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Chen SC, Musat F, Richnow HH, Krüger M. Microbial diversity and oil biodegradation potential of northern Barents Sea sediments. J Environ Sci (China) 2024; 146:283-297. [PMID: 38969457 DOI: 10.1016/j.jes.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 07/07/2024]
Abstract
The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany; Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Florin Musat
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania.
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655, Hannover, Germany
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2
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Jiao JY, Ma SC, Salam N, Zhou Z, Lian ZH, Fu L, Chen Y, Peng CH, OuYang YT, Fan H, Li L, Yi Y, Zhang JY, Wang JY, Liu L, Gao L, Oren A, Woyke T, Dodsworth JA, Hedlund BP, Li WJ, Cheng L. Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. MICROBIOME 2024; 12:123. [PMID: 38971798 PMCID: PMC11227167 DOI: 10.1186/s40168-024-01836-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood. RESULTS We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments. CONCLUSION Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shi-Chun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- National Agri-Food Biotechnology Institute, Sector-81 (Knowledge City), Mohali, 140306, Punjab, India
| | - Zhuo Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Ying Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Cheng-Hui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Ling Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Yue Yi
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jing-Yuan Wang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China.
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de Freitas STF, Silva FG, Bessa LA, de Souza UJB, Augusto DSS, de Faria GS, Vitorino LC. Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta. Sci Rep 2024; 14:15456. [PMID: 38965317 PMCID: PMC11224404 DOI: 10.1038/s41598-024-66161-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.
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Affiliation(s)
- Samylla Tássia Ferreira de Freitas
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil
| | - Fabiano Guimarães Silva
- Laboratory of Plant Mineral Nutrition, Instituto Federal Goiano, campus Rio Verde, Rio Verde, Brazil
| | - Layara Alexandre Bessa
- Laboratory of Plant Mineral Nutrition, Instituto Federal Goiano, campus Rio Verde, Rio Verde, Brazil
| | - Ueric José Borges de Souza
- Bioinformatics and Biotechnology Laboratory, Federal University of Tocantins, Campus of Gurupi, Gurupi, TO, 77410-570, Brazil
| | - Damiana Souza Santos Augusto
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil
| | - Giselle Santos de Faria
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil
| | - Luciana Cristina Vitorino
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil.
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Kawamoto H, Watanabe M, Mochimaru H, Nakahara N, Meng XY, Sakamoto S, Morinaga K, Katayama T, Yoshioka H, Nomura N, Tamaki H. Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota. Syst Appl Microbiol 2024; 47:126515. [PMID: 38776610 DOI: 10.1016/j.syapm.2024.126515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/08/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
A novel anaerobic, thermophilic bacterium of the class Atribacteria, strain M15T, was isolated from a high-temperature gas reservoir, Japan. Cells of strain M15T were gram-negative, short oval-shaped, and lacked flagella. Growth occurred at 45-75 °C (optimum 70-75 °C) and pH 6.5-8.5 (optimum pH 7.5-8.0) and was fast under optimal conditions (doubling time 11.4 h). Yeast extract was required for growth. Fermentative growth with glucose, arabinose, xylose, and cellobiose was observed. The major fermentative end products of glucose were acetate and hydrogen. The major cellular fatty acids were C16:0, iso-C15:0, and C18:0. The genomic G + C content was 46.0 mol%. Fluorescence and electron microscopy observations revealed the intracellular localization of genomic DNA surrounded by a membrane in the cells of strain M15T as reported in a sole validly described species of the class Atribacteria in the phylum Atribacterota, Atribacter laminatus strain RT761T, suggesting that the unique morphological traits are widely shared in this class. Phylogenetic analyses indicated that strain M15T belongs to a distinct family-level lineage in the class Atribacteria and shows low similarities to Atribacter laminatus strain RT761T (16S rRNA gene sequence identity of 90.1 %, average nucleotide identity [ANI] of 66.1 %, average amino acid identity [AAI] of 55.8 %). Phenotypic traits of strain M15T (thermophilic, fast-growing, relatively high G + C content, etc.) were clearly distinct from A. laminatus. Based on these phenotypic and genomic properties, we propose a novel genus and species, Atrimonas thermophila gen. nov., sp. nov. for strain M15T (=JCM39389T, =KCTC25731T) representing a novel family Atrimonadaceae fam., nov. in the class Atribacteria.
