The “dark ocean” – the water column below the photic zone - constitutes 90% of the ocean’s volume and contains three quarters of its microbial biomass. The dark ocean microbiome controls the aphotic end of the ocean’s carbon biological pump, and play a vital role in biogeochemical cycling. It is characterized by elevated taxonomic diversity, pronounced vertical stratification and complex interactions among heterotrophs and chemoautotrophs. There is an urgent need to improve our understanding of the metabolic processes in light of the emerging use of the dark ocean and its seafloor for fishing, carbon sequestration, and industrial mining. However, due to the challenges of conducting research at such depths, relatively little is known about the identity, ecology, evolution, activity and resilience of microorganisms inhabiting the dark ocean. The goal of this session is to assemble scientific presentations that cover deep-sea technology development and cutting-edge science in a broad spectrum of dark ocean microbiology-related research areas.
Lead Organizer: Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences (rstepanauskas@bigelow.org)
Co-organizers:
Maria Pachiadaki, Woods Hole Oceanographic Institution (mpachiadaki@whoi.edu)
Presentations
09:00 AM
A single-cell genome chart of dark ocean prokaryoplankton (8828)
Primary Presenter: Tianyi Chang, Xiamen University (chtianyii@gmail.com)
The “dark ocean”, defined as water column below the sunlight surface layer, contains 90% of the ocean’s volume and three quarters of the marine prokaryoplankton biomass, yet remains underexplored. Here, we report Global Ocean Reference Genome (GORG)-Dark – the first large collection of single amplified genomes (SAGs) of planktonic bacteria and archaea inhabiting this vast environment. GORG-Dark consists of 9,000 curated SAGs representing 43 phyla, 81 classes, and 234 orders of bacteria and archaea. These SAGs were produced using a randomized cell selection strategy from globally sourced samples spanning a latitudinal range from pole to pole, geographic locations from open oceans to inland seas, depth layers from upper mesopelagic to hadal (>10,000 meter), and oxygen regimes from fully oxygenated to anoxic. By leveraging the fine-resolution genome representation of GORG-Dark and the massive gene-level representation of ~800 dark and surface ocean metagenomes through fragment recruitment, we produced a robust map of prokaryoplankton spatial distribution. This revealed pronounced stratification by depth and limited geographic differences in the open, oxygenated ocean. We discovered a previously undescribed SAR11 lineage that is abundant in the deep ocean and predominantly found on particles. Metabolic potential analyses indicated widespread autotrophy and a substantially more diverse capacity for secondary metabolite synthesis as compared to surface ocean. Meanwhile, low-oxygen environments, such as the subphotic zones of the Baltic Sea and the Black Sea, had highly distinct prokaryoplankton, with an unexpected abundance of Patescibacteria and DPANN archaea that may have been underestimated in earlier studies. This study offers a broad overview of the coding potential of the dark ocean prokaryoplankton and an extensive resource for further data exploration.
09:15 AM
Dark ocean chemoautotrophy and other tales from tiny organisms with big impact (9350)
Primary Presenter: Maria Pachiadaki, Woods Hole Oceanographic Institution (mpachiadaki@whoi.edu)
The microbial inhabitants of the dak ocean comprise one of the largest biota on Earth. They mediate all major biogeochemical cycles, and control the “dark end” of ocean’s biological pump. Yet, little is known about the key chemoautotrophic taxa in the aphotic realm. To address this challenge, we employed single cell genomics technology to generate 10,000 partial genomes of planktonic Bacteria and Archaea from all major water masses and the oxygen-depleted seas, Baltic and Black. Two thousand additional genomes were generated from the oxygen-deficient water columns of the Eastern Tropical North and South Pacific. Around a quarter of the recovered genomes are affiliated to Nitrosopumilaceae, and have the potential to fix inorganic carbon through the modified 3-Hydroxyproponate/4-Hydroxybutyrate cycle, confirming the established paradigm that archaeal ammonia oxidizers are the most abundant chemolithotrophs in the ocean. We also detected potential sulfur oxidizing lineages, encoding the genes of the CO2 fixation Calvin-Benson-Bassham cycle, the majority of which belong to Gammaproteobacterial, followed by the SAR324. Nitrite Oxidizing Bacteria using the reductive tricarboxylic acid cycle to fix carbon, are also abundant and ubiquitous. The oxygen-depleted water columns also contain diverse chemoautotrophic lineages using the reductive acetyl-CoA pathway. Genomes affiliated to lineages that are not known to fix inorganic carbon (e.g. Patescibacteria, Nanoarchaeota and Marinisomatota) were also found, but their role in dark CO2 fixation requires further investigation.
