Description: The present study aimed at a first characterization of the enigmatic JTB255 marine benthic group in deep-sea sediments, by: i) confirming the abundance and ubiquitous distribution of JTB255 in deep-sea sediments globally, ii) refining the phylogenetic positioning of the JTB255 clade within the \u03b3-Proteobacteria, iii) distinguishing potential ecotypes within the JTB255 clade, iv) providing first insights into the metabolic potential of deep-sea representatives of this clade. Therefore, two single cell genomes from Arctic HAUSGARTEN deep-se surface sediments were obtained and CARD-FISH counts of total cells, y-Proteobacteria and the JTB255 marine benthic group performed.

Description: We fixed 0.5 g aliquots of sediment with a 4% formaldehyde solution for 2-4 h, washed the fixed sediments three times with 1x phosphate-buffered saline (PBS), before storing them in 50% ethanol/PBS at -20°C. For water samples, we fixed 10 ml (for samples from the deep chlorophyll maximum and 100 m water depth) and 30 ml (for meso- and bathypelagic samples) with formaldehyde to a final concentration of 2-4% for 2-4 h, then filtered over a 0.22 µm polycarbonate filter, and stored samples at -20°C. We performed total cell counts as described by Schauer et al. (2011, doi:10.1111/j.1462-2920.2011.02530.x) using the nucleic acid dye 4'-6-diamidino-2-phenylindole (DAPI). A minimum of 1,000 cells in 20 independent grids were counted using a Zeiss Axio Imager M1 epifluorescence microscope equipped with a 100x/1.25 oil plan-apochromat objective. We used Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH) according to Ishii et al. (2004) to count Gammaproteobacteria and JTB255 cells. We used the GAM42a oligonucleotide probe and the BET42a competitor probe to target members of the Gammaproteobacteria (Manz et al., 1992, doi:10.1016/S0723-2020(11)80121-9). We designed the JTB819a and JTB897 probes to target 16S rRNA gene sequences assigned to JTB255 in SILVA release 128 and the cJTB897 competitor probe to target all non-JTB255 16S sequences in SILVA release 128 that have a single mismatch to JTB819a and JTB897 probes. We obtained total gammaproteobacterial and JTB255 cell counts from duplicate filters derived from each sampling site.

Description: The Fram Strait separates Northeast Greenland from the Svalbard Archipelago, and is the only deep connection to the Arctic Ocean. Therefore, this strait is the only gateway for direct exchange of intermediate and deep waters between the Arctic Ocean and the North Atlantic. Two main currents influence the exchanges: i) the West Spitsbergen Current, bringing Atlantic waters northwards, and ii) the East Greenland Current, which carries cold Arctic waters and ice southwards. These two currents consist of water masses with different origin, generate distinct physical and chemical conditions between the eastern and western parts of the strait, which effects the biological characteristics in this region. Oceanographic observations in the Fram Strait have been carried out for ~15 years with microbial research in the water column focusing mainly on eukaryotes, while very little exploratory work was conducted on pelagic Bacteria and Archaea. Here we present a preliminary report of the first extensive survey across the waters of the Fram Strait focused on Bacterial and Archaeal domains, conducted as part of the Arctic long-term observatory HAUSGARTEN annual expedition in summer 2016. Besides the investigation of “who is out there”, the observations gained in this survey will be integrated with other biological and physical data of the long-term observatory framework and will provide an essential step towards the understanding of the biochemical dynamics in the Fram Strait. In addition, on a long-term plan this project will contribute to the microbial observatory work as part of the FRAM Helmholtz research infrastructure and EU AtlantOS program.

Description: The vast majority of deep-sea ecosystems are sustained by exported organic material from the productive, sunlit surface ocean. Bacteria dominate benthic communities both in biomass and abundance, and have been recognized as the key players in the remineralization of organic material. Since most sediment bacteria remain however uncultivated and represent unknown taxa, we have very limited knowledge of their metabolic capabilities and enzymatic machinery. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1200 m to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA, as well as metagenomic and -transcriptomic sequencing to elucidate total and active bacterial community composition and gain insight into the carbohydrate processing and uptake capabilities of deep-sea benthic bacteria. We identified specific taxa of interest and quantified their cellular abundance using CAtalyzed Reporter Deposition–Fluorescence In Situ Hybridization. Results from the different molecular approaches were in good agreement and suggested similar community structures with the same dominant members. Interestingly, typically predominant sediment taxa, i.e. the JTB255 marine group, the Sh765B.TzT29 group or the OM1 clade, were underrepresented in the active part of the community, while other usually low-abundant taxa, i.e. Flavobacteriia and the SAR202 clade, were overrepresented. At low taxonomic resolution, communities along the slope were similar, yet showed high turnover at species level. Although, the repertoire of carbohydrate-active enzymes (e.g. polysaccharide hydrolases) appeared unchanging along the depth gradient, the relative contribution of distinct enzyme-coding genes varied. Specific glycoside hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) had higher counts at shallow depth, while others responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality.

