Microbial life in the deep ocean thrives despite low temperatures, high pressures, and seemingly scarce sources of organic matter. The identities of microorganisms that comprise deep water and sediment communities, the biogeochemical processes they carry out, and their adaptations have been focal points of deep-sea research, with substantial progress in recent years owing to new technologies and investigations in underexplored deep settings. To synthesize recent progress and gain insight from new inquiries, we broadly invite studies that investigate processes mediated by – and those that sustain – microbial communities in the deep ocean. We will focus on organisms ranging from viruses to microbial eukaryotes and welcome perspectives from any analytical tools, methods, and approaches employed. The topics covered can include (but are not limited to) the following: microbial biogeochemical cycles; community structure, connectivity, and assembly; adaptations to high pressure and low temperature; fluxes of matter to the deep sea; viral infections and influences on microbial ecology and biogeochemistry. We also strongly welcome studies that may focus on processes from other parts of the ocean (e.g. epi- and mesopelagic, coastal environments, etc.), but which are nevertheless crucial to our understanding of microbial processing in the deep sea (e.g. through surface-to-deep transfer of sinking particles, pelagic-benthic coupling, mass wasting events, etc.). Finally, we encourage submissions on developing or newly-developed technologies that facilitate progress in deep sea microbial and biogeochemical research.
Lead Organizer: Ronnie N. Glud, University of Southern Denmark (rnglud@biology.sdu.dk)
Co-organizers:
Chie Amano, University of Vienna (chie.amano@univie.ac.at)
John Paul Balmonte, University of Southern Denmark (jpbalmonte@biology.sdu.dk)
Gerhard J. Herndl, University of Vienna (gerhard.herndl@univie.ac.at)
Presentations
06:30 PM
PRESSURE EFFECTS ON DIVERSE EXTRACELLULAR ENZYMES PRODUCED BY HETEROTROPHIC MICROBIAL COMMUNITIES IN THE OCEAN (4629)
Primary Presenter: Stephanie Caddell, University of North Carolina at Chapel Hill (smc2002@ad.unc.edu)
Heterotrophic microbes consume much of the organic matter (OM) produced in the ocean. Although a considerable part of OM degradation occurs at depth, the effects of hydrostatic pressure on OM degradation in the deep ocean are seldom measured. We investigated the effect of deep ocean pressures on the activities of extracellular enzymes that heterotrophic microbes use to degrade high molecular weight (HMW) organic matter. To distinguish pressure effects on extracellular enzymes released from microbes from the effects on the microbes themselves, we first stimulated enzyme production via HMW OM addition to seawater. Freely released enzymes were isolated by filtration. The free enzymes as well as microbe-containing seawater were then incubated at pressures characteristic of the surface and deep ocean, and activities of peptidases, glucosidase, and chitinase enzymes were measured. For most incubations, activities at high pressure were 30% or more of activities at atmospheric pressure. Pressure enhancement as well as pressure inhibition was evident for both the free enzymes and bulk communities. Free enzymes showed comparatively more consistent pressure effects across sites compared to the bulk communities. These data suggest that despite partial pressure inhibition of enzymes and organisms of the upper ocean, they can still contribute to organic matter degradation at considerable depth. Our data also suggest that pressure effects on enzymes vary by type and class, likely due in part to pressure sensitivities of the enzyme-producing members of the active microbial community.Heterotrophic microbes consume much of the organic matter (OM) produced in the ocean. Although a considerable part of OM degradation occurs at depth, the effects of hydrostatic pressure on OM degradation in the deep ocean are seldom measured. We investigated the effect of deep ocean pressures on the activities of extracellular enzymes that heterotrophic microbes use to degrade high molecular weight (HMW) organic matter. To distinguish pressure effects on extracellular enzymes released from microbes from the effects on the microbes themselves, we first stimulated enzyme production via HMW OM addition to seawater. Freely released enzymes were isolated by filtration. The free enzymes as well as microbe-containing seawater were then incubated at pressures characteristic of the surface and deep ocean, and activities of peptidases, glucosidase, and chitinase enzymes were measured. For most incubations, activities at high pressure were 30% or more of activities at atmospheric pressure. Pressure enhancement as well as pressure inhibition was evident for both the free enzymes and bulk communities. Free enzymes showed comparatively more consistent pressure effects across sites compared to the bulk communities. These data suggest that despite partial pressure inhibition of enzymes and organisms of the upper ocean, they can still contribute to organic matter degradation at considerable depth. Our data also suggest that pressure effects on enzymes vary by type and class, likely due in part to pressure sensitivities of the enzyme-producing members of the active microbial community.
