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Yin X, Chen H, Jiang K, Zhang B, Li R, Zhu X, Sun L, Ng ZL, Su M. Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea. Microorganisms 2024; 12:1901. [PMID: 39338575 PMCID: PMC11434414 DOI: 10.3390/microorganisms12091901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3--N, NO2--N, PO43--P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42-, and Cl-. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2--N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.
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Affiliation(s)
- Xingjia Yin
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Hui Chen
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
| | - Kaixi Jiang
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- Office of Laboratory Safety and Equipment Management, Beijing Normal University, Zhuhai 519087, China
| | - Boda Zhang
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- Center for Environmental Monitoring of Geology, Shenzhen 518034, China
| | - Ruohong Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Xinzhe Zhu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Zhi Lin Ng
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
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2
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024; 6:1209-1224. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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3
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Pattarach K, Surachat K, Liu SL, Mayakun J. Water depth outweighs reef condition in shaping non-geniculate coralline algae-associated microbial communities in coral reefs: A case study from Thailand. Heliyon 2024; 10:e25486. [PMID: 38356583 PMCID: PMC10864967 DOI: 10.1016/j.heliyon.2024.e25486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/05/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Red calcified non-geniculate coralline algae (NGCA) provide habitat structures, stabilize reef structures, and foster coral larval settlement and metamorphosis. Moreover, the microbes associated with NGCA are dependent on the NGCA host species and are affected by environmental factors; however, little is known about the influence of reef conditions and depth gradients on the associated microbial communities and NGCA. In this study, we collected NGCA under different reef conditions and depth gradients and characterized the microbial communities using the V3-V4 hypervariable regions of the 16S rRNA gene. Metagenomic analysis revealed 2 domains, 51 phyla, 123 classes, and 210 genera. The NGCA-associated bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, and Acidobacteriota. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial classes. Differences in microbial diversity and richness were not apparent between reef conditions and depth gradients. However, there was a significant difference in bacterial evenness among the depth gradients. The bacterial abundance associated with NGCA was greater in deep zones than in shallow zones. The shallow zone exhibited a greater relative abundance of all gene functions than the deep zone, indicating differences in the distribution of gene functions. This study showed that the microbial communities associated with red calcified NGCA are diverse, and that the depth gradient affects their abundance and evenness, highlighting the need for further research to understand the functional roles of these microbial communities in coral reef conservation.
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Affiliation(s)
- Kattika Pattarach
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Komwit Surachat
- Department of Biomedical Science & Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Shao-Lun Liu
- Department of Life Science & Center for Ecology and Environment, Tunghai University, Taichung, 40704, Taiwan
| | - Jaruwan Mayakun
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand
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Arai R, Miura S, Nakamura Y, Fujie G, Kodaira S, Kaiho Y, Mochizuki K, Nakata R, Kinoshita M, Hashimoto Y, Hamada Y, Okino K. Upper-plate conduits linked to plate boundary that hosts slow earthquakes. Nat Commun 2023; 14:5101. [PMID: 37730797 PMCID: PMC10511545 DOI: 10.1038/s41467-023-40762-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/07/2023] [Indexed: 09/22/2023] Open
Abstract
In shallow subduction zones, fluid behavior impacts various geodynamic processes capable of regulating slip behaviors and forming mud volcanoes. However, evidence of structures that control the fluid transfer within an overriding plate is limited and the physical properties at the source faults of slow earthquakes are poorly understood. Here we present high-resolution seismic velocity models and reflection images of the Hyuga-nada area, Japan, where the Kyushu-Palau ridge subducts. We image distinct kilometer-wide columns in the upper plate with reduced velocities that extend vertically from the seafloor down to 10-13 km depth. We interpret the low-velocity columns as damaged zones caused by seamount subduction and suggest that they serve as conduits, facilitating vertical fluid migration from the plate boundary. The lateral variation in upper-plate velocity and seismic reflectivity along the plate boundary correlates with the distribution of slow earthquakes, indicating that the upper-plate drainage system controls the complex pattern of seismic slip at subduction faults.
