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Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.

Key Points Biogeography is the study of the distribution of organisms and the ecological and evolutionary processes that shape those distributions. Over the past decade, microbiologists have established the existence of biogeographic patterns among a wide variety of microorganisms, and interest is now shifting towards identifying the mechanisms that shape these patterns. Traditionally, mechanisms that shape the composition and diversity within species are considered to be evolutionary processes, and those that shape the composition and diversity among species are considered to be ecological processes. However, microbial biogeography studies often characterize diversity along a continuous scale of taxonomic resolution using the nucleotide sequences of a single marker gene. In this case, the boundary between ecological and evolutionary processes is particularly blurry. Hence, we merge concepts from both fields to describe the processes that shape microbial biogeographic patterns. Here, we propose a theoretical framework that describes just four processes — selection, drift, dispersal and mutation — which interact to create and maintain microbial biogeographic patterns at all taxonomic scales. As an illustrative example, we show how these processes shape the most commonly studied biogeographic pattern: the distance–decay relationship. We carried out a literature review to assess the evidence for the relative importance of these processes in shaping microbial biogeographic patterns. Although selection imposed by current environmental factors had the strongest influence on microbial spatial distributions, historical processes driven by dispersal limitation also influenced the distribution of at least some microorganisms from all domains of life and from various habitat types, spatial scales and taxonomic resolutions. As different combinations of the same four processes can interact to create the same pattern, we conclude that it remains difficult to disentangle the relative importance of selection, drift, dispersal and mutation by analysing distance–decay patterns alone. We suggest that the field might advance by emphasizing process over pattern: tailoring studies to detect and evaluate specific processes through manipulative experiments, temporal data sets and the incorporation of theoretical models. Like larger organisms, microorganisms display distinct distributions in space and time. Martiny, Hanson and colleagues propose that four processes — selection, drift, dispersal and mutation — can shape such microbial biogeographic patterns, and analyse the literature to assess the evidence for their importance in shaping one pattern, the distance–decay relationship. Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes — selection, drift, dispersal and mutation — create and maintain microbial biogeographic patterns on inseparable ecological and evolutionary scales. We consider how the interplay of these processes affects one biogeographic pattern, the distance–decay relationship, and review evidence from the published literature for the processes driving this pattern in microorganisms. Given the limitations of inferring processes from biogeographic patterns, we suggest that studies should focus on directly testing the underlying processes.

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA-a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L(-1). This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L(-1)), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems.

Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.

The factors driving β-diversity (variation in community composition) yield insights into the maintenance of biodiversity on the planet. Here we tested whether the mechanisms that underlie bacterial β-diversity vary over centimeters to continental spatial scales by comparing the composition of ammonia-oxidizing bacteria communities in salt marsh sediments. As observed in studies of macroorganisms, the drivers of salt marsh bacterial β-diversity depend on spatial scale. In contrast to macroorganism studies, however, we found no evidence of evolutionary diversification of ammonia-oxidizing bacteria taxa at the continental scale, despite an overall relationship between geographic distance and community similarity. Our data are consistent with the idea that dispersal limitation at local scales can contribute to β-diversity, even though the 16S rRNA genes of the relatively common taxa are globally distributed. These results highlight the importance of considering multiple spatial scales for understanding microbial biogeography.

Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.

In recent years, the question of whether microbial life exhibits biogeographical patterns has come under increased scrutiny. In this article, leading scientists in the field review the biogeography of microorganisms and provide a framework for assessing the impact of environmental and historical processes that contribute to microbial biodiversity. Key Points Since the eighteenth century, biologists have investigated plant and animal biogeography, but only recently have the distributions of microorganisms been examined. We consider microbial biogeography in light of habitats types (the contemporary environment) and provinces (legacies of historical events such as dispersal limitation). This framework is useful for addressing whether the distributions of microbial taxa, like those of macroorganisms, reflect the influences of both contemporary environmental conditions and past events. We review a growing body of literature that suggests that microbial assemblages are not only influenced by their current environment, but that some display a degree of provincialism — evidence that these microbial assemblages have diverged and are maintained by genetic isolation. We also find that the relative influence of historical versus environmental factors appears to be related to the scale of sampling. As a first hypothesis, we suggest that the same processes that influence macroorganism biogeography (colonization, diversification and extinction) also apply to microbial life, but that their rates scale with body size, or for single-celled organisms, cell size. Therefore, we use the idea of allometry as a structure for discussing the rates of biogeographic processes in microorganisms. We conclude that the rates of biogeographic processes probably vary more widely for microorganisms of a given size than for macroorganisms of a given size. To tackle the mechanisms generating microbial biogeographic patterns, we recommend that new microbial biogeography studies should systematically sample and record data from various distances, habitats and environmental conditions. We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

The diversity and composition of ecological communities often co-vary with ecosystem productivity. However, the relative importance of productivity, or resource abundance, versus the spatial distribution of resources in shaping those ecological patterns is not well understood, particularly for the bacterial communities that underlie most important ecosystem functions. Increasing ecosystem productivity in lakes has been shown to influence the composition and ecology of bacterial communities, but existing work has only evaluated the effect of increasing resource supply and not heterogeneity in how those resources are distributed. We quantified how bacterial communities varied with the trophic status of lakes and whether community responses differed in surface and deep habitats in response to heterogeneity in nutrient resources. Using ARISA fingerprinting, we found that bacterial communities were more abundant, richer, and more distinct among habitats as lake trophic state and vertical heterogeneity in nutrients increased, and that spatial resource variation produced habitat specific responses of bacteria in response to increased productivity. Furthermore, changes in communities in high nutrient lakes were not produced by turnover in community composition but from additional taxa augmenting core bacterial communities found in lower productivity lakes. These data suggests that bacterial community responses to nutrient enrichment in lakes vary spatially and are likely influenced disproportionately by rare taxa.

A positive power-law relationship between the number of species in an area and the size of that area has been observed repeatedly in plant and animal communities 1 . This species–area relationship, thought to be one of the few laws in ecology 2 , is fundamental to our understanding of the distribution of global biodiversity. However, such a relationship has not been reported for bacteria, and little is known regarding the spatial distribution of bacteria, relative to what is known of plants and animals 3 . Here we describe a taxa–area relationship for bacteria over a scale of centimetres to hundreds of metres in salt marsh sediments. We found that bacterial communities located close together were more similar in composition than communities located farther apart, and we used the decay of community similarity with distance to show that bacteria can exhibit a taxa–area relationship. This relationship was driven primarily by environmental heterogeneity rather than geographic distance or plant composition.