A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

In order to identify patterns in bacterial community composition in freshwater habitats, we analyzed the available database of 16S rDNA sequences from freshwater plankton, including 24 new sequences from Parker River (Massachusetts, USA), 42 from Lake Soyang (South Korea) and 148 from Lake IJssel (The Netherlands). At this point, combined diversity studies using random cloning have deposited 689 bacterial and 75 plastid 16S rDNA sequences from the water column of rivers and lakes in North America, Europe and Asia. Systematic comparisons with the global database showed that the majority of the bacterial sequences were most closely related to other freshwater clones or isolates, while relatively few were closest to sequences recovered from soils or marine habitats. This habitat-specific clustering suggests that the clustered 16S rDNA sequences represent species or groups of species that are indigenous to freshwater. We have discerned 34 phylogenetic clusters of closely related sequences that are either restricted to freshwater or dominated by freshwater sequences. Of these clusters, 23 contained no cultivated organisms. These putative freshwater clusters were found among the alpha-, beta-and gamma-Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides group, the Cyanobacteria, the Actinobacteria, the Verrucomicrobia, the green non-sulfur bacteria and candidate division OP10. This study shows that rivers and lakes have a specific planktonic bacterial community distinct from bacteria in neighboring environments such as soil and sediments. It also points out that these planktonic bacteria are distributed in diverse freshwater ecosystems around the world.KEY WORDS: Microbial diversity · Ribosomal RNA gene · Freshwater · Habitat · Polymerase chain reaction · Phylogeny · Nucleotide sequence database Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 28: [141][142][143][144][145][146][147][148][149][150][151][152][153][154][155] 2002 has made it possible to obtain information on microbial community composition directly, without cultivation (Giovannoni et al. 1990). An environmental sample can be inventoried for taxa present by direct nucleic acid isolation, followed by amplification of particular marker genes and analysis of the sequence of base pairs. The most widely used marker gene is the small subunit rRNA gene (16S rDNA), and the recent application of molecular techniques in a variety of habitats has produced a large set of sequences from this gene. This growing database has taught us that the diversity of the microbial world is much larger than we were able to estimate before the use of molecular techniques (Pace 1997, Hugenholtz et al. 1998). However, a clear view of the species or groups of species that we can expect in particular environments is still lacking. This is due in part to the great diversity of bacteria. In addition, an overview is lacking due to the focused approach followed in many molecular diversity studies. While most studies compare ret...

Carbon in thawing permafrost soils may have global impacts on climate change; however, the factors that control its processing and fate are poorly understood. The dominant fate of dissolved organic carbon (DOC) released from soils to inland waters is either complete oxidation to CO2 or partial oxidation and river export to oceans. Although both processes are most often attributed to bacterial respiration, we found that photochemical oxidation exceeds rates of respiration and accounts for 70 to 95% of total DOC processed in the water column of arctic lakes and rivers. At the basin scale, photochemical processing of DOC is about one-third of the total CO2 released from surface waters and is thus an important component of the arctic carbon budget.

Seasonal shifts in bacterioplankton community composition in Toolik Lake, a tundra lake on the North Slope of Alaska, were related to shifts in the source (terrestrial versus phytoplankton) and lability of dissolved organic matter (DOM). A shift in community composition, measured by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes, occurred at 4°C in near-surface waters beneath seasonal ice and snow cover in spring. This shift was associated with an annual peak in bacterial productivity ([ 14 C]leucine incorporation) driven by the large influx of labile terrestrial DOM associated with snow meltwater. A second shift occurred after the flux of terrestrial DOM had ended in early summer as ice left the lake and as the phytoplankton community developed. Bacterioplankton communities were composed of persistent populations present throughout the year and transient populations that appeared and disappeared. Most of the transient populations could be divided into those that were advected into the lake with terrestrial DOM in spring and those that grew up from low concentrations during the development of the phytoplankton community in early summer. Sequencing of DNA in DGGE bands demonstrated that most bands represented single ribotypes and that matching bands from different samples represented identical ribotypes. Bacteria were identified as members of globally distributed freshwater phylogenetic clusters within the ␣-and ␤-Proteobacteria, the Cytophaga-Flavobacteria-Bacteroides group, and the Actinobacteria.