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Affiliation(s)
- Ryuta Arai
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan.
| | - Seiichi Miura
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan
| | - Yasuyuki Nakamura
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan
| | - Gou Fujie
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan
| | - Shuichi Kodaira
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan
| | - Yuka Kaiho
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan
| | - Kimihiro Mochizuki
- Earthquake Research Institute, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Rie Nakata
- Earthquake Research Institute, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-0032, Japan
- Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Masataka Kinoshita
- Earthquake Research Institute, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yoshitaka Hashimoto
- Faculty of Science and Technology, Kochi University, Akebonocho 2-5-1, Kochi, 780-8520, Japan
| | - Yohei Hamada
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, 200 Monobe Otsu Nankoku, Kochi, 783-8502, Japan
| | - Kyoko Okino
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha Kashiwa, Chiba, 277-8564, Japan
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Webster G, Cragg BA, Rinna J, Watkins AJ, Sass H, Weightman AJ, Parkes RJ. Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments. Front Microbiol 2023; 14:1157337. [PMID: 37293223 PMCID: PMC10244519 DOI: 10.3389/fmicb.2023.1157337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH4) seepage. However, the role of prokaryotes in influencing this CH4 release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM). Prokaryotic populations and activities were variable in these MV sediments reflecting the geochemical heterogeneity within and between them. There were also marked differences between many MV and their reference sites. Overall direct cell numbers below the SMTZ (0.2-0.5 mbsf) were much lower than the general global depth distribution and equivalent to cell numbers from below 100 mbsf. Methanogenesis from methyl compounds, especially methylamine, were much higher than the usually dominant substrates H2/CO2 or acetate. Also, CH4 production occurred in 50% of methylated substrate slurries and only methylotrophic CH4 production occurred at all seven MV sites. These slurries were dominated by Methanococcoides methanogens (resulting in pure cultures), and prokaryotes found in other MV sediments. AOM occurred in some slurries, particularly, those from Captain Arutyunov, Mercator and Carlos Ribeiro MVs. Archaeal diversity at MV sites showed the presence of both methanogens and ANME (Methanosarcinales, Methanococcoides, and ANME-1) related sequences, and bacterial diversity was higher than archaeal diversity, dominated by members of the Atribacterota, Chloroflexota, Pseudomonadota, Planctomycetota, Bacillota, and Ca. "Aminicenantes." Further work is essential to determine the full contribution of Gulf of Cádiz mud volcanoes to the global methane and carbon cycles.
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Affiliation(s)
- Gordon Webster
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Barry A. Cragg
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Joachim Rinna
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
- Aker BP ASA, Lysaker, Norway
| | - Andrew J. Watkins
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
- The Wales Research and Diagnostic Positron Emission Tomography Imaging Centre (PETIC), School of Medicine, Cardiff University, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Henrik Sass
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - R. John Parkes
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
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Mitsutome Y, Toki T, Kagoshima T, Sano Y, Tomonaga Y, Ijiri A. Estimation of the depth of origin of fluids using noble gases in the surface sediments of submarine mud volcanoes off Tanegashima Island. Sci Rep 2023; 13:5051. [PMID: 37024563 PMCID: PMC10079976 DOI: 10.1038/s41598-023-31582-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/14/2023] [Indexed: 04/08/2023] Open
Abstract
The helium isotope ratio (3He/4He), concentration ratio of neon-20 to helium-4 (20Ne/4He), argon (Ar), krypton (Kr), and xenon (Xe) concentrations were measured in the porewater of surface sediments of several submarine mud volcanoes. From the 3He/4He values (0.18-0.93RA), the estimated He origin is almost 90% crustal He, with little contribution from mantle-derived He. The determined Ar, Kr, and Xe concentrations lie within the solubility equilibrium range expected for temperatures from 83 °C up to 230 °C and are consistent with the temperature range of the dehydration origin of clay minerals. Considering the geothermal gradient in the investigated region (25 °C/km), these gases are considered to have reached dissolution equilibrium at a depth of about 3.3 km to 9.2 km below the seafloor. As the depth of the plate boundary is 18 km below the seafloor, the noble gas signatures are likely to originate from the crust, not from the plate boundary. This is consistent with the results presented by the He isotope ratios.
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Affiliation(s)
- Yuki Mitsutome
- Chemistry Biology and Marine Science, Graduate School of Science and Engineering, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Tomohiro Toki
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.