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Affiliation(s)
- Hiroki Kawamoto
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Miho Watanabe
- Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita 010-0195, Japan
| | - Hanako Mochimaru
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nozomi Nakahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; Environmental Management Center, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Xiang-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Sachiko Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Taiki Katayama
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyoshi Yoshioka
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; MiCS (Microbiology Research Center for Sustainability), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; MiCS (Microbiology Research Center for Sustainability), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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5
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Qu Y, Zhao Y, Yao X, Wang J, Liu Z, Hong Y, Zheng P, Wang L, Hu B. Salinity causes differences in stratigraphic methane sources and sinks. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 19:100334. [PMID: 38046178 PMCID: PMC10692758 DOI: 10.1016/j.ese.2023.100334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 12/05/2023]
Abstract
Methane metabolism, driven by methanogenic and methanotrophic microorganisms, plays a pivotal role in the carbon cycle. As seawater intrusion and soil salinization rise due to global environmental shifts, understanding how salinity affects methane emissions, especially in deep strata, becomes imperative. Yet, insights into stratigraphic methane release under varying salinity conditions remain sparse. Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata (15-40 m depth) through in situ and microcosm simulation studies. Coastal strata, exhibiting a salinity level five times greater than terrestrial strata, manifested a 12.05% decrease in total methane production, but a staggering 687.34% surge in methane oxidation, culminating in 146.31% diminished methane emissions. Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics, impacting the methanogenic archaeal, methanotrophic archaeal, and methanotrophic bacterial communities by 16.53%, 27.25%, and 22.94%, respectively. Furthermore, microbial interactions influenced strata system methane metabolism. Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition, facilitating methane production via Methanofastidiosales. This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.
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Affiliation(s)
- Ying Qu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yi Hong
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Lizhong Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
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Jitsuno K, Hoshino T, Nishikawa Y, Kogawa M, Mineta K, Strasser M, Ikehara K, Everest J, Maeda L, Inagaki F, Takeyama H. Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere. mSphere 2024; 9:e0033723. [PMID: 38170974 PMCID: PMC10826368 DOI: 10.1128/msphere.00337-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.
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Affiliation(s)
- Kana Jitsuno
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Yohei Nishikawa
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Masato Kogawa
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Katsuhiko Mineta
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Marine Open Innovation Institute, Shizuoka, Japan
| | - Michael Strasser
- Department of Geology, University of Innsbruck, Innsbruck, Austria
| | - Ken Ikehara
- Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan
| | | | - Lena Maeda
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
| | - Fumio Inagaki
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - IODP Expedition 386 ScientistsBellanovaPieroBrunetMorganeCaiZhirongCattaneoAntonioHochmuthKatharinaHsiungKanhsiIshizawaTakashiItakiTakuyaJitsunoKanaJohnsonJoelKanamatsuToshiyaKeepMyraKiokaArataMaerzChristianMcHughCeciliaMicallefAaronMinLuoPandeyDhananjaiProustJean NoelRasburyTroyRiedingerNataschaBaoRuiSatoguchiYasufumiSawyerDerekSeibertChloeSilverMaxwellStraubSusanneVirtasaloJoonasWangYonghongWuTing-WeiZellersSarahKöllingMartinHuangJyh-Jaan StevenNagahashiYoshitaka
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Marine Open Innovation Institute, Shizuoka, Japan
- Department of Geology, University of Innsbruck, Innsbruck, Austria
- Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan
- British Geological Survey, Edinburgh, United Kingdom
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
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7
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Chen C, Deng Y, Liu Q, Lai H, Zhang C. Effects of microplastics on cold seep sediment prokaryotic communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:123008. [PMID: 38006990 DOI: 10.1016/j.envpol.2023.123008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023]
Abstract
Cold seep sediments are an important reservoir of microplastics (MPs) whose impact on the structure and function of prokaryotic community is not well understood. In this study, the impact of 0.2% and 1% (w/w) polyethylene (PE), polystyrene (PS), and polypropylene (PP) MPs on the cold seep sediment prokaryotic community was investigated in a 120-day laboratory incubation experiment. The results revealed that exposure to MPs altered sedimentary chemical properties in a type- and concentration-dependent manner. Furthermore, MPs significantly altered the structure of bacterial community, with some MPs degradation-associated bacterial phyla significantly increasing (p < 0.05). However, in the case of archaea, the changes in the structure of microbial community were less pronounced (p > 0.05). Co-occurrence network analysis revealed that the addition of MPs reduced the network complexity, while PICRUSt2 and FAPROTAX analyses suggested that 0.2% PP and 1% PS MPs had the most significant effects on the nitrogen and carbon cycles (p < 0.05). Overall, this study provides new insights into the effects of MPs on the structure and function of microbial communities in cold seep sediments.