06:30 PM
TO HELP OR NOT TO HELP? EXPERIMENTAL EVOLUTION OF HOST-VIRUS-VIROPHAGE INTERACTIONS (4967)
Primary Presenter: Ana del Arco, University of Konstanz (ana.del-arco@uni-konstanz.de)
Species interactions lay along a parasitic-mutualistic continuum where cost and benefits change by the interplay of ecological and evolutionary processes. Therefore, mutualistic microbe-host associations to fight pathogens can be a temporal defence strategy that might become costly for the host driving the community to extinction if host is overexploited by both virus and virophage. We use a marine heterotrophic flagellate protected by a virophage (which can integrate into the host genome) against viral infections. First, we studied the role of microbial-mediated protection for species coexistence. Second, we tested if host-virophage interactions evolved towards parasitism. We maintained a microbial community of host-virus-virophage in chemostats for 50 days (~200 host generations). We monitored population dynamics and selected host clones from the end of the experiment. Selected host clone traits diversified from the ancestral host populations, suggesting that they evolved during the experiment. Specifically, we detected an increase in the number of integrated virophages between ancestors and selected clones and differences in virophage reactivation in the selected host clones.
06:30 PM
Variability in bacterial growth efficiency (BGE) of marine bacteria in response to changes in temperatures, pressures, and organic substrates (5426)
Primary Presenter: Devangi Sathe, University of Southern Denmark (SDU) (devangi@biology.sdu.dk)
Bacterial Growth Efficiency (BGE) is a key characteristic of microbial physiology and an important parameter in the evaluation of the quantitative role of bacterioplankton in the microbial food web. Changes in BGE is indicative of the responses of the microbial community to changes in environmental conditions such as temperature, pressure, and substrate availability. Using a batch culture approach, we investigate the effect of these parameters on the BGE of marine microbial communities from different marine environments. We systematically quantify the effects of temperature and pressure in combination with different dissolved organic carbon (DOC) sources on BGE, while varying only one parameter at a time. Our results show that BGE is dynamic, positively correlated to temperature and addition of labile DOC, and regulated by the C and N composition of the added organic carbon sources in both shallow and deep waters. These findings allow us to distinguish between the energy and organic nutrient requirements supporting an efficient transformation of DOC into bacterial biomass. These measurements of BGE regulation across different environmental conditions provide a comprehensive range for BGE values typically observed in marine environments, contributing to our understanding of how microbes adjust their BGE according to environmental parameters. These results in combination with in-situ measurements thus provide important insights into the bacterial carbon demand across marine ecosystems, having implications for estimation of marine carbon budgets.
06:30 PM
Spatial distribution of viruses and prokaryotes in the central Indian Ocean: North-South transect observations between latitudes 5.9N and 65.3S (5596)
Primary Presenter: Taichi Yokokawa, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) (taichi.yokokawa@jamstec.go.jp)
This study investigates the spatial distribution of viruses and prokaryotes in the central Indian Ocean. Samples were collected during cruise MR19-04. Samples for microbial enumeration were determined by flow cytometry. Prokaryotic cell and virus particle densities varied by up to three orders of magnitude (4.3 x 103 - 1.3 x 106 cells mL-1) and one order of magnitude (2.4 x 105 - 8.3 x 106 particles mL-1), respectively. The vertical distribution of the ratio of virus to prokaryote density showed a monotonically increasing trend with depth at all stations. In the surface layer the ratio was 10.2 ± 5.7 (mean ± SD, n = 145), while in the mesopelagic layer it was 14.3 ± 9.8 (n = 153). In the bathypelagic layer the mean ratio was 27.4 ± 14.2 (n = 219) and in the bottom layer 39.6 ± 19.6 (n = 56). The mean values in the bathypelagic and bottom layers were higher and more variable than those in the surface and mesopelagic layers. This variability is mainly due to the horizontal (latitudinal) variation of the ratio. These results suggest that the distribution patterns of viruses and prokaryotes in the central Indian Ocean differ between depth layers. These differences can be attributed to the different mechanisms of reproduction and decay of viruses and prokaryotes. In particular, the latitudinal variation in the ratio in the bathypelagic and the bottom layer (increasing from high to low latitudes) is likely to be explained by the fact that virus particles are less easily removed from the environment (less easily degraded) than prokaryotic cells.