- Research Institute for Humanity and Nature, 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8047, Japan.
| | - Takanori Kagoshima
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Yuji Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Center for Advanced Marie Core Research, Kochi University, 200B Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Yama Tomonaga
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Hydrogeology, Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland
| | - Akira Ijiri
- Graduate School of Maritime Sciences, Kobe University, 5-1-1 Fukaemiinamimachi, Higashinada-ku, Kobe, 658-0022, Japan
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 200B Monobe, Nankoku, Kochi, 783-8502, Japan
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7
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Wang X, Lei Z, Zhang Z, Shimizu K, Lee DJ, Khanal SK. Use of nanobubble water bioaugmented anaerobically digested sludge for high-efficacy energy production from high-solids anaerobic digestion of corn straw. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160825. [PMID: 36502974 DOI: 10.1016/j.scitotenv.2022.160825] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
An increasing attention has been paid to the secure and sustainable management of agricultural wastes, especially lignocellulosic biomass. Nanobubble water (NBW) contains 106-108 bubbles/mL with diameter <1000 nm. Although previous studies have examined the enhancement effects of NBW on methane production from organic solid wastes, the NBW-based anaerobic digestion (AD) system is still restrained from practical application due to the large increase in AD reactor volume, generation of wastewater, and increase in energy consumption as well. In this study, NBW bioaugmentation of anaerobically digested sludge for the first time was performed for high-solids AD of corn straw. Results show that cellulase, xylanases and lignin peroxidase activities were increased by 2-55% during the NBW bioaugmentation process. Significant enrichment of hydrolytic/acidogenic bacteria and methanogenic archaea were noticed in the NBW bioaugmented sludge. This study clearly demonstrated 47% increase in methane production from high-solids AD of corn straw when O2-NBW bioaugmented sludge was applied, achieving a net energy gain of 5138 MJ/t-volatile solids of corn straw with an energy recovery of 34%. The NBW-based high-solids AD system can provide a novel and sustainable management solution for renewable energy production from agricultural wastes, targeting the reduction of environmental pollution and energy crisis.
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Affiliation(s)
- Xuezhi Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; School of Resource and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Zhongfang Lei
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Zhenya Zhang
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuya Shimizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Oura-gun, Itakura, Gunma 374-0193, Japan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Manoa, 1955 East-West Road, Honolulu, HI 96822, USA
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8
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Niu M, Deng L, Su L, Ruff SE, Yang N, Luo M, Qi Q, Li J, Wang F. Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea. Mol Ecol 2023; 32:660-679. [PMID: 36408814 DOI: 10.1111/mec.16786] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 10/10/2022] [Accepted: 11/01/2022] [Indexed: 11/22/2022]
Abstract
Marine cold seeps are unique chemosynthetic habitats fuelled by deeply sourced hydrocarbon-rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface-derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the central role of microbiota in mediating biogeochemical cycles, the factors that govern the assembly and network of prokaryotic communities in cold seeps remain poorly understood. Here we analysed the geochemical and microbiological profiles of 11 different sediment cores from two spatially distant cold seeps of the South China Sea. We show that prokaryotic communities belonging to the same methane-supply regimes (high-methane-supply, low-methane-supply and non-seep control sediments) had a highly similar community structure, regardless of geographical location, seep-associated biota (mussel, clam, microbial mat) and sediment depth. Methane supply appeared to drive the niche partitioning of anaerobic methanotrophic archaea (ANME) at the regional scale, with ANME-1 accounting for >60% sequence abundance of ANME in the high-methane-supply sediments, while ANME-2 dominated (>90%) the low-methane-supply sediments. Increasing methane supply enhanced the contribution of environmental selection but lessened the contributions of dispersal limitation and drift to overall community assembly. High methane supply, moreover, promoted a more tightly connected, less stable prokaryotic network dominated by positive correlations. Together, these results provide a potentially new framework for understanding the niches and network interplay of prokaryotic communities across different methane seepage regimes in cold-seep sediments.
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Affiliation(s)
- Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Longhui Deng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - S Emil Ruff
- Ecosystems Center and Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Na Yang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Min Luo
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qi Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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9
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Lazar CS, Schmidt F, Elvert M, Heuer VB, Hinrichs KU, Teske AP. Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin. Front Microbiol 2022; 13:1043414. [PMID: 36620052 PMCID: PMC9812581 DOI: 10.3389/fmicb.2022.1043414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Frauke Schmidt
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Verena B. Heuer
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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10
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Characterization of archaeal and bacterial communities thriving in methane-seeping on-land mud volcanoes, Niigata, Japan. Int Microbiol 2022; 26:191-204. [PMID: 36329310 DOI: 10.1007/s10123-022-00288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Submarine mud volcanoes (MVs) have attracted significant interest in the scientific community for obtaining clues on the subsurface biosphere. On-land MVs, which are much less focused in this context, are equally important, and they may even provide insights also for astrobiology of extraterrestrial mud volcanism. Hereby, we characterized microbial communities of two active methane-seeping on-land MVs, Murono and Kamou, in central Japan. 16S rRNA gene profiling of those sites recovered the dominant archaeal sequences affiliated with methanogens. Anaerobic methanotrophs (ANME), with the subgroups ANME-1b and ANME-3, were recovered only from the Murono site albeit a greatly reduced relative abundance in the community compared to those of typical submarine MVs. The bacterial sequences affiliated to Caldatribacteriota JS1 were recovered from both sites; on the other hand, sulfate-reducing bacteria (SRB) of Desulfobulbaceae was recovered only from the Murono site. The major difference of on-land MVs from submarine MVs is that the high concentrations of sulfate are not always introduced to the subsurface from above. In addition, the XRD analysis of Murono shows the absence of sulfate-, sulfur-related mineral. Therefore, we hypothesize one scenario of ANME-1b and ANME-3 thriving at the depth of the Murono site independently from SRB, which is similar to the situations reported in some other methane-seeping sites with a sulfate-depleted condition. We note that previous investigations speculate that the erupted materials from Murono and Kamou originate from the Miocene marine strata. The fact that SRB (Desulfobulbaceae) capable of associating with ANME-3 was recovered from the Murono site presents an alternative scenario: the old sea-related juvenile water somehow worked as the source of additional sulfur-related components for the SRB-ANME syntrophic consortium forming at a deeper zone of the site. However, the reason for the differences between Murono and Kamou is still unknown, and this requires further investigation.
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11
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Hydrocarbon Cycling in the Tokamachi Mud Volcano (Japan): Insights from Isotopologue and Metataxonomic Analyses. Microorganisms 2022; 10:microorganisms10071417. [PMID: 35889138 PMCID: PMC9323770 DOI: 10.3390/microorganisms10071417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 12/03/2022] Open
Abstract
Understanding hydrocarbon cycling in the subsurface is important in various disciplines including climate science, energy resources and astrobiology. Mud volcanoes provide insights into biogeochemical processes occurring in the subsurface. They are usually associated with natural gas reservoirs consisting mainly of methane and other hydrocarbons as well as CO2. Stable isotopes have been used to decipher the sources and sinks of hydrocarbons in the subsurface, although the interpretation can be ambiguous due to the numerous processes involved. Here we report new data for hydrocarbon isotope analysis, including position-specific isotope composition of propane, for samples from the Tokamachi mud volcano area, Japan. The data suggest that C2+ hydrocarbons are being biodegraded, with indirect production of methane (“secondary methanogenesis”). Data from chemical and isotopic composition are discussed with regard to 16S rRNA analysis, which exhibits the presence of hydrogenotrophic and acetoclastic methoanogens. Overall, the combination of isotopologue analysis with 16S rRNA gene data allows refining of our understanding of hydrocarbon cycling in subsurface environments.
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12
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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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13
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Distinct methane-dependent biogeochemical states in Arctic seafloor gas hydrate mounds. Nat Commun 2021; 12:6296. [PMID: 34728618 PMCID: PMC8563959 DOI: 10.1038/s41467-021-26549-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/27/2021] [Indexed: 01/04/2023] Open
Abstract
Archaea mediating anaerobic methane oxidation are key in preventing methane produced in marine sediments from reaching the hydrosphere; however, a complete understanding of how microbial communities in natural settings respond to changes in the flux of methane remains largely uncharacterized. We investigate microbial communities in gas hydrate-bearing seafloor mounds at Storfjordrenna, offshore Svalbard in the high Arctic, where we identify distinct methane concentration profiles that include steady-state, recently-increasing subsurface diffusive flux, and active gas seepage. Populations of anaerobic methanotrophs and sulfate-reducing bacteria were highest at the seep site, while decreased community diversity was associated with a recent increase in methane influx. Despite high methane fluxes and methanotroph doubling times estimated at 5-9 months, microbial community responses were largely synchronous with the advancement of methane into shallower sediment horizons. Together, these provide a framework for interpreting subseafloor microbial responses to methane escape in a warming Arctic Ocean.