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Affiliation(s)
- Chunlei Chen
- Institute of Marine Biology and pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Yinan Deng
- Guangzhou Marine Geological Survey, Guangzhou, 510075, Guangdong, China
| | - Qing Liu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541000, Guangxi, China
| | - Hongfei Lai
- Guangzhou Marine Geological Survey, Guangzhou, 510075, Guangdong, China
| | - Chunfang Zhang
- Institute of Marine Biology and pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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8
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Kieft B, Finke N, McLaughlin RJ, Nallan AN, Krzywinski M, Crowe SA, Hallam SJ. Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nat Commun 2023; 14:5380. [PMID: 37666802 PMCID: PMC10477309 DOI: 10.1038/s41467-023-40907-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Niko Finke
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ryan J McLaughlin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Aditi N Nallan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.
- Bradshaw Research Institute for Minerals and Mining (BRIMM), University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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9
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Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Malmstrom R, Hallam SJ. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Sci Data 2023; 10:332. [PMID: 37244914 DOI: 10.1038/s41597-023-02222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.
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Affiliation(s)
- Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Alvaro M Plominsky
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Alyse Kiesser
- School of Engineering, The University of British Columbia, Kelowna, BC, Canada
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, 4070386, Concepción, Chile
- Instituto Milenio de Oceanografía, Casilla 1313, 4070386, Concepción, Chile
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Hallam
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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10
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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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11
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Humphries NH, Thornton SF, Chen X, Bray AW, Stewart DI. Response of soil bacterial populations to application of biosolids under short-term flooding. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27424-0. [PMID: 37184786 DOI: 10.1007/s11356-023-27424-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
Biosolids are applied to agricultural land as a soil conditioner and source of crop nutrients. However, there is concern that bacteria from biosolids may become established in soils, particularly if that soil becomes water-logged. This study examined the microbial community of arable soils cultivated with barley under different applications of biosolids (0, 24t/ha, 48t/ha) in laboratory mesocosms which simulated a 10-day flood. Nutrients (P and N) and organic matter in the soil increased with application rate, but plant growth was not affected by biosolid application. The biosolids contained 10× more genetic material than the soil, with much lower bacterial diversity, yet application did not significantly change the taxonomy of the soil microbiome, with minor changes related to increased nutrients and SOM. Anaerobic conditions developed rapidly during flooding, causing shifts in the native soil microbiome. Some bacterial taxa that were highly abundant in biosolids had slightly increased relative abundance in amended soils during the flood. After flooding, soil bacterial populations returned to their pre-flood profiles, implying that the native microbial community is resilient to transient changes. The short-term changes in the microbiome of biosolid-amended soils during flooding do not appear to increase the environmental risk posed by biosolid application.
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Affiliation(s)
- Nicholas H Humphries
- School of Civil Engineering, University of Leeds, Leeds, LS2 9JT, UK.
- Currently Anglo American plc, 17 Charterhouse St, London, EC1N 6RA, UK.
