High-density element concentrations in fish from subtidal to hadal zones of the Pacific Ocean

Endospores associated with deep seabed geofluid features in the eastern Gulf of Mexico

Recent studies have reported up to 1.9 × 10²⁹ bacterial endospores in the upper kilometre of deep subseafloor marine sediments, however, little is understood about their origin and dispersal. In cold ocean environments, the presence of thermospores (endospores produced by thermophilic bacteria) suggests that distribution is governed by passive migration from warm anoxic sources possibly facilitated by geofluid flow, such as advective hydrocarbon seepage sourced from petroleum deposits deeper in the subsurface. This study assesses this hypothesis by measuring endospore abundance and distribution across 60 sites in Eastern Gulf of Mexico (EGM) sediments using a combination of the endospore biomarker 2,6-pyridine dicarboxylic acid or 'dipicolinic acid' (DPA), sequencing 16S rRNA genes of thermospores germinated in 50°C sediment incubations, petroleum geochemistry in the sediments and acoustic seabed data from sub-bottom profiling. High endospore abundance is associated with geologically active conduit features (mud volcanoes, pockmarks, escarpments and fault systems), consistent with subsurface fluid flow dispersing endospores from deep warm sources up into the cold ocean. Thermospores identified at conduit sites were most closely related to bacteria associated with the deep biosphere habitats including hydrocarbon systems. The high endospore abundance at geological seep features demonstrated here suggests that recalcitrant endospores and their chemical components (such as DPA) can be used in concert with geochemical and geophysical analyses to locate discharging seafloor features. This multiproxy approach can be used to better understand patterns of advective fluid flow in regions with complex geology like the EGM basin.

Ecogenomics reveals viral communities across the Challenger Deep oceanic trench

Despite the environmental challenges and nutrient scarcity, the geographically isolated Challenger Deep in Mariana trench, is considered a dynamic hotspot of microbial activity. Hadal viruses are the least explored microorganisms in Challenger Deep, while their taxonomic and functional diversity and ecological impact on deep-sea biogeochemistry are poorly described. Here, we collect 13 sediment cores from slope and bottom-axis sites across the Challenger Deep (down to ~11 kilometers depth), and identify 1,628 previously undescribed viral operational taxonomic units at species level. Community-wide analyses reveals 1,299 viral genera and distinct viral diversity across the trench, which is significantly higher at the bottom-axis vs. slope sites of the trench. 77% of these viral genera have not been previously identified in soils, deep-sea sediments and other oceanic settings. Key prokaryotes involved in hadal carbon and nitrogen cycling are predicted to be potential hosts infected by these viruses. The detected putative auxiliary metabolic genes suggest that viruses at Challenger Deep could modulate the carbohydrate and sulfur metabolisms of their potential hosts, and stabilize host’s cell membranes under extreme hydrostatic pressures. Our results shed light on hadal viral metabolic capabilities, contribute to understanding deep sea ecology and on functional adaptions of hadal viruses for future research.

Analysis of 13 sediment cores from the Challenger Deep of Marian Trench (down to 11 kilometers depth) identified distinct operational taxonomic units and relevant auxiliary metabolic genes, providing further insight into deep-sea viral metabolic capabilities and ecology.

Microbiomes in the Challenger Deep slope and bottom-axis sediments

Hadal trenches are the deepest and most remote regions of the ocean. The 11-kilometer deep Challenger Deep is the least explored due to the technical challenges of sampling hadal depths. It receives organic matter and heavy metals from the overlying water column that accumulate differently across its V-shaped topography. Here, we collected sediments across the slope and bottom-axis of the Challenger Deep that enable insights into its in situ microbial communities. Analyses of 586 metagenome-assembled genomes retrieved from 37 metagenomes show distinct diversity and metabolic capacities between bottom-axis and slope sites. 26% of prokaryotic 16S rDNA reads in metagenomes were novel, with novelty increasing with water and sediment depths. These predominantly heterotrophic microbes can recycle macromolecules and utilize simple and complex hydrocarbons as carbon sources. Metagenome and metatranscriptome data support reduction and biotransformation of arsenate for energy gain in sediments that present a two-fold greater accumulation of arsenic compared to non-hadal sites. Complete pathways for anaerobic ammonia oxidation are predominantly identified in genomes recovered from bottom-axis sediments compared to slope sites. Our results expand knowledge of microbially-mediated elemental cycling in hadal sediments, and reveal differences in distribution of processes involved in nitrogen loss across the trench.