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14
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Merkel AY, Chernyh NA, Pimenov NV, Bonch-Osmolovskaya EA, Slobodkin AI. Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane. Life (Basel) 2021; 11:life11090953. [PMID: 34575103 PMCID: PMC8470020 DOI: 10.3390/life11090953] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.
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15
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Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ. Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments. Environ Microbiol 2021; 23:4646-4660. [PMID: 34190392 DOI: 10.1111/1462-2920.15656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate-methane transition zone, the metal (iron/manganese) reduction zone, and the gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na+ /H+ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g. high salt brines, high pressure and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K+ -stimulated pyrophosphatase and capsule proteins.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Abigail M Johnson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manlin Xu
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James McManus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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16
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Marlow JJ, Hoer D, Jungbluth SP, Reynard LM, Gartman A, Chavez MS, El-Naggar MY, Tuross N, Orphan VJ, Girguis PR. Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proc Natl Acad Sci U S A 2021; 118:e2006857118. [PMID: 34161255 PMCID: PMC8237665 DOI: 10.1073/pnas.2006857118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample's methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.
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Affiliation(s)
- Jeffrey J Marlow
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
| | - Daniel Hoer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Sean P Jungbluth
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94720
| | - Linda M Reynard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Amy Gartman
- US Geological Survey Pacific Coastal and Marine Science Center, Santa Cruz, CA 95060
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
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17
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Lloyd KG. Time as a microbial resource. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:18-21. [PMID: 33015966 DOI: 10.1111/1758-2229.12892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Karen G Lloyd
- Microbiology Department, University of Tennessee, Mossman Building Rm 307, Knoxville, TN, 37996, USA
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18
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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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19
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Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments. Appl Environ Microbiol 2020; 86:AEM.00877-20. [PMID: 32709727 DOI: 10.1128/aem.00877-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/17/2020] [Indexed: 11/20/2022] Open
Abstract
Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady-state growth rates could be faster to balance cell decay) were estimated as 2 to 25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the fraction read abundance of 16S rRNA genes and total cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28% ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events.IMPORTANCE Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments; rather, they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly nongrowing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 cm, offering a chance for subsurface organisms to undergo natural selection.
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20
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Mardanov AV, Kadnikov VV, Beletsky AV, Ravin NV. Sulfur and Methane-Oxidizing Microbial Community in a Terrestrial Mud Volcano Revealed by Metagenomics. Microorganisms 2020; 8:microorganisms8091333. [PMID: 32878336 PMCID: PMC7565565 DOI: 10.3390/microorganisms8091333] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using a metagenomics approach, we analyzed the microbial community of bubbling fluids retrieved from an active mud volcano in eastern Crimea. The microbial community was dominated by chemolithoautotrophic Campylobacterota and Gammaproteobacteria, which are capable of sulfur oxidation coupled to aerobic and anaerobic respiration. Methane oxidation could be enabled by aerobic Methylococcales bacteria and anaerobic methanotrophic archaea (ANME), while methanogens were nearly absent. The ANME community was dominated by a novel species of Ca. Methanoperedenaceae that lacked nitrate reductase and probably couple methane oxidation to the reduction of metal oxides. Analysis of two Ca. Bathyarchaeota genomes revealed the lack of mcr genes and predicted that they could grow on fatty acids, sugars, and proteinaceous substrates performing fermentation. Thermophilic sulfate reducers indigenous to the deep subsurface, Thermodesulfovibrionales (Nitrospirae) and Ca. Desulforudis (Firmicutes), were found in minor amounts. Overall, the results obtained suggest that reduced compounds delivered from the deep subsurface support the development of autotrophic microorganisms using various electron acceptors for respiration.