06:30 PM
HIGH HETEROTROPHIC PROKARYOTES PRODUCTION SUPPORTED BY CHEMOAUTOTROPHIC COMMUNITIES IN THE PLUME OF THE ULTRAMAFIC-HOSTED HYDROTHERMAL VENT SYSTEM (CHEOEUM) IN THE DEEP INDIAN OCEAN (5764)
Primary Presenter: Jung-Ho Hyun, Hanyang University (hyunjh@hanyang.ac.kr)
The hydrothermal vents distributing along the mid-ocean ridge are geochemical hot-spots playing as a significant source of various elements (e.g., Fe, Mn, Co, Ni, etc.) to sea water, and are characterized by massive biological communities relying on chemosynthetic microbial communities. Although the significance of chemosynthetic processes in the hydrothermal vent ecosystem is well established, microbial and biogeochemical processes around the vent plume are relatively under-represented. We investigated the heterotrophic prokaryotes production (HPP) and microbial community structures associated with the vent plume around the Cheoeum hydrothermal vent system in the central Indian Ocean Ridge. The water in the plume was characterized by high concentrations of Mn (~ 200 nM), Fe (~ 6000 nM) and CH4 (~ 300 nM). The HPP in the plume (average 9.46 µmol C m-3 d-1) was greater than that measured above and below the plume (average 2.34 µmol C m-3 d-1) and in the ambient deep water away from the vent sites (average 2.71 µmol C m-3 d-1). Molecular analysis revealed that microbial communities consist of diverse chemosynthetic ammonia-oxidizing archaea, sulfur-oxidizing bacteria, metal-oxidizing bacteria and methanotrophs, together with heterotrophic bacteria using S0, FeOOH and O2 as an electron acceptor. Our results suggest that chemosynthetic microbial communities are likely to provide a substantial amount of organic substrates for supporting high HPP. Quantitative estimation on the dark CO2 fixation to evaluate if it is enough to support the high HPP remains as a question to be solved.
06:30 PM
INFLUENCE OF PRESSURE ON MICROBIAL COMMUNITIES IN SUBSEAFLOOR SEDIMENTS OF THE PUERTO RICO TRENCH (6068)
Primary Presenter: Miguel Desmarais, Scripps Institution of Oceanography (mdesmarais@ucsd.edu)
Subseafloor sediments, 85% of which are found in the deep sea (<1000 mbsl), host nearly one-third of Earth’s microbial biomass, making them one of the largest ecosystems on our planet. These communities, largely dominated by sulfate reducers and methanogens (>1.5 mbsf), experience extreme environmental conditions including high hydrostatic pressure. However, the impact of pressure on microbial activities and the molecular mechanisms of adaptation to life under these conditions are poorly understood. We collected sediment cores from the hadal, abyssal, and bathyal water-depth zones of the Puerto Rico Trench and hypothesize that 1) microbial communities within these samples are adapted to in situ pressure and 2) anaerobic activities proceed at the same rates observed in shallower waters. To assess this, replicate microcosms were established targeting the enrichment of sulfate reducers and methanogens and incubated at atmospheric (0.1 MPa) and in situ pressure (5-84 MPa, equivalent to 500-8400 mbsl). Differential gene expression (DGE) analyses will be performed to identify genes that potentially contribute to microbial adaptation to high pressure. In addition, sediments were incubated with the methionine analog L-homopropargylglycine to determine microbial activity across water-depth and redox zones using bioorthogonal non-canonical amino acid tagging. Initial results show that 78 microcosms contain elevated cell counts and sulfide concentrations, suggesting enrichment of sulfate reducers. Methanogenic microcosm monitoring, DGE analyses, and activity measurements are ongoing.
