Development of an environmental functional gene microarray for soil microbial communities

Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N2O. A total of 109 genes displayed expression that differed significantly between soils with low and high N2O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities. Copyright © 2010, American Society for Microbiology

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts

While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera "Candidatus Planktophila" (acI-A) and "Candidatus Nanopelagicus" (acI-B) and the proteobacterial genus "Candidatus Fonsibacter" (LD12). While "Ca. Planktophila" and "Ca. Fonsibacter" had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which "Ca. Planktophila" is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain "Ca. Planktophila" population abundance, the success of "Ca. Nanopelagicus" and "Ca. Fonsibacter" is better explained as a community by-product. Ecotype differentiation of "Ca. Fonsibacter" as a means of escaping predation was supported but not for overcoming auxotrophies.IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: "Ca. Planktophila" (acI-A), "Ca. Nanopelagicus" (acI-B), and "Ca. Fonsibacter" (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner–Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.This work was supported by the Swedish Research Council (Grant Numbers 2012-4592 to AE and 2012-3892 to SB) and the Communiy Sequencing Programme of the US Department of Energy Joint Genome Institute. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231

An exploration of freshwater microbial ecology : from streamlined genera to global networks

Microbes are the main drivers of biogeochemical cycles on Earth and even though freshwaters cover only a small area of terrestrial surfaces their contribution to global cycles is important. Global cycles are measured by exchanges between systems e.g. water to atmosphere or lithosphere and are mediated by microbial communities. Cyanobacteria and other photosynthetic microbes can be highly abundant going through cyclic blooms. These blooms are attributed to their ability to harness sunlight and CO2 to outgrow competitors by using their complex and expensive to produce photosystems. In contrast there are microbial lineages termed ‘streamlined’, that are just as abundant as cyanobacteria at times, but who have much smaller cells, small genomes, and grow and replicate slowly. It is not immediately apparent how microbes with such different lifestyles can have similar ‘success’. By investigating individual streamlined lineages and their interactions we see that they appear to have co-evolved dependencies with each other and are highly successful as consortia. By comparing consortia from different lakes we see that streamlined microbes can sit either adjacent or in the middle of carbon cycling end-points and may be more directly involved than thought in mediating methane and CO2 ratios. An analysis of global inland water microbiomes finds that around one third of the core microbial lineages in inland waters are streamlined

An exploration of freshwater microbial ecology : from streamlined genera to global networks

Microbes are the main drivers of biogeochemical cycles on Earth and even though freshwaters cover only a small area of terrestrial surfaces their contribution to global cycles is important. Global cycles are measured by exchanges between systems e.g. water to atmosphere or lithosphere and are mediated by microbial communities. Cyanobacteria and other photosynthetic microbes can be highly abundant going through cyclic blooms. These blooms are attributed to their ability to harness sunlight and CO2 to outgrow competitors by using their complex and expensive to produce photosystems. In contrast there are microbial lineages termed ‘streamlined’, that are just as abundant as cyanobacteria at times, but who have much smaller cells, small genomes, and grow and replicate slowly. It is not immediately apparent how microbes with such different lifestyles can have similar ‘success’. By investigating individual streamlined lineages and their interactions we see that they appear to have co-evolved dependencies with each other and are highly successful as consortia. By comparing consortia from different lakes we see that streamlined microbes can sit either adjacent or in the middle of carbon cycling end-points and may be more directly involved than thought in mediating methane and CO2 ratios. An analysis of global inland water microbiomes finds that around one third of the core microbial lineages in inland waters are streamlined

Biogenic methane cycling is controlled by microbial cohorts

The generation and consumption of methane by aquatic microbial communities is an important contribution to the global carbon budget. We sought to broaden understanding of consortia members and interactions by combining multiple methods including analysis of natural and cultivated microbial communities. By analysing the microbial communit composition and co-occurrence patterns of a lake time-series we were able to identify potential consortia involved in methane cycling. In combination with methane flux, we also analysed the community composition and co-occurrence patterns of reduced microbial model communities with inoculum from the same lake. While the network analyses confirmed many known associations, when combined with results from mixed cultures, we noted new players in methane cycling. Cultivated model communities were shown to be an effective method to explore the rarer but still important players in methane cycling and for identifying new putative members. Here we show that using multiple methods to approach the complex problem of methane cycling consortia yields not just insights into the known taxa but highlights potential new members creating new hypotheses to be tested

Biogenic methane cycling is controlled by microbial cohorts

The generation and consumption of methane by aquatic microbial communities is an important contribution to the global carbon budget. We sought to broaden understanding of consortia members and interactions by combining multiple methods including analysis of natural and cultivated microbial communities. By analysing the microbial communit composition and co-occurrence patterns of a lake time-series we were able to identify potential consortia involved in methane cycling. In combination with methane flux, we also analysed the community composition and co-occurrence patterns of reduced microbial model communities with inoculum from the same lake. While the network analyses confirmed many known associations, when combined with results from mixed cultures, we noted new players in methane cycling. Cultivated model communities were shown to be an effective method to explore the rarer but still important players in methane cycling and for identifying new putative members. Here we show that using multiple methods to approach the complex problem of methane cycling consortia yields not just insights into the known taxa but highlights potential new members creating new hypotheses to be tested

Methane dynamics regulated by microbial community response to permafrost thaw

Permafrost contains about 50% of the global soil carbon1. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions2, 3. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown3 and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ13C signature (10–15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden4, 5 as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus ‘Methanoflorens stordalenmirensis’6 is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models3, 7. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.funded by US Department of Energy Office of Biological and Environmental Research (award DE-SC0004632)IsoGeni

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.

Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner-Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype