Interesting things come in small packages

An unusual uncultivated nitrogen-fixing cyanobacterium lacks many of the signature features of typical cyanobacteria

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host–symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts’ metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts’ interaction with regional-scale differences in geochemistry.National Science Foundation (U.S.) (OCE-0732369)National Science Foundation (U.S.) (GRF grant no. DGE-1144152)Gordon and Betty Moore Foundation (Investigator)Agouron Institut

Metatranscriptomic Analysis of Sulfur Oxidation Genes in the Endosymbiont of Solemya Velum

Thioautotrophic endosymbionts in the Domain Bacteria mediate key sulfur transformations in marine reducing environments. However, the molecular pathways underlying symbiont metabolism and the extent to which these pathways are expressed in situ are poorly characterized for almost all symbioses. This is largely due to the difficulty of culturing symbionts apart from their hosts. Here, we use pyrosequencing of community RNA transcripts (i.e., the metatranscriptome) to characterize enzymes of dissimilatory sulfur metabolism in the model symbiosis between the coastal bivalve Solemya velum and its intracellular thioautotrophic symbionts. High-throughput sequencing of total RNA from the symbiont-containing gill of a single host individual generated 1.6 million sequence reads (500 Mbp). Of these, 43,735 matched Bacteria protein-coding genes in BLASTX searches of the NCBI database. The taxonomic identities of the matched genes indicated relatedness to diverse species of sulfur-oxidizing Gammaproteobacteria, including other thioautotrophic symbionts and the purple sulfur bacterium Allochromatium vinosum. Manual querying of these data identified 28 genes from diverse pathways of sulfur energy metabolism, including the dissimilatory sulfite reductase (Dsr) pathway for sulfur oxidation to sulfite, the APS pathway for sulfite oxidation, and the Sox pathway for thiosulfate oxidation. In total, reads matching sulfur energy metabolism genes represented 7% of the Bacteria mRNA pool. Together, these data highlight the dominance of thioautotrophy in the context of symbiont community metabolism, identify the likely pathways mediating sulfur oxidation, and illustrate the utility of metatranscriptome sequencing for characterizing community gene transcription of uncultured symbionts

Genetic diversity affects the daily transcriptional oscillations of marine microbial populations

Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics

Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016)

Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 543, doi:10.3389/fmicb.2014.00543.Molecular surveys are revealing diverse eukaryotic assemblages in oxygen-limited ocean waters. These communities may play pivotal ecological roles through autotrophy, feeding, and a wide range of symbiotic associations with prokaryotes. We used 18S rRNA gene sequencing to provide the first snapshot of pelagic microeukaryotic community structure in two cellular size fractions (0.2–1.6 μm, >1.6 μm) from seven depths through the anoxic oxygen minimum zone (OMZ) off northern Chile. Sequencing of >154,000 amplicons revealed contrasting patterns of phylogenetic diversity across size fractions and depths. Protist and total eukaryote diversity in the >1.6 μm fraction peaked at the chlorophyll maximum in the upper photic zone before declining by ~50% in the OMZ. In contrast, diversity in the 0.2–1.6 μm fraction, though also elevated in the upper photic zone, increased four-fold from the lower oxycline to a maximum at the anoxic OMZ core. Dinoflagellates of the Dinophyceae and endosymbiotic Syndiniales clades dominated the protist assemblage at all depths (~40–70% of sequences). Other protist groups varied with depth, with the anoxic zone community of the larger size fraction enriched in euglenozoan flagellates and acantharean radiolarians (up to 18 and 40% of all sequences, respectively). The OMZ 0.2–1.6 μm fraction was dominated (11–99%) by Syndiniales, which exhibited depth-specific variation in composition and total richness despite uniform oxygen conditions. Metazoan sequences, though confined primarily to the 1.6 μm fraction above the OMZ, were also detected within the anoxic zone where groups such as copepods increased in abundance relative to the oxycline and upper OMZ. These data, compared to those from other low-oxygen sites, reveal variation in OMZ microeukaryote composition, helping to identify clades with potential adaptations to oxygen-depletion.This work is a contribution of the Center for Microbial Oceanography: Research and Education (C-MORE) and was made possible by generous support from the National Science Foundation (1151698 to Frank J. Stewart and EF0424599 to Edward F. DeLong), the Alfred P. Sloan Foundation (Frank Stewart), the Gordon and Betty Moore Foundation (Edward F. DeLong), and the Agouron Institute (Edward F. DeLong). Edgcomb's involvement was supported by contributions from the Woods Hole Oceanographic Institution Director of Research and Ocean Life Institute

