (SAR11) in the oceans. Dissolved organic carbon found in natural waters is composed by a variety of substrates including sugars, amino acids, humic acids and many others. On the one hand, different phytoplankton species release different carbon compounds, that is, Chryptophytes release more sugars than many Cyanobacteria. On the other hand, there are also numerous other sources of organic carbon, such as bacterial growth and mortality, sloppy-feeding by zooplankton or substrates deriving from terrestrial input. As a consequence, co-occuring heterotrophs have been seen to have very different substrate uptake preferences: whereas some genotypes seem to be specialized in the uptake of amino acids, other prefer glucose, for example. Such differences in meal-preference help explain why so many different bacterial genotypes can co-exist. As we already mentioned, the two main causes of mortality in microbial communities are flagellate predation and viral lysis. The effect of flagellated predators on microbial communities is often seen as a shift in the composition and morphology. Some bacteria are able to change their growth strategy in the presence of predators by, for example, aggregating with other cells or elongating into filamentous shapes, which allow them to avoiding predation due to increased size. But such grazing defense strategies are often evolutionarily costly. This becomes clear when considering an experiment involving a bacterium (Sphingomonas sp.) kept under grazing pressure for a long time: after the experiment, the bacterium aggregates also in absence of the predator, but lost part of its genome related to carbon degradation. In fact, many highly abundant marine and freshwater ultramicrobacteria are characterized by so called streamlined genomes, genomes that contain only the minimum genes needed for survival. Simultaneously, though, flagellate grazing is also known to stimulate bacterial growth, probably also due to the egestion of incompletely digested prey, which can serve as a substrate to other bacteria and regenerate nutrients. In the case of picocyanobacteria, the effect of nanoflagellate predation was to affect the shift from single cell morphotypes to microcolonial aggregates (Fig. 5), thus contrasting the effect of this intrinsic driver. Viruses are potentially able to infect all of the components of aquatic microbial communities, however they primarily infect the most abundant bacteria and eukaryotic microbes (killing-the-winner hypothesis). Due to their ability to infect microbial hosts, in order to survive and replicate they directly affect, at the community level, the structure and composition of the microbial life and, at level of the Aquatic Ecology: Microbial Communities 133 Fig. 5 Synechococcus cells (prey) and Poterioochromonas sp. (mixotrophic nano-flagellate predator) interaction in a culture, giving rise to the presence of microcolonies (photo by C.
Callieri). Fig. 6 Micro-heterogeneity in a drop of lake water (photo by C.
Callieri). single infected hosts, their physiological status. Therefore, viruses also play an important role within the food web. In fact, they lyse the infected bacteria, determining the release of their cellular content, which is converted in particulate and dissolved organic carbon usable by non-infected prokaryotes (viral shunt) (Fig. 4A). The actual consequence of this flow of matter through the food web is the increase of the respiration rate of the community and the decrease of the efficiency of carbon transfer toward the higher trophic layers. Together with carbon, also other nutrients are released, which can sometimes almost satisfy the particular nutrient need of certain organisms. Based on these food web interactions, typical successions of aquatic organisms can be observed (Fig. 4B), initiated by the steep increase of phytoplankton biomass (e.g., early spring). These primary producers exude organic carbon (OC), which serves as a substrate for heterotrophic bacteria. In turn, the increasing numbers of bacteria promote the growth of heterotrophic nanoflagellates (HNF), which feed on the bacterial assemblage and provide a niche for alternative bacterial groups, not affected by grazing. Mortality among these bacteria is probably mainly caused by viral lysis. Generally, phytoplankton blooms are terminated by high abundances of zooplankton species. While these classical food web interactions provide a useful handle to imagine such dynamics, many more interactions characterize microbial communities alongside them; they are termed non-trophic interactions. One example of these interactions can be found in microbes that grow as symbionts, epibionts or parasites. Some parasites can be highly abundant, such as members of the marine Alveolata MALV-IV group that attach to many different higher organisms. Some of these associations are only transient: bacteria may benefit from zooplankton as a refuge from threats such as grazing and abiotic stressors, or use zooplankton as a mean of transport from lower to higher water layers. The association of the cholera-causing agent Vibrio cholerae with planktonic copepods enables the survival, proliferation and transmission of the disease. Attached bacteria and eukaryotes can be metabolically highly active. Since they are preyed upon together with their host, they might form a shortcut through the trophic chain, directly transferring organic carbon from the dissolved fraction to the top predators. Another example is co-aggregation or attachment, through which bacteria can attach, for example, to phytoplankton cells and reduce substrate competition with other bacteria due to their vicinity to the primary producer. 