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Zhou X, Lennon JT, Lu X, Ruan A. Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments. MICROBIOME 2023; 11:191. [PMID: 37626433 PMCID: PMC10464086 DOI: 10.1186/s40168-023-01612-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/04/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Freshwater sediment microbes are crucial decomposers that play a key role in regulating biogeochemical cycles and greenhouse gas emissions. They often exhibit a highly ordered structure along depth profiles. This stratification not only reflects redox effects but also provides valuable insights into historical transitions, as sediments serve as important archives for tracing environmental history. The Anthropocene, a candidate geological epoch, has recently garnered significant attention. However, the human impact on sediment zonation under the cover of natural redox niches remains poorly understood. Dam construction stands as one of the most far-reaching anthropogenic modifications of aquatic ecosystems. Here we attempted to identify the ecological imprint of damming on freshwater sediment microbiome. RESULTS We conducted a year-round survey on the sediment profiles of Lake Chaohu, a large shallow lake in China. Through depth-discrete shotgun metagenomics, metataxonomics, and geophysiochemical analyses, we unveiled a unique prokaryotic hierarchy shaped by the interplay of redox regime and historical damming (labeled by the 137Cs peak in AD 1963). Dam-induced initial differentiation was further amplified by nitrogen and methane metabolism, forming an abrupt transition governing nitrate-methane metabolic interaction and gaseous methane sequestration depth. Using a random forest algorithm, we identified damming-sensitive taxa that possess distinctive metabolic strategies, including energy-saving mechanisms, unique motility behavior, and deep-environment preferences. Moreover, null model analysis showed that damming altered microbial community assembly, from a selection-oriented deterministic process above to a more stochastic, dispersal-limited one below. Temporal investigation unveiled the rapid transition zone as an ecotone, characterized by high species richness, low community stability, and emergent stochasticity. Path analysis revealed the observed emergent stochasticity primarily came from the high metabolic flexibility, which potentially contributed to both ecological and statistical neutralities. CONCLUSIONS We delineate a picture in which dam-induced modifications in nutrient availability and sedimentation rates impact microbial metabolic activities and generate great changes in the community structure, assembly, and stability of the freshwater sediment microbiome. These findings reflect profound ecological and biogeochemical ramifications of human-Earth system interactions and help re-examine the mainstream views on the formation of sediment microbial stratification. Video Abstract.
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Affiliation(s)
- Xiaotian Zhou
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210024, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Xiang Lu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210024, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210024, China.
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China.
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2
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Liu H, Cai X, Luo K, Chen S, Su M, Lu J. Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology. Microbiol Spectr 2023; 11:e0421022. [PMID: 36802161 PMCID: PMC10100816 DOI: 10.1128/spectrum.04210-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xueyu Cai
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Kunwen Luo
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Sihan Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou Guangdong, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou Guangdong, China
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China
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3
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Xiang X, Wang H, Man B, Xu Y, Gong L, Tian W, Yang H. Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China. MICROBIAL ECOLOGY 2023; 85:557-571. [PMID: 35332366 DOI: 10.1007/s00248-022-01990-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.
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Affiliation(s)
- Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Linfeng Gong
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
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4
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Deng L, Meile C, Fiskal A, Bölsterli D, Han X, Gajendra N, Dubois N, Bernasconi SM, Lever MA. Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing. PNAS NEXUS 2022; 1:pgac146. [PMID: 36714871 PMCID: PMC9802194 DOI: 10.1093/pnasnexus/pgac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/25/2022] [Indexed: 06/18/2023]
Abstract
Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer.
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Affiliation(s)
| | - Christof Meile
- Department of Marine Sciences, University of Georgia, 325 Sanford Drive, Athens, GA 30602, USA
| | | | - Damian Bölsterli
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Niroshan Gajendra
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Nathalie Dubois
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Stefano M Bernasconi
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
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5
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Stressors Increase the Impacts of Coastal Macrofauna Biodiversity Loss on Ecosystem Multifunctionality. Ecosystems 2022. [DOI: 10.1007/s10021-022-00775-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThere is substantial evidence that biodiversity underpins ecosystem functioning, but it is unclear how these relationships change with multiple stressors in complex real-world settings. Coastal zones are affected by numerous stressors (for example, sediment input and nutrient runoff from land) and the cumulative effects of these stressors may result in pronounced and unexpected changes in the functioning of ecosystems. To investigate the cumulative effects of turbidity and elevated nutrients on coastal biodiversity-ecosystem functioning relationships, we performed a large-scale field experiment manipulating in situ sediment porewater ammonium concentrations and measured multiple ecosystem functions related to carbon fixation and mineralisation in 15 estuaries with varying levels of turbidity. The results indicated that the benthic macrofauna diversity (species richness, abundance, and functional richness) declined with increased porewater ammonium concentrations and there were clear thresholds in light levels at the seafloor in relation to the biodiversity-ecosystem function relationships. Multifunctionality indices (an integrated index of all measured functions) in moderately turbid and turbid estuaries (daily mean seafloor PAR < 420 µmol m−2 s−1) decreased with the loss of macrofauna biodiversity. Functioning in low-turbidity estuaries (daily mean PAR > 420 µmol m−2 s−1) however remained relatively constant, suggesting that they were more resilient against the nutrient-induced biodiversity loss. Our results demonstrate that ecosystems already stressed by stressors that alter functional performance (turbidity) may be more prone to loss of overall functioning if biodiversity is reduced by another stressor (nutrient enrichment), highlighting the potential snowballing effects of cumulative change.