06:30 PM
CARBON DEGRADATION BY A MESOPELAGIC MICROBIAL COMMUNITY: FOLLOWING PARTICULATE ORGANIC CARBON AND BIOMASS OVER TIME WITH THREE TYPES OF CARBON-14-LABELED ALGAE. (5910)
Primary Presenter: Noah Craft, Old Dominion University (ncraf001@odu.edu)
Knowledge of carbon degradation in the mesopelagic zone is necessary to better understand the marine carbon cycle and specifically processes in the biological pump. Organic particles sink from the surface ocean into the mesopelagic layer, where most of them are microbially degraded. The behavior and speed of this degradation is dependent on both the nature of the sinking substrate and the microbial community itself. In this experiment, particulate organic carbon (POC) from three carbon-14-labeled algae cultures, i.e., Thalassiosira weissflogii, Emiliania huxleyi and Tetraselmis sp., were added to mesopelagic water in triplicate carboys and observed over a period of 87 days in sampling intervals ranging from daily to weekly. Samples were taken for POC, total dissolved carbon (TDC), dissolved organic carbon (DOC), adenosine triphosphate (ATP) and bacterial abundance. Generally, at least two phases of decay were observed: an initial faster rate in the first 10 days which was followed by a period of slower decay for the remainder of the experiment. There was a significant difference in the decay rates among algal species. However, a similar amount of POC, between 7 and 12% of the initial amount, remained undecayed after three months. Our results support the notion that the initial particle composition matters in the rate of decay and determines how far particulate carbon can sink through the water column before it is remineralized.
06:30 PM
A NOVEL GAMMAPROTEOBACTERIAL GROUP POTENTIALLY DOMINATES INORGANIC SULFUR OXIDATION IN THE DEEP OCEAN (6250)
Primary Presenter: José González, University of La Laguna (jmglezh@ull.edu.es)
The dark ocean (>200 m depth) is the largest habitat on Earth. Dissolved inorganic carbon (DIC) fixation in the oxygenated waters of the dark ocean is in the same order of magnitude as heterotrophic microbial biomass production. Recent evidence suggests inorganic sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. In this study we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements. We found that the family classified as UBA868 in the Gammaproteobacteria dominates the total expression of RuBisCO (mainly rcbL type II) genes (average of 34%) and of key sulfur oxidation (soxB and (rdsrA) genes (average of 41% and 71%, respectively) in the global mesopelagic oceanic realm. These organisms were undetectable or at low abundance and activity in surface or bathypelagic layers where other players dominate. Our study also underscores the unrecognized importance of mixotrophic microbes, such as UBA868, in the biogeochemical cycles of the deep ocean.
06:30 PM
A NOVEL PYROLYTIC APPROACH RESOLVING LABILITY OF SEDIMENTARY ORGANIC CARBON – LINKAGE TO MICROBIAL BIOMASS (6452)
Primary Presenter: Marco Sindlev, University of Southern Denmark (marcos@biology.sdu.dk)
Heterotrophic life is fueled by organic material, and Total Organic Carbon (TOC) content has been linked to the distribution of biomass and cell abundance in marine sediments. However, the lability of the available organic material is critical for the respiratory activity and the growth yield of microbial communities. In this study, we present results from a novel pyrolytic approach called Extended Slow Heating (ESH) that provides detailed information on the thermal behavior of different subfractions of organic carbon. The approach is applied to sediments recovered from undisturbed abyssal settings and perturbed complex hadal trench sediments. Using a mathematical model to analyze the pyrolysis data, we show that subfractions of easily degradable organic material better describe the distribution of microbial communities as compared to TOC, which presumably was dominated by resilient organic material. Our results highlight the limitations of using TOC as a predictor for the distribution of microbial life in deep ocean sediments and emphasize the need for more detailed analyses that characterize the nature of the organic material in order to understand the distribution of microbial communities. These findings have important implications for the evaluation of organic matter lability, and the understanding of the processes controlling the preservation and transformation of organic matter in marine sediments.