Abundance and distribution of planktonic Archaea and Bacteria in the waters west of the Antarctic Peninsula

Polyribonucleotide probes targeting planktonic archaeal (Group I and II) and bacterial rRNA revealed that Archaea comprised a significant fraction of total prokaryote cell abundance in the marine waters west of the Antarctic Peninsula. Determinations of Archaea and Bacteria cell abundances were made during two research cruises to the Palmer Long‐Term Ecological Research region during the austral winter and summer of 1999. During the austral summer, surface water abundances of Group I (GI) Archaea were generally low, averaging 4.7 x 103 cells ml−1 and accounting for 1% of the total picoplankton assemblage. The abundance of GI Archaea increased significantly with depth, averaging 2.1 X 104 cells ml−1 and comprising 9–39% of the total picoplankton abundance in the meso‐ (150–1,000 m) and bathypelagic (1,000–3,500 m) circumpolar deep water (CDW). Relative to summertime distributions, GI cells were more evenly distributed throughout the water column during the winter, averaging 10% of the picoplankton in the surface waters and 13% in the CDW. Surface water GI abundance increased 44% between the summer and winter, coincident with a fivefold decrease in GI abundance in the deeper waters. The abundance of Group II (GII) Archaea was persistently \u3c2% of the total picoplankton throughout the water column in both summer and winter. Bacterial abundance was greatest in the upper water column (0–100 m) during the summer, averaging 3.9 x 105 cells ml−1 and comprised 89% of the total picoplankton assemblage. Generally, GI Archaea varied seasonally in the deeper waters, whereas bacterial abundance varied more in the upper waters. The observed variability in bacterial and archaeal abundance suggests that these two groups of marine picoplankton are dynamic components of Southern Ocean microbial food webs

Evidence for Circumpolar Distribution of Planktonic Archaea in the Southern Ocean

Surveys using rRNA-targeted probes specific for the 3 domains of life (Eucarya, Archaea, and Bacteria) indicated the presence, and at times high abundance, of archaeal rRNA in a variety of water masses surrounding Antarctica. Hybridization signals of archaeal rRNA contributed significantly to that of total picoplankton rRNA both north and south of the Polar Front in Drake Passage. Late winter surface water populations collected around the South Shetland Islands also yielded relatively high archaeal rRNA hybridization signals, approaching 10% or greater of the total rRNA. Summer samples collected in the western region of the Antarctic Peninsula and at McMurdo Sound in the Ross Sea region of Antarctica yielded lower amounts of archaeal rRNA in the surface waters, and higher levels of archaeal rRNA at depth (150 to 500 m). The hybridization data were compared to biological, chemical, and hydrographic information when possible. In surface waters, archaeal rRNA and chlorophyll a varied inversely. The data presented here further supports the hypothesis that planktonic archaea are a common, widespread and likely ecologically important component of Antarctic picoplankton assemblages. The presence of these archaea in circumpolar deep water suggests a conduit for their circumpolar transport around Antarctica via the Antarctic Circumpolar Current, as well as their export to the deep sea, or to intermediate waters of the South Atlantic via mixing at the polar front

Microbial sources of exocellular DNA in the ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Linney, M. D., Eppley, J. M., Romano, A. E., Luo, E., DeLong, E. F., & Karl, D. M. Microbial sources of exocellular DNA in the ocean. Applied and Environmental Microbiology, 88(7), (2022): e02093-21, https://doi.org/10.1128/aem.02093-21.Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism.This work was supported by the Simons Collaboration on Ocean Processes and Ecology (awards 329108 to D.M.K. and E.F.D., 721252 to D.M.K., and 721223 to E.F.D.)