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6
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Møller TE, Le Moine Bauer S, Hannisdal B, Zhao R, Baumberger T, Roerdink DL, Dupuis A, Thorseth IH, Pedersen RB, Jørgensen SL. Mapping Microbial Abundance and Prevalence to Changing Oxygen Concentration in Deep-Sea Sediments Using Machine Learning and Differential Abundance. Front Microbiol 2022; 13:804575. [PMID: 35663876 PMCID: PMC9158483 DOI: 10.3389/fmicb.2022.804575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/09/2022] [Indexed: 12/28/2022] Open
Abstract
Oxygen constitutes one of the strongest factors explaining microbial taxonomic variability in deep-sea sediments. However, deep-sea microbiome studies often lack the spatial resolution to study the oxygen gradient and transition zone beyond the oxic-anoxic dichotomy, thus leaving important questions regarding the microbial response to changing conditions unanswered. Here, we use machine learning and differential abundance analysis on 184 samples from 11 sediment cores retrieved along the Arctic Mid-Ocean Ridge to study how changing oxygen concentrations (1) are predicted by the relative abundance of higher taxa and (2) influence the distribution of individual Operational Taxonomic Units. We find that some of the most abundant classes of microorganisms can be used to classify samples according to oxygen concentration. At the level of Operational Taxonomic Units, however, representatives of common classes are not differentially abundant from high-oxic to low-oxic conditions. This weakened response to changing oxygen concentration suggests that the abundance and prevalence of highly abundant OTUs may be better explained by other variables than oxygen. Our results suggest that a relatively homogeneous microbiome is recruited to the benthos, and that the microbiome then becomes more heterogeneous as oxygen drops below 25 μM. Our analytical approach takes into account the oft-ignored compositional nature of relative abundance data, and provides a framework for extracting biologically meaningful associations from datasets spanning multiple sedimentary cores.
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Affiliation(s)
- Tor Einar Møller
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Rui Zhao
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamara Baumberger
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State University, Newport, OR, United States
| | - Desiree L Roerdink
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | | | - Ingunn H Thorseth
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Rolf Birger Pedersen
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Steffen Leth Jørgensen
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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7
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Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment. Commun Biol 2021; 4:1006. [PMID: 34433861 PMCID: PMC8387401 DOI: 10.1038/s42003-021-02507-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below. Lagostina et al. show that relative abundances of Bacteria and Archaea in sediments of Guaymas Basin, Gulf of California, are controlled by temperature, while energy flux explains microbial community structure at the phylum-level and below. Hot diffusion-dominated and energy-depleted sediments are dominated by taxa with relatives in cold subseafloor sediments, while hot sediments with high energy supply from fluid seepage are dominated by taxa also found at hydrothermal vents and in hot springs.
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8
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Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM. Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments. Front Microbiol 2021; 12:631621. [PMID: 33679659 PMCID: PMC7935538 DOI: 10.3389/fmicb.2021.631621] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/05/2022] Open
Abstract
Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.
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Affiliation(s)
- Anna J. Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Caroline P. Slomp
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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9
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Abstract
Marine sediment covers 70% of Earth’s surface and harbors as much biomass as seawater. However, the global taxonomic diversity of marine sedimentary communities, and the spatial distribution of that diversity remain unclear. We investigated microbial composition from 40 globally distributed sampling locations, spanning sediment depths of 0.1 to 678 m. Statistical analysis reveals that oxygen presence or absence and organic carbon concentration are key environmental factors for defining taxonomic composition and diversity of marine sedimentary communities. Global marine sedimentary taxonomic richness predicted by species–area relationship models is 7.85 × 103 to 6.10 × 105 for Archaea and 3.28 × 104 to 2.46 × 106 for Bacteria as amplicon sequence variants, which is comparable to the richness in seawater and that in topsoil. Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ∼47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 103 to 6.10 × 105 and 3.28 × 104 to 2.46 × 106 amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.