The V-shaped Challenger Deep in the Mariana Trench is the deepest part of the world’s oceans. Using 586 prokaryotic metagenome-assembled genomes and metatranscriptomic data, this study explores metabolic capabilities and activities of microorganisms involved in elemental cycling in hadal sediments, and reveals the different distribution of processes between its bottom-axis and slope.

Evidence for Long-Term Anthropogenic Pollution: The Hadal Trench as a Depository and Indicator for Dissemination of Antibiotic Resistance Genes

Knowledge of the distribution and dissemination of antibiotic resistance genes (ARGs) is essential for understanding anthropogenic impacts on natural ecosystems. The transportation of ARGs via aquatic environments is significant and has received great attention, but whether there has been anthropogenic ARG pollution to the hadal ocean ecosystem has not been well explored. For investigating ecological health concerns, we profiled the ARG occurrence in sediments of the Mariana Trench (MT) (10 890 m), the deepest region of the ocean. Metagenomic-based ARG profiles showed a sudden increase of abundance and diversity in the surface layer of MT sediments reaching 2.73 × 10^-2 copy/cell and 81 subtypes, and a high percentage of ∼63.6% anthropogenic pollution sources was predicted by the Bayesian-modeling classification method. These together suggested that ARG accumulation and anthropogenic impacts have already permeated into the bottom of the deepest corner on the earth. Moreover, six ARG-carrying draft genomes were retrieved using a metagenomic binning strategy, one of which assigned as Streptococcus was identified as a potential bacterial host to contribute to the ARG accumulation in MT, carrying ermF, tetM, tetQ, cfxA2, PBP-2X, and PBP-1A. We propose that the MT ecosystem needs further long-term monitoring for the assessment of human impacts, and our identified three biomarkers (cfxA2, ermF, and mefA) could be used for the rapid monitoring of anthropogenic pollution. Together our findings imply that anthropogenic pollution has penetrated into the deepest region of the ocean and urge for better pollution control to reduce the risk of ARG dissemination to prevent the consistent accumulation and potential threat to the natural environment.

Geology, environment, and life in the deepest part of the world's oceans

The hadal zone, mostly comprising of deep trenches and constituting of the deepest part of the world’s oceans, represents the least explored habitat but one of the last frontiers on our planet. The present scientific understanding of the hadal environment is still relatively rudimentary, particularly in comparison with that of shallower marine environments. In the last 30 years, continuous efforts have been launched in deepening our knowledge regarding the ecology of the hadal trench. However, the geological and environmental processes that potentially affect the sedimentary, geochemical and biological processes in hadal trenches have received less attention. Here, we review recent advances in the geology, biology, and environment of hadal trenches and offer a perspective of the hadal science involved therein. For the first time, we release high-definition images taken by a new full-ocean-depth manned submersible Fendouzhe that reveal novel species with an unexpectedly high density, outcrops of mantle and basaltic rocks, and anthropogenic pollutants at the deepest point of the world’s ocean. We advocate that the hydration of the hadal lithosphere is a driving force that influences a variety of sedimentary, geochemical, and biological processes in the hadal trench. Hadal lithosphere might host the Earth’s deepest subsurface microbial ecosystem. Future research, combined with technological advances and international cooperation, should focus on establishing the intrinsic linkage of the geology, biology, and environment of the hadal trenches.