| | - Steven F Thornton
- Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK
| | - Xiaohui Chen
- School of Civil Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew W Bray
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
- Currently Calder Rivers Trust, Halifax, HX1 5ER, UK
| | - Douglas I Stewart
- School of Civil Engineering, University of Leeds, Leeds, LS2 9JT, UK
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12
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Su L, Teske AP, MacGregor BJ, McKay LJ, Mendlovitz H, Albert D, Ma Z, Li J. Thermal Selection of Microbial Communities and Preservation of Microbial Function in Guaymas Basin Hydrothermal Sediments. Appl Environ Microbiol 2023; 89:e0001823. [PMID: 36847505 PMCID: PMC10057036 DOI: 10.1128/aem.00018-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, hydrothermal activity, and organic matter accumulation on the seafloor due to high sedimentation rates. In the hydrothermal sediments of Guaymas Basin, microbial community compositions and coexistence patterns change across steep gradients of temperature, potential carbon sources, and electron acceptors. Nonmetric multidimensional scaling and guanine-cytosine percentage analyses reveal that the bacterial and archaeal communities adjust compositionally to their local temperature regime. Functional inference using PICRUSt shows that microbial communities consistently maintain their predicted biogeochemical functions in different sediments. Phylogenetic profiling shows that microbial communities retain distinct sulfate-reducing, methane-oxidizing, or heterotrophic lineages within specific temperature windows. The preservation of similar biogeochemical functions across microbial lineages with different temperature adaptations stabilizes the hydrothermal microbial community in a highly dynamic environment. IMPORTANCE Hydrothermal vent sites have been widely studied to investigate novel bacteria and archaea that are adapted to these extreme environments. However, community-level analyses of hydrothermal microbial ecosystems look beyond the presence and activity of particular types of microbes and examine to what extent the entire community of bacteria and archaea is adapted to hydrothermal conditions; these include elevated temperatures, hydrothermally generated carbon sources, and inorganic electron donors and acceptors that are characteristic for hydrothermal environments. In our case study of bacterial and archaeal communities in hydrothermal sediments of Guaymas Basin, we found that sequence-inferred microbial function was maintained in differently structured bacterial and archaeal communities across different samples and thermal regimes. The resulting preservation of biogeochemical functions across thermal gradients is an important factor in explaining the consistency of the microbial core community in the dynamic sedimentary environment of Guaymas Basin.
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Affiliation(s)
- Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Andreas P. Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Barbara J. MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Earth Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Luke J. McKay
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Howard Mendlovitz
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel Albert
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zhonglin Ma
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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13
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Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment. Microorganisms 2022; 10:microorganisms10122505. [PMID: 36557758 PMCID: PMC9784657 DOI: 10.3390/microorganisms10122505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.
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14
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Xin Y, Wu N, Sun Z, Wang H, Chen Y, Xu C, Geng W, Cao H, Zhang X, Zhai B, Yan D. Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158213. [PMID: 36028040 DOI: 10.1016/j.scitotenv.2022.158213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Shallow methane/sulfate transition zones in cold seeps are hotspots to study microbially mediated geochemical cycles due to high methane fluxes. However, our knowledge about the microbial communities in remote seafloor cold seep ecosystems with different methane seepage intensity is still sparse due to the challenge for sampling and visual observations. In this work, three remotely operated vehicle (ROV) video-guided push sediment cores were sampled from cold seep fields with different methane seepage intensity (low-intensity seepage, R5-C1; moderate-intensity seepage, R6-C2; high-intensity seepage, R6-C3) at the western slope of Mid-Okinawa Trough (Mid-OT) and subjected to high throughput sequencing of 16S rRNA genes for bacteria and archaea. Vesicomyid clams and white microbial mats are visible by video at R6-C3 with methane bubbles. The high relative abundances of anaerobic methanotrophic archaea (ANME-1, -2, and -3), δ-Proteobacteriacea and Campylobacteria in R6-C3 indicated that the processes of anaerobic methane oxidation (AOM), sulfate reduction and sulfur oxidation might occur in this active seeping site. In contrast, Bathyarchaeia, Nitrosopumilales, Sphingomonadales, and Burkholderiales were enriched in bubble-free sites, which commonly involved in the degradation of organic compounds. Principal coordinate analysis showed that both bacterial and archaeal communities were clustered according to sampling sites, also indicating the impact of methane seepage intensity on microbial communities. The co-occurrence network analysis revealed that microbes at the site with high methane fluxes mainly cooperated with each other to sustain the ecosystems, whereas competition enhanced at sites with low methane fluxes. Detection of thermophiles Thermoanaerobaculia and Hydrothermarchaeota may indicate microbial transmission from nearby hydrothermal vents, suggesting potential interactions between cold seepage and hydrothermal vent ecosystems. These results expand our knowledge about the composition and distribution of bacteria and archaea with different methane seepage intensity in cold seep field at the Mid-OT, contributing to the ongoing efforts in understanding carbon cycling in the cold seep ecosystems.