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10
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Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLoS One 2020; 15:e0234839. [PMID: 32853201 PMCID: PMC7451513 DOI: 10.1371/journal.pone.0234839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
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Affiliation(s)
- Joy Buongiorno
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Karen G. Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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11
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Super Resolution by Deep Learning Improves Boulder Detection in Side Scan Sonar Backscatter Mosaics. REMOTE SENSING 2020. [DOI: 10.3390/rs12142284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In marine habitat mapping, a demand exists for high-resolution maps of the seafloor both for marine spatial planning and research. One topic of interest is the detection of boulders in side scan sonar backscatter mosaics of continental shelf seas. Boulders are oftentimes numerous, but encompass few pixels in backscatter mosaics. Therefore, both their automatic and manual detection is difficult. In this study, located in the German Baltic Sea, the use of super resolution by deep learning to improve the manual and automatic detection of boulders in backscatter mosaics is explored. It is found that upscaling of mosaics by a factor of 2 to 0.25 m or 0.125 m resolution increases the performance of small boulder detection and boulder density grids. Upscaling mosaics with 1.0 m pixel resolution by a factor of 4 improved performance, but the results are not sufficient for practical application. It is suggested that mosaics of 0.5 m resolution can be used to create boulder density grids in the Baltic Sea in line with current standards following upscaling.
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12
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Macrofaunal control of microbial community structure in continental margin sediments. Proc Natl Acad Sci U S A 2020; 117:15911-15922. [PMID: 32576690 PMCID: PMC7376573 DOI: 10.1073/pnas.1917494117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O2 introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.
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13
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Han X, Schubert CJ, Fiskal A, Dubois N, Lever MA. Eutrophication as a driver of microbial community structure in lake sediments. Environ Microbiol 2020; 22:3446-3462. [PMID: 32510812 DOI: 10.1111/1462-2920.15115] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 11/27/2022]
Abstract
Lake sediments are globally important carbon sinks. Although the fate of organic carbon in lake sediments depends significantly on microorganisms, only few studies have investigated controls on lake sedimentary microbial communities. Here we investigate the impact of anthropogenic eutrophication, which affects redox chemistry and organic matter (OM) sources in sediments, on microbial communities across five lakes in central Switzerland. Lipid biomarkers and distributions of microbial respiration reactions indicate strong increases in aquatic OM contributions and microbial activity with increasing trophic state. Across all lakes, 16S rRNA genes analyses indicate similar depth-dependent zonations at the phylum- and class-level that follow vertical distributions of OM sources and respiration reactions. Yet, there are notable differences, such as higher abundances of nitrifying Bacteria and Archaea in an oligotrophic lake. Furthermore, analyses at the order-level and below suggest that changes in OM sources due to eutrophication cause permanent changes in bacterial community structure. By contrast, archaeal communities are differentiated according to trophic state in recently deposited layers, but converge in older sediments deposited under different trophic regimes. Our study indicates an important role for trophic state in driving lacustrine sediment microbial communities and reveals fundamental differences in the temporal responses of sediment Bacteria and Archaea to eutrophication.
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Affiliation(s)
- Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, Zurich, 8092, Switzerland
| | - Carsten Johnny Schubert
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, Kastanienbaum, 6047, Switzerland
| | - Annika Fiskal
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, Zurich, 8092, Switzerland
| | - Nathalie Dubois
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, Zurich, 8092, Switzerland.,Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, Dübendorf, 8600, Switzerland
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, Zurich, 8092, Switzerland
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14
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Mhatre SS, Kaufmann S, Marshall IPG, Obrochta S, Andrèn T, Jørgensen BB, Lomstein BA. Microbial biomass turnover times and clues to cellular protein repair in energy-limited deep Baltic Sea sediments. FEMS Microbiol Ecol 2020; 95:5490327. [PMID: 31095297 DOI: 10.1093/femsec/fiz068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/14/2019] [Indexed: 11/14/2022] Open
Abstract
The discovery of active microbial life deeply buried beneath the seafloor has opened important questions: how do microorganisms cope with extreme energy limitation, what is their metabolic activity, and how do they repair damages to essential biomolecules? We used a D:L-amino acid model to calculate microbial biomass turnover times. We used a metagenome and metatranscriptome analysis to investigate the distribution of the gene that encodes Protein-L-iso aspartate(D-aspartate) O-methyltransferase (PCMT), an enzyme which recognizes damaged L-isoapartyl and D-aspartyl residues in proteins and catalyzes their repair. Sediment was retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347 from Landsort Deep and the Little Belt in the Baltic Sea. The study covers the period from the Baltic Ice Lake ca. 13 000 years ago to the present. Our results provide new knowledge on microbial biomass turnover times and protein repair in relation to different regimes of organic matter input. For the first time, we show that the PCMT gene was widely distributed and expressed among phylogenetically diverse groups of microorganisms. Our findings suggest that microbial communities are capable of repairing D-amino acids within proteins using energy obtained from the degradation of a mixture of labile compounds in microbial necromass and more recalcitrant organic matter.