09:30 AM
Trans-Pacific explorations of pelagic microbial communities unveil factors affecting the biogeochemical cycles in the dark ocean (9029)
Primary Presenter: Takuro Nunoura, Japan Agency for Marine-Earth Science & Technology (JAMSTEC) (takuron@jamstec.go.jp)
Microbial community drives the oceanic biogeochemical cycles through primary production and organic degradation, and thus, local microbial communities interact spatiotemporal biogeochemical cycles. Here, we observed SSU rRNA gene-based community compositions in combination with cell counts and comprehensive physical and geochemical measurements throughout the water columns (0–9758 m) at 49 stations along the three subarctic, subtropical and antarctic transect sampling campaigns in the Pacific Ocean. The results revealed that vertical microbial diversity transition was affected by quality of organic matter, but neither concentrations of oxygen, nutrients, nor organic carbon flux. Moreover, microbial ecosystem below the bathypelagic zone can mostly be explained by a combination of the 8 ubiquitous microbial communities. In contrast, oceanic region-specific communities dominated in the epi- and meso-pelagic zones. The distribution patterns of the microbial communities suggested that the quality of organic matter were varied above the mesopelagic zone, the variable organic matter converged on certain states below the bathypelagic zone, and the ubiquitous microbial communities likely represent degree of organic matter maturation. Moreover, the comparison of the microbial communities among the three transects revealed the impacts of organic matter transportation by antarctic bottom water formation and that with bottom current. The study unveiled the structure of geochemical cycles in deep ocean and the impacts of deep water circulation on geochemical cycles.
09:45 AM
OPENING A (META)GENOMIC WINDOW INTO MODULAR DENITRIFICATION PATHWAY COMPONENTS IN SUNLIT AND DARK OCEAN WATERS (9359)
Primary Presenter: Julia Anstett, University of British Columbia (julia.anstett@alumni.ubc.ca)
An invisible majority of life on Earth comprised of interacting bacterial and archaeal cells (the Prokaryotes) plays integral roles in driving global-scale biogeochemical cycles. Despite their outsize roles and two decades of shotgun sequence exploration, we know surprisingly little about the fine structure of uncultivated prokaryotic communities. This is especially true in marine environments where most studies have focused on sunlit waters that comprise only a small fraction of total ocean volume. Recent advances in culture independent methods enable identification and analysis of prokaryotic cells through construction of single-cell amplified genomes (SAGs) with increased coverage and precise taxonomic resolution. Here, we utilize 9,000 globally sourced SAGs of dark ocean planktonic Prokaryotes as taxonomic anchors to expand gene-centric phylogenies for denitrification pathway components (NapA/NarG, NirK/NirS, NorBC, and NosZ) relevant to biological nitrogen loss and greenhouse gas production using the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP). By iteratively adding environmentally relevant SAGs in combination with metagenome assembled genomes and raw sequencing reads from the same locations, we explored the spatiotemporal distribution and expression of denitrification genes in the Northeastern subarctic Pacific (NESAP) ocean waters providing quantitative resolution on the modularity of this pathway along gradients of oxygen and nitrate that are increasingly sensitive to the forcing effects of climate change.