06:30 PM
Giant viruses from a pelagic deep sea incubation experiment (6543)
Primary Presenter: Theo Krüger, GEOMAR Helmholtz Centre for Ocean Research Kiel (tkrueger@geomar.de)
The deep sea is the largest ecosystem on Earth, but despite its size it is one of the least explored. While benthic systems such as hydrothermal vents, cold seeps, and sediments have received attention, the deep pelagic biome is less understood. Viruses have repeatedly been recognized to play a bigger role in ecosystems than previously assumed, e.g. in their impact on biogeochemical cycles and on community structures by ending bloom events and facilitating nutrient availability through lysis. Giant viruses have been studied intensively in the surface ocean. However, deep sea pelagic systems remain understudied in terms of viruses. Here, we used a unique in-situ incubation system to introduce detrital phytoplankton material to the natural microbial community in the pelagic deep sea, 1040 m below sea level. Over the course of the experiment, taxonomic composition of the resident microbes shifted, in particular by the 4-month time point. Metagenomic sequencing and assembly recovered multiple giant virus genomes. Phylogenetic reconstructions indicate that several of these viruses represent new viruses that are relatively distant within known giant viruses. Similarly, initial analyses indicate presence of auxiliary metabolic genes encoding functions not yet known in giant viruses.
06:30 PM
When life gives you cyanide, make carbon and nitrogen substrates: microbial poisoning and detoxification during organic matter degradation in deep-sea (6656)
Primary Presenter: Yu-Chen Ling, Ocean EcoSystems Biology (lchacol@gmail.com)
Deep-sea ecosystems play a crucial role in global carbon cycles, and microbes there are the primary drivers of biogeochemical cycling. However, our understanding of microbial ecological roles in deep-sea ecosystems remains limited due to the challenges of collecting samples and performing experimental manipulations. In this study, we examined in-situ degradation of detrital diatom cells at 1,040 meters below sea level for 4 months in a submarine canyon, to investigate microbial responses to organic matter from (simulated) descending bloom detritus. Among the 107 high quality prokaryotic metagenomic assembled genomes (MAGs), 39 have higher abundances in terms of coverage at the latest time point. Four Alpha- and one Gamma-proteobacteria Five MAGs encoded hydrogen cyanide synthases, which generates the compound fatal for most of life. Yet, MAGs encoded capabilities for detoxifying this poison via the cyanide hydratase and a rhodanese are found. Rhodanese generates a less toxic metabolic product, thiocyanate, and we found MAGs that then degrade thiocyanate using cyanase and thiocyanate hydrolase. We also observed that genes encoding proteins responsible for arsenic- and mercuric-resistance were widespread across MAGs. MAGs that increased abundance with time contained more of the poisoning and detoxification genes above than those that had decreased abundances during organic matter degradation. Compared to deep-sea hydrothermal vents as research hotspots, much less attention was paid to pelagic deep-sea microbes, and our study revealed that microbes encode diverse metabolisms for managing environmental toxicity.
06:30 PM
Enhanced sediment phosphorus recycling at a deep-sea methane seep (6777)
Primary Presenter: Yuxuan Lin, The Hong Kong University of Science and Technology (yuxuan.lin@connect.ust.hk)
Sediment recycles the key nutrient phosphorus (P) to support marine productivity. In contrast to coastal marine environments where the sediment P recycling is largely controlled by iron (Fe) geochemistry, effluxes of bioavailable P (i.e., soluble reactive phosphorus, SRP) from low-Fe deep-sea sediments are considered decoupled from the Fe cycle and mostly driven by decomposition of organic matter. At methane (CH4)-rich cold seeps in the South China Sea, however, we observed a strong coupling of Fe and P cycling similar to that in Fe and organic-rich coastal sediments. Higher P effluxes were found in high-CH4 seep sediments, where Fe reduction occurred at the surface. Unlike coastal sediments where heterotrophic Fe reduction relies on the availability of reactive organic matter, at the CH4 seeps, Fe reduction is coupled to the anaerobic oxidation of methane (AOM), a process independent of the organic matter supply. Our finding suggests the importance of chemoautotrophy in driving the benthic nutrient cycling and fluxes in the deep-sea cold seeps.