Description: Microbial observation is of high relevance in assessing marine phenomena of scientific and societal concern including ocean productivity, harmful algal blooms, and pathogen exposure. However, we have yet to realise its potential to coherently and comprehensively report on global ocean status. The ability of satellites to monitor the distribution of phytoplankton has transformed our appreciation of microbes as the foundation of key ecosystem services; however, more in-depth understanding of microbial dynamics is needed to fully assess natural and anthropogenically induced variation in ocean ecosystems. While this first synthesis shows that notable efforts exist, vast regions such as the ocean depths, the open ocean, the polar oceans, and most of the Southern Hemisphere lack consistent observation. To secure a coordinated future for a global microbial observing system, existing long-term efforts must be better networked to generate shared bioindicators of the Global Ocean's state and health.

Description: The vast majority of deep-sea ecosystems are sustained by exported organic material from the productive, sunlit surface ocean. Bacteria dominate benthic communities both in biomass and abundance, and have been recognized as the key players in the remineralization of organic material. Since most sediment bacteria remain however uncultivated and represent unknown taxa, we have very limited knowledge of their metabolic capabilities and enzymatic machinery. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1200 m to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA, as well as metagenomic and -transcriptomic sequencing to elucidate total and active bacterial community composition and gain insight into the carbohydrate processing and uptake capabilities of deep-sea benthic bacteria. We identified specific taxa of interest and quantified their cellular abundance using CAtalyzed Reporter Deposition–Fluorescence In Situ Hybridization. Results from the different molecular approaches were in good agreement and suggested similar community structures with the same dominant members. Interestingly, typically predominant sediment taxa, i.e. the JTB255 marine group, the Sh765B.TzT29 group or the OM1 clade, were underrepresented in the active part of the community, while other usually low-abundant taxa, i.e. Flavobacteriia and the SAR202 clade, were overrepresented. At low taxonomic resolution, communities along the slope were similar, yet showed high turnover at species level. Although, the repertoire of carbohydrate-active enzymes (e.g. polysaccharide hydrolases) appeared unchanging along the depth gradient, the relative contribution of distinct enzyme-coding genes varied. Specific glycoside hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) had higher counts at shallow depth, while others responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality.

Description: The majority of the Earth’s surface is covered by fine-grained deep-sea sediments, with bacteria dominating total benthic biomass. These benthic bacterial communities depend on organic matter input from the upper ocean, but as they comprise mostly unknown and uncultivated taxa, we have very limited knowledge of their enzymatic machinery to break down this material. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1000 to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA and metagenomic sequencing to elucidate total and active bacterial community composition, and the key functional potentials. Some sequence-dominant taxa of the total community (e.g. members of the Gamma- and Deltaproteobacteria) were underrepresented in the cDNA fraction, while other groups (e.g. Flavobacteriaceae; SAR202 clade) were overrepresented in the active fraction when compared to total community reads. We used the Carbohydrate Active Enzymes database (http://www.cazy.org) to identify protein families in the generated metagenomes, which are associated with polysaccharide degradation, e.g. glycoside hydrolases. We found the same families of glycoside hydrolases in all metagenomes, but their relative contribution to glycoside hydrolase-coding genes varied according to depth. A larger number of hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) was found at shallower depths, while those responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality.

Description: Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named “JTB255-Marine Benthic Group” (now the candidate order Woeseiales), accounts for 1–22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and specific ecological niches in the deep sea, which constitutes the largest biome globally. Here, we characterized the phylogeny, environmental distribution patterns, abundance, and metabolic potential of Woeseiales bacteria with a focus on representatives from the deep sea. From a phylogenetic analysis of publicly available 16S rRNA gene sequences (≥1400 bp, n = 994), we identified lineages of Woeseiales with greater prevalence in the deep sea than in coastal environments, a pattern corroborated by the distribution of 16S oligotypes recovered from 28 globally distributed sediment samples. Cell counts revealed that Woeseiales bacteria accounted for 5 ± 2% of all microbial cells in deep-sea surface sediments at 23 globally distributed sites. Comparative analyses of a genome, metagenome bins, and single-cell genomes suggested that members of the corresponding clades are likely to grow on proteinaceous matter, potentially derived from detrital cell membranes, cell walls, and other organic remnants in marine sediments.