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Affiliation(s)
- Youzhi Xin
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China; Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Nengyou Wu
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Zhilei Sun
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.
| | - Ye Chen
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Cuiling Xu
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Wei Geng
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Hong Cao
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Xilin Zhang
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Bin Zhai
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Dawei Yan
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
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15
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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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16
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Addition of Conductive Materials to Support Syntrophic Microorganisms in Anaerobic Digestion. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Syntrophy and interspecies electron transfer among different microbial groups occurs in anaerobic digestion, and many papers recently reported their positive effect on biogas and methane production. In this paper, we present the results on the effect of conductive material, i.e., graphene, PAC and biochar addition in 3.5 L batch experiments, analyzing the biogas production curve. A peculiar curve pattern occurred in the presence of conductive materials. Compared to the respective controls, the addition of graphene produced a biogas surplus of 33%, PAC 20% and biochar 8%. Microbial community molecular analysis showed that syntrophic microorganisms present in the inoculum were stimulated by the conductive material addition. Graphene also appears to promote an interspecies electron transfer between Geobacter sp. and ca. Methanofastidiosum. This paper contributes to the understanding of the DIET-related microbial community dynamic in the presence of graphene and PAC, which could be exploited to optimize biogas and methane production in real-scale applications.
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17
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Chen Y, Xu C, Wu N, Sun Z, Liu C, Zhen Y, Xin Y, Zhang X, Geng W, Cao H, Zhai B, Li J, Qin S, Zhou Y. Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough. Front Microbiol 2022; 13:819187. [PMID: 35495656 PMCID: PMC9048799 DOI: 10.3389/fmicb.2022.819187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Active cold seeps in the Okinawa Trough (OT) have been widely identified, but the sediment microbial communities associated with these sites are still poorly understood. Here, we investigated the distribution and biomass of the microbial communities, particularly those associated with the anaerobic oxidation of methane (AOM), in sediments from an active cold seep in the mid-Okinawa Trough. Methane-oxidizing archaea, including ANME-1a, ANME-1b, ANME-2a/b, ANME-2c, and ANME-3, were detected in the OT cold seep sediments. Vertical stratification of anaerobic methanotrophic archaea (ANME) communities was observed in the following order: ANME-3, ANME-1a, and ANME-1b. In addition, the abundance of methyl coenzyme M reductase A (mcrA) genes corresponded to high levels of dissolved iron, suggesting that methane-metabolizing archaea might participate in iron reduction coupled to methane oxidation (Fe-AOM) in the OT cold seep. Furthermore, the relative abundance of ANME-1a was strongly related to the concentration of dissolved iron, indicating that ANME-1a is a key microbial player for Fe-AOM in the OT cold seep sediments. Co-occurrence analysis revealed that methane-metabolizing microbial communities were mainly associated with heterotrophic microorganisms, such as JS1, Bathy-1, and Bathy-15.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Cuiling Xu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- *Correspondence: Nengyou Wu,
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Zhilei Sun,
| | - Changling Liu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Youzhi Xin
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xilin Zhang
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wei Geng
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hong Cao
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bin Zhai
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jing Li
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuangshuang Qin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Yucheng Zhou
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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18
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 142] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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19
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Westerholm M, Calusinska M, Dolfing J. Syntrophic propionate-oxidizing bacteria in methanogenic systems. FEMS Microbiol Rev 2022; 46:fuab057. [PMID: 34875063 PMCID: PMC8892533 DOI: 10.1093/femsre/fuab057] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/03/2021] [Indexed: 12/04/2022] Open
Abstract
The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology and metabolic capacities of syntrophic propionate-oxidizing bacteria (SPOB) is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. SPOB are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of SPOB and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes.
