In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). ...The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.
Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for ...this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (~50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.
Uncovering which biogeochemical processes have a critical role controlling dissolved organic matter (DOM) compositional changes in complex estuarine environments remains a challenge. In this context, ...the aim of this study is to characterize the dominant patterns of variability modifying the DOM composition in an estuary off the Southeastern U.S. We collected water samples during three seasons (July and October 2014 and April 2015) at both high and low tides and conducted short- (1 day) and long-term (60 days) dark incubations. Samples were analyzed for bulk DOC concentration, and optical (CDOM) and molecular (FT-ICR MS) compositions and bacterial cells were collected for metatranscriptomics. Results show that the dominant pattern of variability in DOM composition occurs at seasonal scales, likely associated with the seasonality of river discharge. After seasonal variations, long-term biodegradation was found to be comparatively more important in the fall, while tidal variability was the second most important factor correlated to DOM composition in spring, when the freshwater content in the estuary was high. Over shorter time scales, however, the influence of microbial processing was small. Microbial data revealed a similar pattern, with variability in gene expression occurring primarily at the seasonal scale and tidal influence being of secondary importance. Our analyses suggest that future changes in the seasonal delivery of freshwater to this system have the potential to significantly impact DOM composition. Changes in residence time may also be important, helping control the relative contribution of tides and long-term biodegradation to DOM compositional changes in the estuary.
Dissolved primary production released into seawater by marine phytoplankton is a major source of carbon fueling heterotrophic bacterial production in the ocean. The composition of the organic ...compounds released by healthy phytoplankton is poorly known and difficult to assess with existing chemical methods. Here, expression of transporter and catabolic genes by three model marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) was used as a biological sensor of metabolites released from the picoeukaryote Micromonas commoda RCC299. Bacterial expression responses indicated that the three species together recognized 38 picoeukaryote metabolites. This was consistent with the Micromonas expression of genes for starch metabolism and synthesis of peptidoglycan-like intermediates. A comparison of the hypothesized Micromonas exometabolite pool with that of the diatom Thalassiosira pseudonana CCMP1335, analyzed previously with the same biological sensor method, indicated that both phytoplankton released organic acids, nucleosides, and amino acids, but differed in polysaccharide and organic nitrogen release. Future ocean conditions are expected to favor picoeukaryotic phytoplankton over larger-celled microphytoplankton. Results from this study suggest that such a shift could alter the substrate pool available to heterotrophic bacterioplankton.
Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have ...been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical changes as porewater salinity was increased from 0 to 10 over 35 days. As reported in Weston et al. (Biogeochemistry, 77:375-408, 62), porewater chemistry was monitored, and cores were sacrificed at 0, 9, 15, and 35 days, at which time we completed terminal restriction fragment length polymorphism and 16S rRNA clone library analyses of sediment microbial communities. The biogeochemical study documented changes in mineralization pathways in response to artificial seawater additions, with a decline in methanogenesis, a transient increase in iron reduction, and finally a dominance of sulfate reduction. Here, we report that, despite these dramatic and significant changes in microbial activity at the biogeochemical level, no significant differences were found between microbial community composition of control vs. seawater-amended treatments for either Bacterial or Archaeal members. Further, taxa in the seawater-amended treatment community did not become more “marine-like” through time. Our experiment suggests that, as seawater intrudes into freshwater sediments, observed changes in metabolic activity and carbon mineralization on the time scale of weeks are driven more by shifts in gene expression and regulation than by changes in the composition of the microbial community.
Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and ...concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.
To characterize bacterioplankton functional assemblages that transform specific components of the coastal seawater dissolved organic carbon (DOC) pool, bromodeoxyuridine (BrdU) was used to label the ...bacterioplankton cells that were active following addition of single-DOC model compounds: two organic osmolytes dimethylsulfoniopropionate (DMSP) and glycine betaine (GlyB) and two aromatic monomers para-hydroxybenzoic acid (pHBA) and vanillic acid (VanA). Bacterial populations were analysed based on in situ fluorescent immunodetection of BrdU incorporation followed by fluorescence-activated cell sorting (FACS). Sorted cells were then characterized by 16S rDNA-based analysis. Populations with high BrdU incorporation level (HI) developed within 8 h of introduction of 100 nM model compound. Terminal restriction fragment length polymorphisms (T-RFLP) analysis indicated that the HI populations in all four amendments were composed of bacteria from the same major taxa (phylum and subphylum levels), but the relative abundance of each differed. High-resolution clone libraries (each containing ~200 clones) showed that the HI populations in the GlyB and VanA amendments consisted of both metabolic generalists and specialists within the α-Proteobacteria (mainly members of the Roseobacter clade), β-Proteobacteria and γ-Proteobacteria (mainly members of Altermonadaceae, Chromatiaceae, Oceanospirillaceae and Pseudomonadaceae). The presence of members of OM60/241, OM185, SAR11, SAR86 and SAR116 in the HI populations indicated that members of these groups can assimilate the model DOC compounds, providing some of the first glimpses into heterotrophy by members of these poorly understood environmental clusters.
Abstract
Bacteria and Archaea of the air–water surface microlayer (neuston) and plankton from three high mountain lakes (Limnological Observatory of the Pyrenees, Spain) were analysed by 16S rRNA ...gene 454 pyrosequencing (V6 region) in two dates with different atmospheric aerosol loading conditions: (1) under a Saharan dust plume driven by southern winds; and (2) under northern winds with oceanic influence. In general, bacterial communities were richer than archaea, with estimated total richness of c. 2500 OTUs for Bacteria and c. 900 OTUs for Archaea equivalent to a sequencing effort of c. 250 000 and c. 20 000 sequences, respectively. The dominant bacterial OTU was affiliated to Actinobacteria. Archaea were one to two orders of magnitude less abundant than bacteria but were more evenly distributed. Apparently, Bacteroidetes and Thaumarchaeota sequences were preferentially found at the neuston, but no consistent pattern in either total microbial abundance or richness was found in any sample. However, we observed more marked changes in microbial relative abundances between neuston and plankton in the dust-influenced scenario. Higher community dissimilarities between neuston and plankton were also found during the Saharan dust episode, and such differences were higher for Bacteria than for Archaea. Nonetheless, relatively few (< 0.05%) of the neuston sequences matched previously identified airborne microorganisms, and none became important in the dates analysed.
Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an ...intense dinoflagellate bloom in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16S rRNA amplicon libraries from samples collected on 41 dates. The dataset also includes 88 18S rRNA amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom. Accompanying the sequence data are chemical and biological measurements associated with each sample. These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.
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