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Affiliation(s)
- Snehit S Mhatre
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.,NordCEE, Department of Biology, University of Southern Denmark, Compusvej 55, 5230 Odense M, Denmark
| | - Stefan Kaufmann
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Stephen Obrochta
- Graduate School of International Resource Sciences, Department of Earth Resource Science, Akita University, 1-1 Tegatagakuen-machi, Akita City 010-8502, Japan
| | - Thomas Andrèn
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels all 7, Flemingsberg, 14189 Huddinge, Sweden
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Bente Aa Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.,Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
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15
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Sandfeld T, Marzocchi U, Petro C, Schramm A, Risgaard-Petersen N. Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments. THE ISME JOURNAL 2020; 14:1233-1246. [PMID: 32042102 PMCID: PMC7174387 DOI: 10.1038/s41396-020-0607-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/08/2022]
Abstract
Cable bacteria are filamentous members of the Desulfobulbaceae family that oxidize sulfide with oxygen or nitrate by transferring electrons over centimeter distances in sediments. Recent studies show that freshwater sediments can support populations of cable bacteria at densities comparable to those found in marine environments. This is surprising since sulfide availability is presumably low in freshwater sediments due to sulfate limitation of sulfate reduction. Here we show that cable bacteria stimulate sulfate reduction in freshwater sediment through promotion of sulfate availability. Comparing experimental freshwater sediments with and without active cable bacteria, we observed a three- to tenfold increase in sulfate concentrations and a 4.5-fold increase in sulfate reduction rates when cable bacteria were present, while abundance and community composition of sulfate-reducing microorganisms (SRM) were unaffected. Correlation and ANCOVA analysis supported the hypothesis that the stimulation of sulfate reduction activity was due to relieve of the kinetic limitations of the SRM community through the elevated sulfate concentrations in sediments with cable bacteria activity. The elevated sulfate concentration was caused by cable bacteria-driven sulfide oxidation, by sulfate production from an indigenous sulfide pool, likely through cable bacteria-mediated dissolution and oxidation of iron sulfides, and by enhanced retention of sulfate, triggered by an electric field generated by the cable bacteria. Cable bacteria in freshwater sediments may thus be an integral component of a cryptic sulfur cycle and provide a mechanism for recycling of the scarce resource sulfate, stimulating sulfate reduction. It is possible that this stimulation has implication for methanogenesis and greenhouse gas emissions.
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Affiliation(s)
- Tobias Sandfeld
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Ugo Marzocchi
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Department of Chemistry, Vrije Universiteit Brussel, Brussel, Belgium
| | - Caitlin Petro
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Nils Risgaard-Petersen
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark.
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark.
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark.
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16
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Okuku EO, Kiteresi LI, Wanjeri VO, Owato GO. Baseline survey of sediment contamination with 210Polonium in three peri-urban creeks of Mombasa, Kenya. MARINE POLLUTION BULLETIN 2020; 154:111040. [PMID: 32319890 DOI: 10.1016/j.marpolbul.2020.111040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
210Po in marine sediment from three peri-urban creeks in Mombasa was analyzed by alpha spectrometry in order to determine its baseline contamination levels. The mean 210Po activity in marine sediment from Mtwapa, Tudor and Makupa creeks were 18.67 ± 1.8, 21.17 ± 2.2 and 13.09 ± 1.6 Bq Kg-1 dw, for surface sediment and 37.56 ± 2.14, 28.64 ± 2.86 and 30.42 ± 2.1 Bq Kg-1 dw respectively, for sediment cores. Comparison of 210Po activity in surface sediment indicated that 210Po in the creeks could be originating from the same source. However, comparison of activities in the entire cores from the three creeks indicated that 210Po sources could have been different in the past. 210Po activities in this study were relatively elevated compared to marine environments under similar anthropogenic influence and there is need to understand its source and fate.
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Affiliation(s)
- Eric Ochieng Okuku
- Kenya Marine and Fisheries Research Institute, P.O. Box 81651, Mombasa, Kenya.