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Affiliation(s)
- Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCentre, Almas allé 5, SE-75007 Uppsala, Sweden
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, rue du Brill 41, L-4422 Belvaux, Luxembourg
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Wynne Jones 2.11, Ellison Place, Newcastle-upon-Tyne NE1 8QH, UK
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20
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Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
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Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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21
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Kiaghadi A, Rifai HS, Crum M, Willson RC. Longitudinal patterns in sediment type and quality during daily flow regimes and following natural hazards in an urban estuary: a Hurricane Harvey retrospective. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:7514-7531. [PMID: 34476713 DOI: 10.1007/s11356-021-15912-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Understanding the transport of sediments in urban estuaries and their effects on water quality and microorganisms is a convergent challenge that has yet to be addressed especially as a result of natural hazards that affect the hydrodynamics of estuarine systems. This study provides a holistic view of the longitudinal nature and character of sediment in an urban estuary, the Galveston Bay Estuary System (GBES), under daily and extreme flow regimes and presents the results of water and sediment sampling after Hurricane Harvey. The sediment sampling quantified total suspended sediment (TSS) concentrations, metal concentrations, and the diversity of microbial communities. The results revealed the impact of the substantial sediment loads that were transported into the GBES in terms of sediment grain type, the spatial distribution of trace metals, and the diversity of microbial communities. A measurable shift in the percentage of silt relative to historical norms was noted in the GBES after Hurricane Harvey. Not only did sediment metal data confirms this shift and its ensuing impact on metal concentrations; microbial data provided ample evidence of the effect of leaks and spills from wastewater treatment plants, superfund sites, and industrial runoff on microbial diversity. The research demonstrates the importance of understanding longitudinal sediment transport and deposition in estuarine systems under daily flow regimes but more critically, following natural hazard events to ensure sustainability and resilience of systems such as the GBES that encounter numerous acute and chronic stresses.
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Affiliation(s)
- Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Room N138, Engineering Building 1, 4726 Calhoun, Houston, TX, 77204-4003, USA
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Room N138, Engineering Building 1, 4726 Calhoun, Houston, TX, 77204-4003, USA.
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Room S222, Engineering Building 1, 4726 Calhoun, Houston, TX, 77204-4004, USA
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Room S222, Engineering Building 1, 4726 Calhoun, Houston, TX, 77204-4004, USA
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22
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Iasakov TR, Kanapatskiy TA, Toshchakov SV, Korzhenkov AA, Ulyanova MO, Pimenov NV. The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation. MARINE ENVIRONMENTAL RESEARCH 2022; 173:105533. [PMID: 34875513 DOI: 10.1016/j.marenvres.2021.105533] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/11/2021] [Accepted: 11/21/2021] [Indexed: 05/20/2023]
Abstract
Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.
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Affiliation(s)
- Timur R Iasakov
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054, Ufa, Russia.
| | - Timur A Kanapatskiy
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Leninsky prospect 33/2, 119071, Moscow, Russia
| | - Stepan V Toshchakov
- Kurchatov Center for Genome Research, NRC "Kurchatov Institute", Ac. Kurchatov square, 1, 123098, Moscow, Russia
| | - Aleksei A Korzhenkov
- Kurchatov Center for Genome Research, NRC "Kurchatov Institute", Ac. Kurchatov square, 1, 123098, Moscow, Russia
| | - Marina O Ulyanova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow, 117997, Russia; Immanuel Kant Baltic Federal University, 14, Nevskogo str., Kaliningrad, 236016, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Leninsky prospect 33/2, 119071, Moscow, Russia
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23
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Voskuhl L, Akbari A, Müller H, Pannekens M, Brusilova D, Dyksma S, Haque S, Graupner N, Dunthorn M, Meckenstock RU, Brauer VS. Indigenous microbial communities in heavy oil show a threshold response to salinity. FEMS Microbiol Ecol 2021; 97:6447536. [PMID: 34864985 PMCID: PMC8684454 DOI: 10.1093/femsec/fiab157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.
