ABSTRACT We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ∼80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly α- and γ- Proteobacteria ) and Archaea (mainly Euryarchaeota ). Many transcripts could be linked to environmentally important processes such as sulfur oxidation ( soxA ), assimilation of C1 compounds ( fdh1B ), and acquisition of nitrogen via polyamine degradation ( aphA ). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.
Uncovering the metabolic capabilities of microbes is key to understanding global energy flux and nutrient transformations. Since the vast majority of environmental microorganisms are uncultured, metagenomics has become an important tool to genotype the microbial community. This study uses a recently developed computational method to confidently assign metagenomic reads to microbial clades without the requirement of metagenome assembly by comparing the evolutionary pattern of nucleotide sequences at non-synonymous sites between metagenomic and orthologous reference genes. We found evidence for new, ecologically relevant metabolic pathways in several lineages of surface ocean bacterioplankton using the Global Ocean Survey (GOS) metagenomic data, including assimilatory sulfate reduction and alkaline phosphatase capabilities in the alphaproteobacterial SAR11 clade, and proteorhodopsin-like genes in the cyanobacterial genus Prochlorococcus. These findings raise new hypotheses about microbial roles in energy flux and organic matter transformation in the ocean.
Microbially-mediated transformations of dissolved organic matter (DOM) in a marsh-dominated estuarine system were investigated at the molecular level using ultrahigh resolution mass spectrometry. In addition to observing spatial and temporal variability in DOM sources in the estuary, multiple incubations with endogenous microorganisms identified the influence of DOM composition on biodegradation. A clear microbial preference for degradation of compounds associated with marine DOM relative to those of terrestrial origin was observed, resulting in an overall shift of the remaining DOM toward a stronger terrigenous signature. During short, one-day long incubations of samples rich in marine DOM, the molecular formulae that were enriched had slightly smaller mass (20-30 Da) and number of carbon atoms compared to the molecular formulae that were depleted. Over longer time scales (70 days), the mean differences in molecular mass between formulae that were depleted and enriched were substantially larger (~270 Da). The differences in elemental composition over daily time scales were consistent with transformations in functional groups; over longer time scales, the differences in elemental composition may be related to progressive transformations of functional groups of intermediate products and/or other reactions. Our results infused new data toward the understanding of DOM processing by bacterioplankton in estuarine systems.
Summary of parameters measured in experimental and control microcosms as part of the Dauphin Island Cubitainer Experiment (DICE). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3857
The saltmarshes of the Georgia, USA, Atlantic coast are expansive and highly productive. The marshes form the intertidal ecosystem 5–10 km wide extending from the barrier-island chain to the mainland. The predominant macrophyte of the marshes is smooth cordgrass (Spartina alterniflora Loisel.). Cross-marsh average annual production of smooth cordgrass shoots in Georgia has been measured at approximately 1.3 kg m− 2 of marsh (Newell, 2001a, from Dai & Wiegert, 1996). Like most grasses, smooth cordgrass does not abscise its leaf blades; they remain attached to the leaf sheath after senescence and death (Newell, 1993, and references therein). As new blades are produced at the apex of shoots, the bottom blades senesce and die, until the whole shoot dies after flowering. Therefore, a large crop of standing-dead litter is available to microbes for decomposition for much of the year (for leaf blades alone, up to 538 g dry mass m− 2) (Newell et al., 1998).
The ubiquitous algal metabolite dimethylsulfoniopropionate (DMSP) is a major source of carbon and reduced sulfur for marine bacteria. Recently, the enzyme responsible for the demethylation of DMSP, designated DmdA, was identified, and homologs were found to be common in marine bacterioplankton cells. The recombinant DmdA proteins from the cultured marine bacteria Pelagibacter ubique HTCC1062 and Silicibacter pomeroyi DSS-3 were purified with a three-step procedure using anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies. The P. ubique enzyme possessed an M(r) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 38,500. Under nondenaturing conditions, the M(r) was 68,000, suggesting that the enzyme was likely to be a dimer. The purified enzyme exhibited strict substrate specificity for DMSP, as DmdA from both S. pomeroyi and P. ubique possessed no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity was found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate. The apparent K(m)s for DMSP were 13.2 +/- 2.0 and 5.4 +/- 2.3 mM for the P. ubique and S. pomeroyi enzymes, respectively. In cell extracts of S. pomeroyi DSS-3, the apparent K(m) for DMSP was 8.6 +/- 1.2 mM, similar to that of purified recombinant DmdA. The intracellular concentration of DMSP in chemostat-grown S. pomeroyi DSS-3 was 70 mM. These results suggest that marine bacterioplankton may actively accumulate DMSP to osmotically significant concentrations that favor near-maximal rates of DMSP demethylation activity.
Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate-relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a 3-week time period spanning September-October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harboured mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study. Novel members of the DMSP-degrading community emerged from dmdA sequences recovered from metagenome assemblies and single-cell sequencing, including largely uncharacterized gammaproteobacteria and alphaproteobacteria taxa. In the DMSP cleavage pathway, the SAR11 gene dddK was the most abundant early in the study, but was supplanted by dddP over time. SAR11 members, especially those harbouring genes for both DMSP degradation pathways, had a strong positive relationship with the abundance of dinoflagellates, and DMSP-degrading gammaproteobacteria co-occurred with haptophytes. This in situ study of the drivers of DMSP fate in a coastal ecosystem demonstrates for the first time correlations between specific groups of bacterial DMSP degraders and phytoplankton taxa.