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This paper provides a comprehensive review on hadal geology, environment, and biology, as well as potential interactions among them

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For the first time, we release high-definition images taken by a new full-ocean-depth manned submersible Fendouzhe

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The hydration of the hadal lithosphere is a driving force that influences a variety of sedimentary, geochemical, and biological processes in the hadal trench

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The development of deep-sea technology and international cooperation will greatly promote the progress of hadal science

Occurrence of Halogenated Organic Pollutants in Hadal Trenches of the Western Pacific Ocean

The hadal trenches are the most remote and inaccessible habitats on earth and were once believed to be pristine. A recent study has reported the detection of high levels of persistent organic pollutants (POPs), including polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs), in endemic amphipods from two hadal trenches (Mariana and Kermadec) in the Western Pacific, implicating that the trenches are indeed polluted. However, a fundamental question remains unanswered, if and to what extent such the physical environment of the trenches is polluted by POPs. In this study, we sampled Mariana, Mussau, and New Britain trenches and analyzed samples of amphipods, sediment, and suspended particulate matter (SPM). Our results show that the amphipods contained elevated levels of PCBs and PBDEs, comparable to those reported in the earlier study. We also detected significantly high concentrations (up to 1343 ng g^-1 lw) of chlorinated pesticides, such as dichlorodiphenyltrichloroethanes and chlordanes. Furthermore, four brominated natural products (BNPs), which structurally resembled methoxylated brominated diphenyl ethers or polybrominated biphenyls, were identified in the endemic amphipods. However, neither POPs nor BNPs were detected in sediments or SPM. Taken together, we propose that the POPs detected in endemic amphipods likely resulted from bioaccumulation by feeding on polluted large detritus (e.g., carrion) falling to the trench bottoms from the surface ocean.

Mercury isotopes identify near-surface marine mercury in deep-sea trench biota

Mercury is a globally distributed neurotoxic pollutant that can be biomagnified in marine fish to levels that are harmful for consumption by humans and other animals. The degree to which mercury has infiltrated the oceans yields important information on the biogeochemistry of mercury and its expected effects on fisheries during changing mercury emissions scenarios. Mercury isotope measurement of biota from deep-sea trenches was used to demonstrate that surface-ocean-derived mercury has infiltrated the deepest locations in the oceans. It was found that when fish living in the surface ocean die and their carcasses sink (along with marine particles), they transfer large amounts of mercury to the trench foodwebs leading to high concentrations of mercury in trench biota.

Mercury isotopic compositions of amphipods and snailfish from deep-sea trenches reveal information on the sources and transformations of mercury in the deep oceans. Evidence for methyl-mercury subjected to photochemical degradation in the photic zone is provided by odd-mass independent isotope values (Δ¹⁹⁹Hg) in amphipods from the Kermadec Trench, which average 1.57‰ (±0.14, n = 12, SD), and amphipods from the Mariana Trench, which average 1.49‰ (±0.28, n = 13). These values are close to the average value of 1.48‰ (±0.34, n = 10) for methyl-mercury in fish that feed at ∼500-m depth in the central Pacific Ocean. Evidence for variable contributions of mercury from rainfall is provided by even-mass independent isotope values (Δ²⁰⁰Hg) in amphipods that average 0.03‰ (±0.02, n = 12) for the Kermadec and 0.07‰ (±0.01, n = 13) for the Mariana Trench compared to the rainfall average of 0.13 (±0.05, n = 8) in the central Pacific. Mass-dependent isotope values (δ²⁰²Hg) are elevated in amphipods from the Kermadec Trench (0.91 ±0.22‰, n = 12) compared to the Mariana Trench (0.26 ±0.23‰, n = 13), suggesting a higher level of microbial demethylation of the methyl-mercury pool before incorporation into the base of the foodweb. Our study suggests that mercury in the marine foodweb at ∼500 m, which is predominantly anthropogenic, is transported to deep-sea trenches primarily in carrion, and then incorporated into hadal (6,000-11,000-m) food webs. Anthropogenic Hg added to the surface ocean is, therefore, expected to be rapidly transported to the deepest reaches of the oceans.

Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses

Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.

Atmospheric Deposition of Coal-Related Pollutants in the Pacific Northwest of the United States from 1950 to 2016

Coal-related elements are toxic and persistent pollutants that have spread globally since the industrial revolution, mainly from point-source emissions. A sediment core was collected from Deep Lake in northeastern Washington State (USA) by the Washington State Department of Ecology, with the aim of assessing recent changes in atmospheric deposition in the US Pacific Northwest. The core was divided into depth intervals and dated by lead-210. A sample from each cross section was digested and analyzed for toxic metals and metalloids using inductively coupled plasma-mass spectrometry. Data show recent increases in the concentrations of arsenic, barium, selenium, and mercury. Comparison with 1993 US Geological Survey ice core data from the Upper Fremont Glacier in Wyoming (USA), Asian coal consumption data, and weather patterns suggests that pollutant inputs to Deep Lake sediments are the result of coal-burning activities in the Asia-Pacific region. Most notably, mercury deposition in Deep Lake has increased from approximately 20 ppb in 1996 to 9470 ppb in 2014 (an ~400-fold increase), and since 1993 when the ice core was analyzed. Environ Toxicol Chem 2020;39:335-342. © 2019 SETAC.

Assessment of metal concentrations in oysters and shrimp from Atlantic Coast of the Democratic Republic of the Congo

Oysters and shrimp are abundant and commonly consumed seafood by the indigenous population of the Kongo central region of the Democratic Republic of the Congo (DRC). Literature reviews suggest that no data were available for the metal concentrations in these species. Consequently, the purpose of this study is to determine the metal concentrations in tissues of oysters (Egeria congica) and shrimp (Macrobrachium spp., Parapenaeus spp., Penaeus spp.) collected in November 2017 from the Atlantic Ocean Coast of DRC in the territory of Muanda. Metal levels in the seafood species studied here were put into context using international regulation for human consumption set by the Food and Agriculture Organization (FAO), Canadian Food Inspection Agency (CFIA), European Union (EU), and World Health Organization (WHO). Our results demonstrated that the concentration of heavy metals varied considerably between sampling sites and analyzed species (P < 0.05), with the values (in mg kg1) ranged between 0.05-0.41, 0.03-2.25, Collapse

Key Words

• Atlantic Ocean
• Bioaccumulation
• Congo DR
• Environmental pollution
• Environmental risk assessment
• Environmental science
• Heavy metal
• Oysters
• Shrimp
• Water pollution
• Water quality

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Affiliation(s)

Robert B. Suami University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo University of Kinshasa (UNIKIN), Faculty of Pharmaceutical Sciences, B.P. 212, Kinshasa XI, Democratic Republic of the Congo
Dhafer Mohammed M. Al Salah Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, Geneva 4, CH-1211, Switzerland King Abdulaziz City for Science and Technology, Joint Centers of Excellence Program, Prince Turki the 1st Street, Riyadh, 11442, Saudi Arabia
César D. Kabala University of Kinshasa (UNIKIN), Faculty of Pharmaceutical Sciences, B.P. 212, Kinshasa XI, Democratic Republic of the Congo
J.-P. Otamonga Université Pédagogique Nationale (UPN). Croisement Route de Matadi et Avenue de la Libération. Quartier Binza/UPN, B.P. 8815, Kinshasa, République Démocratique du Congo
Crispin K. Mulaji University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo
Pius T. Mpiana University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo
John W. Poté University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, Geneva 4, CH-1211, Switzerland Université Pédagogique Nationale (UPN). Croisement Route de Matadi et Avenue de la Libération. Quartier Binza/UPN, B.P. 8815, Kinshasa, République Démocratique du Congo

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