10:00 AM
Genomic Insights into Chemotaxis of the Ubiquitous SAR324 Bacteria in the Pelagic Deep Ocean (9088)
Primary Presenter: Paula Ruiz-Fernández, Instituto Milenio de Oceanografía IC120019 (sofpaula@gmail.com)
In the deep, cold, pelagic ocean, where organic matter is typically scarce, chemotaxis likely plays a crucial role in enabling heterotrophic microorganisms to locate and acquire it. Here, we examine the genomic features of chemotaxis machinery under high hydrostatic pressure conditions. Single Amplified Genomes (SAGs) of the Atacama Trench water column were analyzed, focusing on the SAR324 bacteria lineage. This lineage was detected at all sampled depths and exhibited genetic potential to encode a complete set of proteins related to chemotaxis, similar to those found in model bacteria. Phylogenomic analysis clustered SAR324 SAGs into two groups: one associated with Antarctic Intermediate Water (AAIW; 500 and 1,000 m) and the other with deep Pacific Ocean Water masses (PWD; >2,000 m). Notably, PWD samples contained a higher proportion of SAGs with sequences related to chemoreceptors and intracellular signaling components, including CheA, CheB, CheW, and CheR. This finding suggests a potential strategy for capturing attractant compounds, such as organic matter via chemotaxis in the dark ocean. Read recruitment of SAR324 chemotaxis-related sequences to public ocean metagenomes and metatranscriptomes revealed a cluster enriched in bathypelagic waters (>2,800 m). The predicted amino acid composition of these sequences was similar to those found in shallower waters for most of the genes. However, notable exceptions included the predicted proteins MCP (chemoreceptors), FlhF (flagellar biosynthesis), FliN (flagellar motor switch), and FliK (flagellar hook-length control), which exhibited distinct differences in the deep-bathypelagic waters. Additionally, sequences enriched in deep metagenomes exhibited distinct nucleotide compositions and significant differences in synonymous codon usage patterns. These findings suggest specific adaptations of the chemotaxis system to low temperatures and high pressures, providing SAR324 with a selective advantage in extreme deep-sea environments.
10:15 AM
Exploring Viral Impacts on Dark Carbon Fixation at Deep-Sea Hydrothermal Vents using DNA-SIP (9395)
Primary Presenter: Paulo Freire, University of North Carolina at Charlotte (UNC Charlotte) (pfreire@uncc.edu)
Chemosynthetic microbes form the base of the food web at deep-sea hydrothermal vents by fixing dissolved inorganic carbon (DIC) into organic carbon that can flow into other trophic levels. In this ecosystem, viruses convert organic carbon from the host into dissolved and particulate organic carbon pools through host lysis. Moreover, viruses enhance the host's nutrient uptake by transferring auxiliary metabolic genes (AMGs), which support viral replication. However, the key viruses infecting microbes in the deep sea remain understudied relative to the surface ocean. This study combines metagenomics and stable-isotope probing (SIP) to identify the diversity and activity of viruses infecting primary producers at deep-sea vents. Samples from the Axial Seamount (Oregon coast) were incubated with 13C-DIC or 12C-DIC. DNA was extracted and separated based on density to quantify microbial hosts' and viruses' carbon cycling activity. Recovered metagenomic-assembled genomes uncovered diverse chemoautotrophic prokaryotes, including the phyla Campylobacteria and Aquificota. The majority of retrieved viruses were novel bacteriophages not reported before. Diverse AMGs from energy and carbon metabolism were identified, demonstrating the viruses' potential for manipulating host metabolism. This uncharacterized diversity showed that DNA-SIP can be a powerful approach for linking genomic diversity to the biogeochemical cycle. Our results emphasize the importance of linking novel taxonomic diversity to key biogeochemical processes to advance our understanding of the deep-sea biosphere.
SS10A - Microbial processes of the dark ocean
Description
Time: 9:00 AM
Date: 28/3/2025
Room: W201CD