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17
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Zou D, Pan J, Liu Z, Zhang C, Liu H, Li M. The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient. Front Microbiol 2020; 11:285. [PMID: 32174899 PMCID: PMC7056671 DOI: 10.3389/fmicb.2020.00285] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/07/2020] [Indexed: 01/05/2023] Open
Abstract
Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Metabolic pathways of the Bathyarchaeota members are diverse and, hence, this phylum has been proposed to play an important role in global biogeochemical cycles. Bathyarchaeota members are distributed in the estuarine environments. However, limited information is available about their detailed community structure, abundance, and functions in the Pearl River estuary (PRE). In the current study, we performed a comprehensive investigation of the archaeal community in the PRE surface sediments along a salinity gradient, with a focus on Bathyarchaeota. Bathyarchaeota was the dominant archaeal phylum, with the abundance of the bathyarchaeotal 16S rRNA gene ranging from 1.43 × 108 to 1.22 × 109 copies/g sediment dry weight (d.w.), and Bathy-8 was the dominant subgroup. Thaumarchaeota, Lokiarchaeota, and Euryarchaeota, including Thermoprofundales (MBG-D archaea), were the other major archaeal groups in the PRE. The differences of community distributions in the high- and low-salinity sediments were hence investigated. Statistical analysis revealed that besides salinity, ammonium, and total organic carbon were the most important environmental factors influencing the archaea community structure, including that of Bathyarchaeota, in the PRE. The archaeal network indicated the cooccurrence among Bathyarchaeota, Lokiarchaeota, and Euryarchaeota, while Bathy-6 presented unique correlations compared with other bathyarchaeotal subgroups. These observations indicate that Bathyarchaeota may play a role in ecosystem function through microbe-microbe interactions, revealing a possible different lifestyle for Bathy-6 in eutrophic estuarine sediments.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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18
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Jørgensen BB, Andrén T, Marshall IPG. Sub-seafloor biogeochemical processes and microbial life in the Baltic Sea. Environ Microbiol 2020; 22:1688-1706. [PMID: 31970880 DOI: 10.1111/1462-2920.14920] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
Abstract
The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins.
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Affiliation(s)
- Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Thomas Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Ian P G Marshall
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Center for Electromicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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19
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Targeting Remediation Dredging by Ecological Risk Assessment of Heavy Metals in Lake Sediment: A Case Study of Shitang Lake, China. SUSTAINABILITY 2019. [DOI: 10.3390/su11247251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding the spatial distribution and pollution characteristics of heavy metals in lake sediment is crucial for studying deposition and migration processes, assessing lake conditions, and determining the extent of remediation dredging. The present work is a case study of heavy metal pollution in Shitang Lake in Anhui province, China. Heavy metal concentrations were determined in sediment at locations across the lake to a depth of 100 cm, and pollution levels were assessed on the basis of the Geoaccumulation Index (Igeo) and Potential Ecological Risk Index (RI). Hg and Cd were the predominant heavy metals in the sediment, and the Igeo and RI indicated high pollution levels in the northern and southern zones of the lake. These findings can be used to guide the prioritization of dredging operations.
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20
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Overholt WA, Schwing P, Raz KM, Hastings D, Hollander DJ, Kostka JE. The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills. Environ Microbiol 2019; 21:4316-4329. [PMID: 31469487 DOI: 10.1111/1462-2920.14794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/20/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.
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Affiliation(s)
- Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patrick Schwing
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Kala M Raz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David Hastings
- Department of Marine Science, Eckerd College, St. Petersburg, FL, USA
| | - David J Hollander
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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21
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Klasek SA, Torres ME, Loher M, Bohrmann G, Pape T, Colwell FS. Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion. Front Microbiol 2019; 10:1436. [PMID: 31281306 PMCID: PMC6596357 DOI: 10.3389/fmicb.2019.01436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li+ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K+ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats.
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Affiliation(s)
- Scott A Klasek
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Marta E Torres
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Markus Loher
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Frederick S Colwell
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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22
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Cupit C, Lomstein BA, Kjeldsen KU. Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:352-360. [PMID: 30043505 DOI: 10.1111/1758-2229.12679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.
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Affiliation(s)
- Carina Cupit
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bente Aagaard Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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23
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019; 10:849. [PMID: 31105660 PMCID: PMC6492693 DOI: 10.3389/fmicb.2019.00849] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.
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Affiliation(s)
- Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
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25
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Petro C, Zäncker B, Starnawski P, Jochum LM, Ferdelman TG, Jørgensen BB, Røy H, Kjeldsen KU, Schramm A. Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay. Front Microbiol 2019; 10:758. [PMID: 31031732 PMCID: PMC6474314 DOI: 10.3389/fmicb.2019.00758] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/26/2019] [Indexed: 11/30/2022] Open
Abstract
Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0–6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.
