Manganese (Mn) oxides are highly reactive minerals that play an important role in elemental biogeochemical cycles, controlling the speciation and availability of many metals and organic compounds. Microbes catalyze the transformation of soluble Mn(II) into solid-phase Mn(III/ IV) oxides, however the identity of the organisms responsible and mechanism of this biomineralization are unknown. Field work was carried out in deep-sea hydrothermal vent plumes at Guaymas Basin (GB) in the Gulf of California, where previous studies suggested that microbes play a major role in the oxidation precipitation of Mn. Mn(II) oxidation rates were measured using ⁵⁴Mn as a radioactive tracer and were found to be the fastest ever recorded in a deep-sea hydrothermal plume. This rapid Mn(II) oxidation is catalyzed by microbial enzymes and is specific to the GB plume, suggesting that a distinct community of microbes is present in the plume compared to background deep-seawater. However, molecular methods revealed that there are only subtle differences in the microbial community in the plume versus background deep- seawater, indicating that the unique biogeochemistry of the plume is due to unique activities of plume microbes rather than unique types of plume microbes. Mn(II)- oxidizing isolates were not well represented in plume clone libraries, suggesting that the organisms responsible for Mn(II) oxidation in the plume have not yet been identified. Laboratory investigations of model Mn(II)- oxidizers in the lab further elucidated the mechanism of Mn(II) oxidation. The Mn-oxidizing enzyme from spores of a marine Bacillus species was partially purified and identified by tandem mass spectrometry (MS/MS), providing a conclusive match to the protein MnxG, a multicopper oxidase. These results demonstrate that MnxG directly catalyzes the oxidation of Mn(II) to Mn(IV) oxides, a novel biochemical reaction for a multicopper oxidase. Genome sequence analysis of the Mn(II)-oxidizing [alpha]- proteobacterium strain SI85-9A1 provided genomic insights into Mn(II) oxidation. The genome encodes metabolic versatility, including pathways for heterotrophy, lithotrophy (on sulfur, methanol, CO), and authotrophy (via the Calvin cycle). Genes encoding the putative Mn(II) oxidase were identified and found to be widespread in completed proteobacterial genomes and in environmental datasets, suggesting that Mn(II) oxidation is more widespread that previously recognized

Abstract Background Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. Results We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH ~5) versus extracellular (pH ~1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. Conclusions An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.

The National Science Foundation's EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on 'omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, "big-data capable" analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean 'omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the 'omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.

Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1-2 mm thick layer of 50 µmol L-1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. A metagenome-assembled genome of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, the ability of the organism to reduce Photosystem I via sulfide quinone reductase while Photosystem II is sulfide-inhibited, thereby performing anoxygenic photosynthesis in the presence of sulfide, has yet to be demonstrated.

This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.