The Columbia River estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. Particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. PCR-amplified 16S rRNA genes from particle-attached and free-living bacteria in the Columbia River, its estuary, and the adjacent coastal ocean were cloned, and 239 partial sequences were determined. A wide diversity was observed at the species level within at least six different bacterial phyla, including most subphyla of the classProteobacteria. In the estuary, most particle-attached bacterial clones (75%) were related to members of the genusCytophaga or of the α, γ, or δ subclass of the classProteobacteria. These same clones, however, were rare in or absent from either the particle-attached or the free-living bacterial communities of the river and the coastal ocean. In contrast, about half (48%) of the free-living estuarine bacterial clones were similar to clones from the river or the coastal ocean. These free-living bacteria were related to groups of cosmopolitan freshwater bacteria (β-proteobacteria, gram-positive bacteria, andVerrucomicrobium spp.) and groups of marine organisms (gram-positive bacteria and α-proteobacteria [SAR11 andRhodobacter spp.]). These results suggest that rapidly growing particle-attached bacteria develop into a uniquely adapted estuarine community and that free-living estuarine bacteria are similar to members of the river and the coastal ocean microbial communities. The high degree of diversity in the estuary is the result of the mixing of bacterial communities from the river, estuary, and coastal ocean.

Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([ 14 C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and Actinobacteria. Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil.Estuarine waters contain strong biological and chemical gradients established by the mixing of freshwater and seawater and modified by autochthonous biological activity. Many of these gradients, including salinity, nutrient concentration, organic matter composition, and bacteriovore community composition, are thought to influence the composition of natural bacterioplankton communities (2, 11). Such changes in environmental conditions, when recreated in mesocosm and microcosm experiments, caused shifts in the phylogenetic composition of bacterioplankton communities (10,19,32,41). It is therefore reasonable to predict that similar shifts will occur in natural freshwater and marine bacterioplankton communities when they encounter estuarine gradients, leading to the development of an estuarine community.Several studies have described estuarine microbial diversity and some have demonstrated how freshwater and marine bacterioplankton communities mix along estuarine gradients (3,4,8,14,21,37), but few reports have provided evidence of a unique estuarine bacterioplankton community. This is partly due to the dynamic nature of estuaries and the difficulty in distinguishing estuarine populations from those that wash in from adjacent environments. Crump et al. (6) identified putative estuarine bacteria associated with particles in the Columbia River estuarine turbidity maximum (ETM) by comparing environmental clone libraries of PCR-amplified 16S ribosomal DNA (rDNA) from the river, the estuary, and the coastal ocean. Similarly, Hollibaugh et al. (14) demonstrated the mixing of bacter...

Microbes are transported in hydrological networks through many environments, but the nature and dynamics of underlying microbial metacommunities and the impact of downslope inoculation on patterns of microbial diversity across landscapes are unknown. Pyrosequencing of small subunit ribosomal RNA gene hypervariable regions to characterize microbial communities along a hydrological continuum in arctic tundra showed a pattern of decreasing diversity downslope, with highest species richness in soil waters and headwater streams, and lowest richness in lake water. In a downstream lake, 58% and 43% of the bacterial and archaeal taxa, respectively, were also detected in diverse upslope communities, including most of the numerically dominant lake taxa. In contrast, only 18% of microbial eukaryotic taxa in the lake were detected upslope. We suggest that patterns of diversity in surface waters are structured by initial inoculation from microbial reservoirs in soils followed by a species-sorting process during downslope dispersal of both common and rare microbial taxa. Our results suggest that, unlike for metazoans, a substantial portion of bacterial and archaeal diversity in surface freshwaters may originate in complex soil environments.

The bacterioplankton community composition (measured with denaturing gradient gel electrophoresis of 16S ribosomal DNA [rDNA]) of two nonintersecting temperate rivers was nearly identical and changed synchronously over 2.5 yr, suggesting that intrinsic controls on bacteria were similar in the two rivers and that seasonal changes were driven by extrinsic factors such as climate. Most potential controls on community composition also exhibited synchrony; these included bacterial production rate (leucine incorporation), water temperature, river flow rate, and a suite of chemical measurements. Temperature and river flow rate were the best predictors of temporal patterns in diversity. However, diversity patterns also correlated with bacterial production and concentrations of dissolved organic nitrogen and nitrate, suggesting that diversity is directly or indirectly influenced by complex seasonal shifts in environmental conditions. Winter and summer communities were somewhat predictable over 3 yr, although these communities were not identical. Two polymerase chain reaction (PCR)-amplified clone libraries of 16S rDNA, constructed with summer samples from each river, were not significantly different and contained typical freshwater bacterioplankton of the beta-Proteobacteria, Bacteroidetes, and Actinobacteria, including members of five new freshwater bacterioplankton clusters. However, libraries also included several phylotypes related to bacteria from soil and sediment, indicating the potential importance of allochthonous organisms in river diversity.