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Affiliation(s)
- Caitlin Petro
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Birthe Zäncker
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Piotr Starnawski
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lara M Jochum
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Timothy G Ferdelman
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Deng L, Fiskal A, Han X, Dubois N, Bernasconi SM, Lever MA. Improving the Accuracy of Flow Cytometric Quantification of Microbial Populations in Sediments: Importance of Cell Staining Procedures. Front Microbiol 2019; 10:720. [PMID: 31024498 PMCID: PMC6465615 DOI: 10.3389/fmicb.2019.00720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/21/2019] [Indexed: 12/12/2022] Open
Abstract
The accuracy of flow cytometric (FCM) quantifications of microbial populations in sediments varies with FCM settings, cell extraction and staining protocols, as well as sample types. In the present study, we improve the accuracy of FCM for enumerating microorganisms inhabiting diverse lake and marine sediment types based on extensive tests with FCM settings, extraction buffer chemical compositions, cell separation methods, and staining procedures. Tests on the FCM settings, (e.g., acquisition time, rates of events) and salinity of extraction solutions show minor impacts on FCM enumerations and yields of cell extraction, respectively. Existing methods involving hydrofluoric acid (HF) treatment to release sediment-attached cells into solution prove effective on both marine and freshwater samples. Yet, different staining techniques (direct staining of cell extracts, staining of membrane-filtered cell extracts) produce clear differences in cell number estimates. We demonstrate that, while labor-intensive membrane-staining generates high cell staining efficiency and accurate cell counts that are consistent across FCM and epifluorescence microscopy-based (EFM) quantification methods, accurate cell counts determined by more time- and labor-efficient direct staining require consideration of dye concentration, sample dilution, and lithology. Yet, good agreement between the two staining methods can be achieved through sample-specific adjustments of dye concentrations and sample dilutions during direct staining. We thus present a complete protocol for FCM-based cell quantification, that includes all steps from the initial sample fixation to the final enumeration, with recommendations for buffer compositions, direct and membrane-based staining procedures, and the final FCM assay. This protocol is versatile, accurate, and reliable, as is evident from good agreement with cell quantifications by EFM and quantitative polymerase chain reaction (qPCR) of 16S rRNA genes across a wide range of sedimentary sample types.
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Affiliation(s)
- Longhui Deng
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Annika Fiskal
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Nathalie Dubois
- Surface Waters Research-Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Department of Earth Sciences, ETH Zürich, Zurich, Switzerland
| | | | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
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Chen X, Ottosen LDM, Kofoed MVW. How Low Can You Go: Methane Production of Methanobacterium congolense at Low CO 2 Concentrations. Front Bioeng Biotechnol 2019; 7:34. [PMID: 30899758 PMCID: PMC6416169 DOI: 10.3389/fbioe.2019.00034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/05/2019] [Indexed: 01/21/2023] Open
Abstract
Autotrophic hydrogenotrophic methanogens use H2/CO2 as sole carbon and energy source. In contrast to H2, CO2 is present in high concentrations in environments dominated by methanogens e.g., anaerobic digesters (AD), and is therefore rarely considered to be a limiting factor. Nonetheless, potential CO2 limitation can be relevant in the process of biomethanation, a power-to-gas technology, where biogas is upgraded by the addition of H2 and ideally reduce the CO2 concentration in the produced biogas to 0–6%. H2 is effectively utilized by methanogens even at very low concentrations, but little is known about the impact of low CO2 concentrations on methanogenic activity. In this study, CO2 consumption and CH4 production kinetics under low CO2 concentrations were studied, using a hydrogenotrophic methanogen, Methanobacterium congolense, as model organism. We found that both cellular growth and methane production were limited at low CO2 concentrations (here expressed as Dissolved Inorganic Carbon, DIC). Maximum rates (Vmax) were reached at [DIC] of 100 mM (extrapolated), with a CO2 consumption rate of 69.2 fmol cell−1 d−1 and a CH4 production rate of 48.8 fmol cell−1 d−1. In our experimental setup, 80% of Vmax was achieved at [DIC] >9 mM. DIC half-saturation concentrations (Km) was about 2.5 mM for CO2 consumption and 2.2 mM for CH4 production. No CH4 production could be detected below 44.4 μM [DIC]. These data revealed that the limiting concentration of DIC may be much higher than that of H2 for a hydrogenotrophic methanogen. However, DIC is not a limiting factor in ADs running under standard operating conditions. For biomethanation, the results are applicable for both in situ and ex situ biomethanation reactors and show that biogas can be upgraded to concentrations of 2% CO2 (98% CH4) while still retaining 80% Vmax at pH 7.5 evaluated from M. congolense. Since DIC concentration can vary significantly with pH and pCO2 during biomethanation, monitoring DIC concentration through pH and pCO2 is therefore important for keeping optimal operational conditions for the biomethanation process.