06:30 PM
UNCOVERING THE HIDDEN POTENTIAL OF DEEP SEA MICROBES TO PRODUCE ESSENTIAL POLYUNSATURATED FATTY ACIDS (6832)
Primary Presenter: Raquel Liébana, AZTI (rliebana@azti.es)
Long chain polyunsaturated fatty acids (PUFAs), such as the omega-3 fatty acids eicosapentaeonic (EPA) and docosahexaenoic (DHA), are produced by a seemingly small fraction of marine microorganisms, which supply these essential lipids to the rest of the food web. While microalgae typically use FA desaturases to produce omega-3 PUFAs in the surface ocean, a pathway involving polyketide synthases, encoded by the pfa gene cluster, has been found in unicellular eukaryotes and a few bacterial isolates. However, the contribution of these taxa to the production of PUFAs in the global ocean remains unknown. To determine the global diversity, abundance, and activity of potential marine microbial PUFA producers, we have examined more than 35,000 microbial genomes from the Ocean Microbiomics database and the eukaryotic fraction of Tara Oceans. We detected 240 potential PUFA producers, some of them featuring a novel domain architecture of the pfa gene cluster. Known producers of omega-3 PUFAs (e.g., Shewanella, Colwellia, Vibrio) did not show high abundance or activity in marine metagenomes and metatranscriptomes. By contrast, we uncovered the presence of the pfa gene cluster in ecologically relevant lineages such as SAR324, which presented high cumulative abundance and activity in all ocean layers, especially at depth. Our results broaden the current knowledge on potential PUFA suppliers to the marine trophic web, including the mesopelagic and bathypelagic realm. For these microorganisms, PUFAs may have a key role in their adaptation to cold temperature or high-pressure conditions.
06:30 PM
PARTICLE NUMBERS IN A VOLUME OF WATER ARE ILL DEFINED DUE TO THE PARTICLE-GEL CONTINUUM: CONSEQUENCES FOR DEEP-SEA PARTICLE INVENTORIES (6872)
Primary Presenter: Alexander Bochdansky, Old Dominion University (abochdan@odu.edu)
By any method, it is surprisingly difficult to determine in a volume of water the number of particles in a size range from micrometers to several millimeters. Imaging systems are especially suitable to demonstrate this problem as the particle numbers greatly depend on the sensitivity threshold of the combined optomechanical - image analysis protocols. The ill-defined particle numbers can be largely attributed to gels that are orders of magnitude more abundant than denser particles. Standard optical tools are calibrated to render suitable images of plankton and other dense particles but are ill-equipped to record the abundance of gels that come in a variety of densities depending on factors such as sediment entrapment and microbial colonization. This problem is magnified in the deep sea where amorphous particles far exceed the abundance of live plankton. Here we suggest methods of tying particle numbers to objectively determined optical densities. We also explore techniques that accurately capture a group of enigmatic particles forming a large portion of the total particle volume in the deep ocean.
06:30 PM
MICROBIAL ACTIVITY IN SUBSURFACE SEDIMENTS REFLECTS ADAPTATIONS TO STRESS AND CONTINUED RECYCLING OF BURIED ORGANIC CARBON FROM THE GUAYMAS BASIN WATER COLUMN (7115)
Primary Presenter: Virginia Edgcomb, Woods Hole Oceanographic Institution (vedgcomb@whoi.edu)
International Ocean Discovery Program 385 (IODP 385) drilled 8 sites in Guaymas Basin, Gulf of California, Mexico (Fig. 1). Hydrothermal alteration of buried organic matter produces complex hydrocarbons that together with high temperature, pressure, and variations in nutrient pools present a dynamic and challenging habitat for subsurface microbiota. RNA and DNA recovery declined with depth as did cell counts at all sites. Transcripts support active metabolisms used for energy gain (e.g., methane/acetate cycling, sulfur/nitrogen metabolisms and chemoautotrophy). Expression of genes for genome modifications, DNA maintenance and repair, protein homeostasis and degradation, and tRNA, rRNA and mRNA editing are observed that enable metabolic flexibility and mediate stress-related adaptations of Guaymas microbiota to these deep biosphere conditions. The concerted interaction of many of these genes may be crucial for survival, and in some cases, for activity in the Guaymas Basin subsurface.
SS013P Microbial Life and Elemental Cycling in the Deep Ocean: Progress on Processes and Players
Description
Time: 6:30 PM
Date: 8/6/2023
Room: Mezzanine