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21
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Abstract
The marine subsurface is one of the largest habitats on Earth composed exclusively of microorganisms and harboring on the order of 1029 microbial cells. It is unclear if deep subsurface life impacts overlying seafloor diversity and biogeochemical cycling in the deep ocean. We analyzed the microbial communities of 172 seafloor surface sediment samples, including gas and oil seeps as well as sediments not subject to upward fluid flow. A strong correlation between typical subsurface clades and active geofluid seepage suggests that subsurface life is injected into the deep ocean floor at hydrocarbon seeps, a globally widespread hydrogeological phenomenon. This supply of subsurface-derived microbial populations, biomass, and metabolic potential thus increases biodiversity and impacts carbon cycling in the deep ocean. Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.
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22
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Þorsteinsdóttir GV, Blischke A, Sigurbjörnsdóttir MA, Òskarsson F, Arnarson ÞS, Magnússon KP, Vilhelmsson O. Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland. Can J Microbiol 2019; 66:25-38. [PMID: 31557445 DOI: 10.1139/cjm-2019-0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ13C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ13C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.
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Affiliation(s)
- Guðný Vala Þorsteinsdóttir
- Faculty of Natural Resource Sciences, University of Akureyri, Borgir v. Norðurslóð, 600 Akureyri, Iceland.,Icelandic Institute of Natural History, Borgir v. Norðurslóð, 600 Akureyri, Iceland
| | - Anett Blischke
- Iceland GeoSurvey, Branch at Akureyri, Rangarvollum, 603 Akureyri, Iceland
| | - M Auður Sigurbjörnsdóttir
- Faculty of Natural Resource Sciences, University of Akureyri, Borgir v. Norðurslóð, 600 Akureyri, Iceland
| | - Finnbogi Òskarsson
- Iceland GeoSurvey, Department of Geothermal Engineering, Grensásvegi 9, 108 Reykjavík, Iceland
| | | | - Kristinn P Magnússon
- Faculty of Natural Resource Sciences, University of Akureyri, Borgir v. Norðurslóð, 600 Akureyri, Iceland.,Icelandic Institute of Natural History, Borgir v. Norðurslóð, 600 Akureyri, Iceland.,Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland
| | - Oddur Vilhelmsson
- Faculty of Natural Resource Sciences, University of Akureyri, Borgir v. Norðurslóð, 600 Akureyri, Iceland.,Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland.,School of Biological Sciences, University of Reading, Earley, Reading RG6 6AS, UK
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23
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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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24
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Gründger F, Carrier V, Svenning MM, Panieri G, Vonnahme TR, Klasek S, Niemann H. Methane-fuelled biofilms predominantly composed of methanotrophic ANME-1 in Arctic gas hydrate-related sediments. Sci Rep 2019; 9:9725. [PMID: 31278352 PMCID: PMC6611871 DOI: 10.1038/s41598-019-46209-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/25/2019] [Indexed: 11/21/2022] Open
Abstract
Sedimentary biofilms comprising microbial communities mediating the anaerobic oxidation of methane are rare. Here, we describe two biofilm communities discovered in sediment cores recovered from Arctic cold seep sites (gas hydrate pingos) in the north-western Barents Sea, characterized by steady methane fluxes. We found macroscopically visible biofilms in pockets in the sediment matrix at the depth of the sulphate-methane-transition zone. 16S rRNA gene surveys revealed that the microbial community in one of the two biofilms comprised exclusively of putative anaerobic methanotrophic archaea of which ANME-1 was the sole archaeal taxon. The bacterial community consisted of relatives of sulphate-reducing bacteria (SRB) belonging to uncultured Desulfobacteraceae clustering into SEEP-SRB1 (i.e. the typical SRB associated to ANME-1), and members of the atribacterial JS1 clade. Confocal laser scanning microscopy demonstrates that this biofilm is composed of multicellular strands and patches of ANME-1 that are loosely associated with SRB cells, but not tightly connected in aggregates. Our discovery of methanotrophic biofilms in sediment pockets closely associated with methane seeps constitutes a hitherto overlooked and potentially widespread sink for methane and sulphate in marine sediments.