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Affiliation(s)
- Xihan Chen
- Section for Biological and Chemical Engineering, Department of Engineering, Aarhus University, Aarhus, Denmark
| | - Lars Ditlev Mørck Ottosen
- Section for Biological and Chemical Engineering, Department of Engineering, Aarhus University, Aarhus, Denmark
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Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments. ISME JOURNAL 2019; 13:1920-1932. [PMID: 30894690 DOI: 10.1038/s41396-019-0387-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/22/2019] [Accepted: 02/28/2019] [Indexed: 01/09/2023]
Abstract
Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.
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Torti A, Jørgensen BB, Lever MA. Preservation of microbial DNA in marine sediments: insights from extracellular DNA pools. Environ Microbiol 2018; 20:4526-4542. [PMID: 30198168 DOI: 10.1111/1462-2920.14401] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/04/2018] [Accepted: 09/05/2018] [Indexed: 01/15/2023]
Abstract
Marine sediments harbour extracellular DNA (exDNA) not associated with currently living organisms. Including this exDNA in genetic surveys may distort abundance and diversity estimates of living prokaryotic communities. We separately extract exDNA and intracellular DNA (inDNA) from 11 horizons in a 10-m deep sediment core from Aarhus Bay (Denmark) that spans > 9000 years of Holocene sedimentation. We compare depth profiles of bacterial and archaeal 16S rRNA gene compositions to those of macrofaunal activity (bioturbation), sulfate and methane concentrations, sediment age and lithology. Among these variables, bioturbation shows the strongest relationship with the two DNA pools. In bioturbated surface sediments, the majority of Operational Taxonomic Units (OTUs) present in exDNA is absent from inDNA, thus belonging to microorganisms that were not alive at the time of sampling. Below the bioturbation zone, the two DNA pools display a much higher phylogenetic similarity. At all depths, the majority of exDNA and inDNA sequences show highest sequence similarities to sediment microorganisms, a finding that is additionally supported by separate analyses on low- and high-molecular weight exDNA. Our results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.
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Affiliation(s)
- Andrea Torti
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Mark Alexander Lever
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark.,Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
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30
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Cryptic CH 4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea. ISME JOURNAL 2018; 13:250-262. [PMID: 30194429 DOI: 10.1038/s41396-018-0273-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/10/2018] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO2 by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.
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31
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Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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32
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Hoshino T, Inagaki F. Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. ISME JOURNAL 2018; 13:227-231. [PMID: 30116037 PMCID: PMC6298964 DOI: 10.1038/s41396-018-0253-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 12/12/2022]
Abstract
Subseafloor sedimentary environments harbor a remarkable number of microorganisms that constitute anaerobic and aerobic microbial ecosystems beneath the ocean margins and open-ocean gyres, respectively. Microbial biomass and diversity richness generally decrease with increasing sediment depth and burial time. However, there has been a long-standing debate over the contribution and distribution of Archaea in the subseafloor sedimentary biosphere. Here we show the global quantification of archaeal and bacterial 16S rRNA genes in 221 sediment core samples obtained from diverse oceanographic settings through scientific ocean drilling using microfluidic digital PCR. We estimated that archaeal cells constitute 37.3% of the total microbial cells (40.0% and 12.8% in the ocean margin and open-ocean sites, respectively), corresponding to 1.1 × 1029 cells on Earth. In addition, the relative abundance of archaeal 16S rRNA genes generally decreased with the depth of water in the overlying sedimentary habitat, suggesting that Archaea may be more sensitive to nutrient quality and quantity supplied from the overlying ocean.
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Affiliation(s)
- Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan. .,Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, 236-0001, Japan.
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Otte JM, Harter J, Laufer K, Blackwell N, Straub D, Kappler A, Kleindienst S. The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients. Environ Microbiol 2018; 20:2483-2499. [DOI: 10.1111/1462-2920.14260] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Julia M. Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
| | - Johannes Harter
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
| | - Katja Laufer
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
- Center for Geomicrobiology, Department of BioscienceAarhus University Denmark
| | - Nia Blackwell
- Microbial Ecology, Center for Applied GeosciencesUniversity of Tübingen Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied GeosciencesUniversity of Tübingen Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
- Center for Geomicrobiology, Department of BioscienceAarhus University Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied GeosciencesUniversity of Tübingen Germany
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Lacoste É, Piot A, Archambault P, McKindsey CW, Nozais C. Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities. MARINE ENVIRONMENTAL RESEARCH 2018; 136:62-70. [PMID: 29503107 DOI: 10.1016/j.marenvres.2018.02.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Given concerns of increasing rates of species extinctions, the relationship between biodiversity and ecosystem functioning has become a major research focus over the past two decades. Many studies have shown that biodiversity per se (e.g. species richness) or species-specific traits may be good predictors of changes in ecosystem function. Although numerous studies on this subject have focused on terrestrial systems, few have evaluated benthic marine systems. We used the Limecola balthica community as a model to test whether the number or identity of three well-studied macrofaunal species influence the sediment bacterial compartment, which drives important biogeochemical processes and influence ecosystem functioning. We also investigated the poorly known role of meiofauna in the interactions between macrofauna and bacteria. Eight combinations of 0-3 species were maintained in microcosms for 34 days in the presence or absence of meiofauna. The abundance and composition of the bacterial community, defined by the relative percentage of cells with a high (HNA) vs low (LNA) nucleic acid content, were measured. Species identity of macrofauna was a better indicator of changes in the microbial compartment than was species richness per se. In particular, the gallery-diffuser behaviour of the polychaete Alitta virens likely induced strong changes in sediment physical and geochemical properties with a major impact on the bacterial compartment. Moreover, the presence of meiofauna modulated the influence of macrofauna on bacterial communities. This study provides evidence that species identity provides greater explanatory power than species richness to predict changes in the bacterial compartment. We propose that multi-compartment approaches to describe interactions amongst different size classes of organisms and their ecological roles should be further developed to improve our understanding of benthic ecosystem functioning.
