ABSTRACT SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world’s oceans, where they play a major role in ocean carbon cycle. Correlations between phylogenetic branching order spatiotemporal patterns cell distributions from planktonic environments indicate has evolved into perhaps dozen or more specialized ecotypes span evolutionary distances equivalent to bacterial order. We isolated sequenced genomes cultures represent three lineages...

Significance Thaumarchaeota are among the most abundant microbial cells in ocean, but to date, complete genome sequences for marine lacking. Here, we report 1.23-Mbp of pelagic ammonia-oxidizing thaumarchaeon “ Candidatus Nitrosopelagicus brevis” str. CN25. We present first proteomic data, our knowledge, from this phylum, which show a high proportion proteins translated oligotrophic conditions. Metagenomic fragment recruitment using data open ocean indicate ubiquitous presence Ca. N....

Although bacteria within the Verrucomicrobia phylum are pervasive in soils around world, they under-represented both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 found this spartobacterial phylotype be ubiquitous consistently one of most abundant soil bacterial phylotypes, particularly grasslands, where it was typically abundant....

Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. Nonetheless, phylogenetic accuracy improves more refined tools and expanded taxon sampling. We investigated mitochondrial benefit of new, deeply branching genome sequences from prolific SAR11 clade Alphaproteobacteria publicly available alphaproteobacterial sequences. Using...

Significance Nonphosphorus lipids produced by heterotrophic bacteria have been measured in marine ecosystems without an understanding of their origins or role. This work shows SAR11 chemoheterotrophic synthesize multiple nonphosphorus response to phosphate depletion. Because this process results a reduced cellular P:C ratio, it impacts our ocean processes related elemental stoichiometry showing how different environmental parameters alter ratios heterotrophs. Also, grown with excess...

Particles in aquatic environments host distinct communities of microbes, yet the evolution particle-specialized taxa and extent to which specialized microbial metabolism is associated with particles largely unexplored. Here, we investigate hypothesis that a widely distributed uncultivated group--the marine group II euryarchaea (MGII)--interacts living detrital particulate organic matter (POM) euphotic zone central California Current System. Using fluorescent situ hybridization, verified...

Abstract It is implicitly assumed that the microbial DNA recovered from soil originates living cells. However, because relic (DNA dead cells) can persist in for weeks to years, it could impact DNA-based analyses of diversity. We examined a wide range soils and found that, on average, 40% prokaryotic fungal was derived pool. Relic inflated observed diversity by as much 55%, caused misestimation taxon abundances, including taxa integral key ecosystem processes. These findings imply obscure...

Thaumarchaea are ubiquitous in marine habitats where they participate carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea active microbes waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization activity. Here, report the global transcriptional response of ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 ammonia limitation using RNA-Seq. We further describe genome transcriptome Ca. N....

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that belowground environment is dynamic. In part, this stems from challenges associated with high degree of spatial heterogeneity and because presence relic DNA (DNA dead cells or secreted extracellular DNA) may dampen signals. Here, we disentangle relationships among spatial, temporal, effects on prokaryotic fungal soils collected contrasting hillslopes...

Sunlight is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in biochemical composition communities over diel light cycles attendant consequences for carbon flux environments remain poorly elucidated. Here we use lipidomic data from North Pacific subtropical gyre to show that biosynthesis energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during day subsequent consumption at night drives...

The ability to grow a microbe in the laboratory enables reproducible study and engineering of its genetics. Unfortunately, majority microbes tree life remain uncultivated because effort required identify culturing conditions. Predictions viable growth conditions guide experimental testing would be highly desirable. While carbon energy sources can computationally predicted with annotated genes, it is harder predict other requirements for such as oxygen, temperature, salinity, pH. Here, we...

Sometimes, to move ahead, you must take a look at where have been. Culturing microbes is foundational underpinning of microbiology.

Nitrogen is one of the major nutrients limiting microbial productivity in ocean, and as a result, most marine microorganisms have evolved systems for responding to nitrogen stress. The highly abundant alphaproteobacterium "Candidatus Pelagibacter ubique," cultured member order Pelagibacterales (SAR11), lacks canonical GlnB, GlnD, GlnK, NtrB/NtrC genes regulating assimilation, raising questions about how these organisms respond limitation. A survey 266 Alphaproteobacteria genomes found five...

The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating may persist because in deeper soils are adapted to low nutrient availability quality. Here, we use high-throughput dilution-to-extinction culturing isolate from a conifer forest Arizona, USA. We hypothesized that concentration heterotrophic substrates microbiological growth medium...

Non-symbiotic Bradyrhizobium are among the most abundant and ubiquitous microbes in bulk soils globally. Despite this, available genomic resources for derived from plant-associated strains. We present high-quality draft genomes 17 four Nitrobacteraceae cultures isolated semiarid Arizona, USA. The genome sizes range 5.99 to 10.4 Mbp. Phylogenomic analysis of 21 indicates they fall into clades. Two clades nested within genus. other two were associated with outgroups basal . All lack genes...

Abstract Methane is a potent greenhouse gas commonly supersaturated in the oxic surfaces waters of oceans and lakes, yet canonical microbial methanogens are obligate anaerobes. One proposed methane production pathway involves degradation methylphosphonate (MPn), which can proceed presence oxygen. Directly tracing dissolved to its source waters, however, remains challenge. To address this knowledge gap, we quantified carbon isotopic fractionation between substrate MPn product (1.3‰) lab...

The alphaproteobacterium "Candidatus Pelagibacter ubique" strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown defined medium containing either limiting or nonlimiting amounts dimethylsulfoniopropionate (DMSP) as sole source. Protein mRNA expression measured before, during,...

ABSTRACT The genomic expression patterns of Methanosarcina mazei growing with trimethylamine were measured in comparison to those cells grown methanol. We identified a total 72 genes either an increased level (49 genes) or decreased (23 mRNA during growth on methanol-grown as the control. Major differences transcript levels observed for mta , mtb mtt and mtm genes, which encode enzymes involved methane formation from methanol trimethylamine, respectively. Other abundance found encoding...