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Affiliation(s)
- Friederike Gründger
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Vincent Carrier
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Giuliana Panieri
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tobias R Vonnahme
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Scott Klasek
- Department of Microbiology, College of Sciences, Oregon State University, Corvallis, OR, USA
| | - Helge Niemann
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Marine Microbiology & Biogeochemistry, and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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25
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Liu YF, Qi ZZ, Shou LB, Liu JF, Yang SZ, Gu JD, Mu BZ. Anaerobic hydrocarbon degradation in candidate phylum 'Atribacteria' (JS1) inferred from genomics. ISME JOURNAL 2019; 13:2377-2390. [PMID: 31171858 PMCID: PMC6776118 DOI: 10.1038/s41396-019-0448-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/11/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023]
Abstract
The hydrocarbon-enriched environments, such as oil reservoirs and oil sands tailings ponds, contain a broad diversity of uncultured microorganisms. Despite being one of the few prokaryotic lineages that is consistently detected in both production water from oil reservoirs and stable hydrocarbon-degrading enrichment cultures originated from oil reservoirs, the physiological and ecological roles of candidate phylum “Atribacteria” (OP9/JS1) are not known in deep subsurface environments. Here, we report the expanded metabolic capabilities of Atribacteria as inferred from genomic reconstructions. Seventeen newly assembled medium-to-high-quality metagenomic assembly genomes (MAGs) were obtained either from co-assembly of two metagenomes from an Alaska North Slope oil reservoir or from previous studies of metagenomes coming from different environments. These MAGs comprise three currently known genus-level lineages and four novel genus-level groups of OP9 and JS1, which expands the genomic coverage of the major lineages within the candidate phylum Atribacteria. Genes involved in anaerobic hydrocarbon degradation were found in seven MAGs associated with hydrocarbon-enriched environments, and suggest that some Atribacteria could ferment short-chain n-alkanes into fatty acid while conserving energy. This study expands predicted metabolic capabilities of Atribacteria (JS1) and suggests that they are mediating a key role in subsurface carbon cycling.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Zhen-Zhen Qi
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Li-Bin Shou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China. .,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 200237, Shanghai, P.R. China.
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26
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In situ development of a methanotrophic microbiome in deep-sea sediments. ISME JOURNAL 2018; 13:197-213. [PMID: 30154496 PMCID: PMC6298960 DOI: 10.1038/s41396-018-0263-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/06/2018] [Accepted: 08/04/2018] [Indexed: 01/11/2023]
Abstract
Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of a methanotrophic microbiome following subsurface mud eruptions at Håkon Mosby mud volcano (1250 m water depth). Freshly erupted muds hosted deep-subsurface communities that were dominated by Bathyarchaeota, Atribacteria and Chloroflexi. Methanotrophy was initially limited to a thin surface layer of Methylococcales populations consuming methane aerobically. With increasing distance to the eruptive center, anaerobic methanotrophic archaea, sulfate-reducing Desulfobacterales and thiotrophic Beggiatoaceae developed, and their respective metabolic capabilities dominated the biogeochemical functions of the community. Microbial richness, evenness, and cell numbers of the entire microbial community increased up to tenfold within a few years downstream of the mud flow from the eruptive center. The increasing diversity was accompanied by an up to fourfold increase in sequence abundance of relevant metabolic genes of the anaerobic methanotrophic and thiotrophic guilds. The communities fundamentally changed in their structure and functions as reflected in the metagenome turnover with distance from the eruptive center, and this was reflected in the biogeochemical zonation across the mud volcano caldera. The observed functional succession provides a framework for the response time and recovery of complex methanotrophic communities after disturbances of the deep-sea bed.
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27
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Orsi WD. Ecology and evolution of seafloor and subseafloor microbial communities. Nat Rev Microbiol 2018; 16:671-683. [DOI: 10.1038/s41579-018-0046-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Ijiri A, Inagaki F, Kubo Y, Adhikari RR, Hattori S, Hoshino T, Imachi H, Kawagucci S, Morono Y, Ohtomo Y, Ono S, Sakai S, Takai K, Toki T, Wang DT, Yoshinaga MY, Arnold GL, Ashi J, Case DH, Feseker T, Hinrichs KU, Ikegawa Y, Ikehara M, Kallmeyer J, Kumagai H, Lever MA, Morita S, Nakamura KI, Nakamura Y, Nishizawa M, Orphan VJ, Røy H, Schmidt F, Tani A, Tanikawa W, Terada T, Tomaru H, Tsuji T, Tsunogai U, Yamaguchi YT, Yoshida N. Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex. SCIENCE ADVANCES 2018; 4:eaao4631. [PMID: 29928689 PMCID: PMC6007163 DOI: 10.1126/sciadv.aao4631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Microbial life inhabiting subseafloor sediments plays an important role in Earth's carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm-3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated.