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Affiliation(s)
- Élise Lacoste
- Institut des Sciences de la mer, Université du Québec à Rimouski, Rimouski, Canada; Québec-Océan, Département de Biologie, Université Laval, Québec, Canada.
| | - Adeline Piot
- Institut des Sciences de la mer, Université du Québec à Rimouski, Rimouski, Canada
| | | | - Christopher W McKindsey
- Institut des Sciences de la mer, Université du Québec à Rimouski, Rimouski, Canada; Fisheries and Oceans Canada, Institut Maurice Lamontagne, Mont-Joli, Canada
| | - Christian Nozais
- Québec-Océan, Département de Biologie, Université du Québec à Rimouski, Rimouski, Canada
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Cozzoli F, Bouma TJ, Ottolander P, Lluch MS, Ysebaert T, Herman PMJ. The combined influence of body size and density on cohesive sediment resuspension by bioturbators. Sci Rep 2018; 8:3831. [PMID: 29497095 PMCID: PMC5832813 DOI: 10.1038/s41598-018-22190-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 02/19/2018] [Indexed: 11/18/2022] Open
Abstract
We propose an empirical framework to scale the effects of bioturbation on sediment resuspension to population bioturbation activity, approximated as population metabolic rate. Individual metabolic rates have been estimated as functions of body size and extrapolated to population level. We used experimental flumes to test this approach across different types of marine, soft-sediment bioturbators. We observed that a large part of the variance in biota-mediated sediment resuspension can be explained by a positive relationship with population metabolic rate. Other mechanisms can strongly influence the outcome, such as bioturbation of deep sediment strata, biotic interactions with hydrodynamic stress and overlapping areas of influence must be further investigated. By relating the biota-mediated changes in resuspended sediment to metabolism, we can place our observations within the broader context of the metabolic theory of ecology and to formulate general expectations about changes in biota-mediated sediment resuspension in response to changes in population structure and climate change.
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Affiliation(s)
- Francesco Cozzoli
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research (NIOZ) and Utrecht University, Yerseke, The Netherlands.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Centro Ecotekne Pal. B S.P. 6, Lecce, Monteroni, Lecce, Italy.
| | - Tjeerd J Bouma
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research (NIOZ) and Utrecht University, Yerseke, The Netherlands
| | - Pauline Ottolander
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research (NIOZ) and Utrecht University, Yerseke, The Netherlands
| | - Maria Salvador Lluch
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research (NIOZ) and Utrecht University, Yerseke, The Netherlands
| | - Tom Ysebaert
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research (NIOZ) and Utrecht University, Yerseke, The Netherlands
- Institute for Marine Resources and Ecosystem Studies (IMARES), Wageningen University, Wageningen, The Netherlands
| | - Peter M J Herman
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research (NIOZ) and Utrecht University, Yerseke, The Netherlands
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Marshall IP, Karst SM, Nielsen PH, Jørgensen BB. Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition. Mar Genomics 2018; 37:58-68. [DOI: 10.1016/j.margen.2017.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 02/04/2023]
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37
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Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay. Appl Environ Microbiol 2017; 83:AEM.01547-17. [PMID: 28939599 DOI: 10.1128/aem.01547-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.
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Zinke LA, Mullis MM, Bird JT, Marshall IPG, Jørgensen BB, Lloyd KG, Amend JP, Kiel Reese B. Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:528-536. [PMID: 28836742 DOI: 10.1111/1758-2229.12578] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.
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Affiliation(s)
- Laura A Zinke
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, USA
| | - Megan M Mullis
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, USA
| | - Jordan T Bird
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, USA
| | | | | | - Karen G Lloyd
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, USA
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