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The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, nonparametric, and parametric analyses, and they rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation, but the individual responses to these environmental variables differ for each lineage. The models estimate global biogeographic patterns and seasonal variability of cell abundance, with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans and minima at higher latitudes. The annual mean global abundances of Prochlorococcus and Synechococcus are 2.9 ± 0.1 × 10 ²⁷ and 7.0 ± 0.3 × 10 ²⁶ cells, respectively. Using projections of sea surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 29% and 14% for Prochlorococcus and Synechococcus , respectively. The changes are geographically uneven but include an increase in area. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes as a result of projected future climate conditions. Because of the high abundances and contributions to primary production of Prochlorococcus and Synechococcus , these changes may have large impacts on ocean ecosystems and biogeochemical cycles.

Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. These large-scale consequences result from the combined effect of countless interactions occurring at the level of the individual cells. At these small scales, the ocean is surprisingly heterogeneous, and microbes experience an environment of pervasive and dynamic chemical and physical gradients. Many species actively exploit this heterogeneity, while others rely on gradient-independent adaptations. This is an exciting time to explore this frontier of oceanography, but understanding microbial behavior and competition in the context of the water column's microarchitecture calls for new ecological frameworks, such as a microbial optimal foraging theory, to determine the relevant trade-offs and global consequences of microbial life in a sea of gradients.

Soil heterotrophic respiration and nutrient mineralization are strongly affected by environmental conditions, in particular by moisture fluctuations triggered by rainfall events. When soil moisture decreases, so does decomposers' activity, with microfauna generally undergoing stress sooner than bacteria and fungi. Despite differences in the responses of individual decomposer groups to moisture availability (e.g., bacteria are typically more sensitive than fungi to water stress), we show that responses of decomposers at the community level are different in soils and surface litter, but similar across biomes and climates. This results in a nearly constant soil-moisture threshold corresponding to the point when biological activity ceases, at a water potential of about −14 MPa in mineral soils and −36 MPa in surface litter. This threshold is shown to be comparable to the soil moisture value where solute diffusion becomes strongly inhibited in soil, while in litter it is dehydration rather than diffusion that likely limits biological activity around the stress point. Because of these intrinsic constraints and lack of adaptation to different hydro-climatic regimes, changes in rainfall patterns (primary drivers of the soil moisture balance) may have dramatic impacts on soil carbon and nutrient cycling.

The ocean is an important global source of nitrous oxide (N₂O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N₂O, but the isotopic signatures of N₂O produced by these processes are not consistent with the marine contribution to the global N₂O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N₂O. Natural-abundance stable isotope measurements indicate that the produced N₂O had bulk δ¹⁵N and δ¹⁸O values higher than observed for ammonia-oxidizing bacteria but similar to the δ¹⁵N and δ¹⁸O values attributed to the oceanic N₂O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N₂O source.

Miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in sea-floor sediments; single-cell genomics reveals that these archaea belong to new branches of the archaeal tree and probably have a role in protein remineralization in anoxic marine sediments. Marine archaeans as protein recyclers Sediments on the sea floor are home to almost half of the microorganisms in the ocean, including a large number of Archaea that have not been cultured in the laboratory. Here Karen Lloyd et al . identify uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) organisms as the predominant archaeans in sediments. Single-cell genomic analysis of four different cell types indicates that they belong to new branches of the archaeal tree. All cells tested encode extracellular protein-degrading enzymes, pointing to a possible role in protein remineralization in anoxic marine sediments. Half of the microbial cells in the Earth’s oceans are found in sediments 1 . Many of these cells are members of the Archaea 2 , single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota 3 and Aigarchaeota 4 , for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.

Superoxide and other reactive oxygen species (ROS) originate from several natural sources and profoundly influence numerous elemental cycles, including carbon and trace metals. In the deep ocean, the permanent absence of light precludes currently known ROS sources, yet ROS production mysteriously occurs. Here, we show that taxonomically and ecologically diverse heterotrophic bacteria from aquatic and terrestrial environments are a vast, unrecognized, and light-independent source of Superoxide, and perhaps other ROS derived from Superoxide. Superoxide production by a model bacterium within the ubiquitous Roseobacter clade involves an extracellular oxidoreductase that is stimulated by the reduced form of nicotinamide adenine dinucleotide (NADH), suggesting a surprising homology with eukaryotic organisms. The consequences of ROS cycling in immense aphotic zones representing key sites of nutrient regeneration and carbon export must now be considered, including potential control of carbon remineralization and metal bioavailability.

The composition and prevalence of microorganisms in the middle-to-upper troposphere (8–15 km altitude) and their role in aerosol-cloud-precipitation interactions represent important, unresolved questions for biological and atmospheric science. In particular, airborne microorganisms above the oceans remain essentially uncharacterized, as most work to date is restricted to samples taken near the Earth’s surface. Here we report on the microbiome of low- and high-altitude air masses sampled onboard the National Aeronautics and Space Administration DC-8 platform during the 2010 Genesis and Rapid Intensification Processes campaign in the Caribbean Sea. The samples were collected in cloudy and cloud-free air masses before, during, and after two major tropical hurricanes, Earl and Karl. Quantitative PCR and microscopy revealed that viable bacterial cells represented on average around 20% of the total particles in the 0.25- to 1-μm diameter range and were at least an order of magnitude more abundant than fungal cells, suggesting that bacteria represent an important and underestimated fraction of micrometer-sized atmospheric aerosols. The samples from the two hurricanes were characterized by significantly different bacterial communities, revealing that hurricanes aerosolize a large amount of new cells. Nonetheless, 17 bacterial taxa, including taxa that are known to use C1–C4 carbon compounds present in the atmosphere, were found in all samples, indicating that these organisms possess traits that allow survival in the troposphere. The findings presented here suggest that the microbiome is a dynamic and underappreciated aspect of the upper troposphere with potentially important impacts on the hydrological cycle, clouds, and climate.

Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.

BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like hybrid type ll/lll ribulose-l, 5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO₂ fixation, a pathway not previously described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-type hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.

Permafrost microbes await the thaw Permafrost soil in the Arctic contains a huge reservoir of carbon. If the climate warms and the permafrost thaws, this carbon would become accessible to microbial degradation, releasing greenhouse gases in the process. The microbes responsible for this process are largely unknown. Metagenomic analysis of DNA isolated from two permafrost soils collected in Alaska reveals a rapid microbial response to thawing, with many functional gene abundances increasing. A draft genome of a novel methanogen was constructed from the sequence data. This study highlights the importance of rapid cycling of methane and nitrogen in thawing permafrost. Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere 1 , 2 , 3 . This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw 2 . During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions 4 , 5 . Despite recent advances in the use of molecular tools to study permafrost microbial communities 6 , 7 , 8 , 9 , their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.