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Affiliation(s)
- Akira Ijiri
- 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 Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- 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 Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - Yusuke Kubo
- Center for Deep Earth Exploration, JAMSTEC, Yokohama 236-0001, Japan
| | - Rishi R. Adhikari
- Department of Earth and Environmental Sciences, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Shohei Hattori
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Tatsuhiko Hoshino
- 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 Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Hiroyuki Imachi
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Shinsuke Kawagucci
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Yuki Morono
- 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 Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Yoko Ohtomo
- 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 Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Shuhei Ono
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Ken Takai
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Tomohiro Toki
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - David T. Wang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marcos Y. Yoshinaga
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Gail L. Arnold
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Juichiro Ashi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - David H. Case
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tomas Feseker
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Yojiro Ikegawa
- Civil Engineering Research Laboratory, Central Research Institute of Electric Power Industry, Abiko, Chiba 270-1194, Japan
| | - Minoru Ikehara
- Center for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Jens Kallmeyer
- Department of Earth and Environmental Sciences, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Hidenori Kumagai
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Mark A. Lever
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sumito Morita
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | | | - Yuki Nakamura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hans Røy
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Frauke Schmidt
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Atsushi Tani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Wataru Tanikawa
- 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 Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | | | - Hitoshi Tomaru
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Takeshi Tsuji
- Department of Earth Resources Engineering, Kyushu University, Fukuoka 819-0395, Japan
- International Institute for Carbon-Neutral Energy Research, Department of Earth Resources Engineering, Kyushu University, 744 Motooka, Fukuoka-shi, Fukuoka 819-0395, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, Japan
| | - Yasuhiko T. Yamaguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Naohiro Yoshida
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
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29
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Thermophilic endospores associated with migrated thermogenic hydrocarbons in deep Gulf of Mexico marine sediments. ISME JOURNAL 2018; 12:1895-1906. [PMID: 29599524 PMCID: PMC6052102 DOI: 10.1038/s41396-018-0108-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/16/2018] [Accepted: 03/12/2018] [Indexed: 12/31/2022]
Abstract
Dormant endospores of thermophilic bacteria (thermospores) can be detected in cold marine sediments following high-temperature incubation. Thermospores in the cold seabed may be explained by a dispersal history originating in deep biosphere oil reservoir habitats where upward migration of petroleum fluids at hydrocarbon seeps transports viable cells into the overlying ocean. We assessed this deep-to-shallow dispersal hypothesis through geochemical and microbiological analyses of 111 marine sediments from the deep water Eastern Gulf of Mexico. GC-MS and fluorescence confirmed the unambiguous presence of thermogenic hydrocarbons in 71 of these locations, indicating seepage from deeply sourced petroleum in the subsurface. Heating each sediment to 50 °C followed by 16S rRNA gene sequencing revealed several thermospores with a cosmopolitan distribution throughout the study area, as well as thermospores that were more geographically restricted. Among the thermospores having a more limited distribution, 12 OTUs from eight different lineages were repeatedly detected in sediments containing thermogenic hydrocarbons. A subset of these were significantly correlated with hydrocarbons (p < 0.05) and most closely related to Clostridiales previously detected in oil reservoirs from around the world. This provides evidence of bacteria in the ocean being dispersed out of oil reservoirs, and suggests that specific thermospores may be used as model organisms for studying warm-to-cold transmigration in the deep sea.
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30
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Cabrol NA. The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures. ASTROBIOLOGY 2018; 18:1-27. [PMID: 29252008 PMCID: PMC5779243 DOI: 10.1089/ast.2017.1756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/27/2017] [Indexed: 05/09/2023]
Abstract
Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.
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31
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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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