134 Aquatic Ecology: Microbial Communities Conclusions and Perspectives In this article, we focused on the broader processes that characterize microbial communities in aquatic environments. This scope provides a better grasp of the main questions and concerns informing the study of these organisms, and allows to foreground their impact on a global scale. This is also because much research on these communities concentrated on such more readily apparent dynamics. These planetary biogeochemical transformations are the results of processes working at the microscale and resulting in a fragmented and diverse micro-heterogeneity of aquatic habitats (Fig. 6). The prevalence of the microscale gradients in aquatic systems forces us to seriously reconsider the importance of studying aquatic microbes at single-cell level, and at a scale that is more commensurate with their own dynamics and lives. The new opportunities offered by genomics, single-cell technologies like nanoSIMS (nano secondary ion mass spectrometry), microfluidics, and atomic-force microscopy opened new frontiers for understanding the functioning of microorganisms and their interactions with the environment, paving the way to a micro-scale focus on microbial communities. Despite these novel approaches, and the vast range of molecular and computational techniques that revolutionized our understanding of microbial life since the 1980s, our understanding of these life forms and the vital processes they shape still faces many challenges, and constantly stumbles upon surprising findings that redefine how we understand life on Earth and beyond. For this reason, the study of the microbiota, its micro-scale dynamics, and its interactions with the macrobiota require us to think outside the box, to work collaboratively across disciplinary boundaries, and to remain open to the awe-inspiring workings of our planet's ecosystems. This is the hard and yet rewarding task inherited by the younger generations of scientists, thinkers and explorers to whom this article is dedicated. See also: Aquatic Ecology: Dead Zones: Low Oxygen in Coastal Waters; Ecosystem Health Indicators—Freshwater Environments. Conservation Ecology: Ecological Health Indicators. Ecological Processes: Biological Nitrogen Fixation; Decomposition and Mineralization; Nitrification; Ammonification. General Ecology: Detritus. Global Change Ecology: Microbial Cycles Further Reading Amann, R., Rosselló-Móra, R., 2016. After all, only millions? MBio 7.e00999-16. Azam, F., Fenchel, T., Field, J.G., Gray, J.S., Meyer-Reil, L.A., Thingstad, F., 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series 10, 257–263. Doblin, M.A., van Sebille, E., 2016. Drift in ocean currents impacts intergenerational microbial exposure to temperature. Proceedings of the National Academy of Sciences of the United States of America 113, 5700–5705. Giovannoni, S.J., Stingl, U., 2005. Molecular diversity and ecology of microbial plankton. Nature Reviews Microbiology 437, 343–348. Jürgens, K., 1994. Impact of Daphnia on planktonic microbial food web. A review. Marine Microbial Food Webs 8, 295–324. Kent, A.D., Yannarel, A.C., Rusak, J.A., Triplett, E.W., McMahon, K.D., 2007. Synchrony in aquatic microbial community dynamics. The ISME Journal 1, 38–47. Locey, K.J., Lennon, J.T., 2016. Scaling laws predict global microbial diversity. Proceedings of the National Academy of Sciences 113, 5970–5975. Newton, R.J., Jones, S.E., Eiler, A., McMahon, K.D., Bertilsson, S., 2011. A guide to the natural history of freshwater lake bacteria. Microbiology and Molecular Biology Reviews 75, 14–49. Pedros-Alio, C., 2012. The rare bacterial biosphere. Annual Review of Marine Science 4, 449–466. Pernthaler, J., 2005. Predation on prokaryotes in the water column and its ecological implications. Nature Reviews Microbiology 3, 537–546. Ruiz-González, C., Niño-García, J.P., del Giorgio, P.A., 2015. Terrestrial origin of bacterial communities in complex boreal freshwater networks. Ecology Letters 18, 1198–1206. Seymour, J.R., Amin, S.A., Raina, J.B., Stocker, R., 2017. Zooming in on the phycosphere: The ecological interface for phytoplankton-bacteria relationships. Nature Microbiology 2.17065 Stocker, R., 2012. Marine microbes see a sea of gradients. Science 338, 628. Sunagawa, S., Coelho, L.P., Chaffron, S., Kultima, J.R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D.R., Alberti, A., 2015. Structure and function of the global ocean microbiome. Science 348, 1261359. Suttle, C.A., 2005. Viruses in the sea. Nature Reviews Microbiology 437, 356–361.