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Affiliation(s)
- Lisa Voskuhl
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Ali Akbari
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Hubert Müller
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Darya Brusilova
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.,German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Shirin Haque
- Faculty of Science and Technology, Department of Physics, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Nadine Graupner
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Micah Dunthorn
- Eukaryotic Microbiology, Natural History Museum of Oslo, P.O. Box 1172, Blindern, Oslo 0318, Norway
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Verena S Brauer
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
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24
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Wu YT, Chiang PW, Tandon K, Rogozin DY, Degermendzhy AG, Tang SL. Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia. Microb Genom 2021; 7:000712. [PMID: 34860152 PMCID: PMC8767323 DOI: 10.1099/mgen.0.000712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 10/11/2021] [Indexed: 01/18/2023] Open
Abstract
Meromictic lakes usually harbour certain prevailing anoxygenic phototrophic bacteria in their anoxic zone, such as the purple sulfur bacterium (PSB) Thiocapsa sp. LSW (hereafter LSW) in Lake Shunet, Siberia. PSBs have been suggested to play a vital role in carbon, nitrogen and sulfur cycling at the oxic-anoxic interface of stratified lakes; however, the ecological significance of PSBs in the lake remains poorly understood. In this study, we explored the potential ecological role of LSW using a deep-sequencing analysis of single-cell genomics associated with flow cytometry. An approximately 2.7 Mb draft genome was obtained based on the co-assembly of five single-cell genomes. LSW might grow photolithoautotrophically and could play putative roles not only as a carbon fixer and diazotroph, but also as a sulfate reducer/oxidizer in the lake. This study provides insights into the potential ecological role of Thiocapsa sp. in meromictic lakes.
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Affiliation(s)
- Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Denis Yu Rogozin
- Institute of Biophysics, Siberian Division of the Russian Academy of Sciences, Krasnoyarsk, Russia
- Siberian Federal University, Krasnoyarsk, Russia
| | - Andrey G. Degermendzhy
- Institute of Biophysics, Siberian Division of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
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25
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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26
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Begmatov S, Savvichev AS, Kadnikov VV, Beletsky AV, Rusanov II, Klyuvitkin AA, Novichkova EA, Mardanov AV, Pimenov NV, Ravin NV. Microbial Communities Involved in Methane, Sulfur, and Nitrogen Cycling in the Sediments of the Barents Sea. Microorganisms 2021; 9:2362. [PMID: 34835487 PMCID: PMC8625253 DOI: 10.3390/microorganisms9112362] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
A combination of physicochemical and radiotracer analysis, high-throughput sequencing of the 16S rRNA, and particulate methane monooxygenase subunit A (pmoA) genes was used to link a microbial community profile with methane, sulfur, and nitrogen cycling processes. The objects of study were surface sediments sampled at five stations in the northern part of the Barents Sea. The methane content in the upper layers (0-5 cm) ranged from 0.2 to 2.4 µM and increased with depth (16-19 cm) to 9.5 µM. The rate of methane oxidation in the oxic upper layers varied from 2 to 23 nmol CH4 L-1 day-1 and decreased to 0.3 nmol L-1 day-1 in the anoxic zone at a depth of 16-19 cm. Sulfate reduction rates were much higher, from 0.3 to 2.8 µmol L-1 day-1. In the surface sediments, ammonia-oxidizing Nitrosopumilaceae were abundant; the subsequent oxidation of nitrite to nitrate can be carried out by Nitrospira sp. Aerobic methane oxidation could be performed by uncultured deep-sea cluster 3 of gamma-proteobacterial methanotrophs. Undetectable low levels of methanogenesis were consistent with a near complete absence of methanogens. Anaerobic methane oxidation in the deeper sediments was likely performed by ANME-2a-2b and ANME-2c archaea in consortium with sulfate-reducing Desulfobacterota. Sulfide can be oxidized by nitrate-reducing Sulfurovum sp. Thus, the sulfur cycle was linked with the anaerobic oxidation of methane and the nitrogen cycle, which included the oxidation of ammonium to nitrate in the oxic zone and denitrification coupled to the oxidation of sulfide in the deeper sediments. Methane concentrations and rates of microbial biogeochemical processes in sediments in the northern part of the Barents Sea were noticeably higher than in oligotrophic areas of the Arctic Ocean, indicating that an increase in methane concentration significantly activates microbial processes.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Alexey A. Klyuvitkin
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Ekaterina A. Novichkova
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
- Il’ichev Pacific Institute of Oceanology, Far East Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
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27
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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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Liu H, Chen Y, Ye J, Xu H, Zhu Z, Xu T. Effects of different amino acids and their configurations on methane yield and biotransformation of intermediate metabolites during anaerobic digestion. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 296:113152. [PMID: 34217942 DOI: 10.1016/j.jenvman.2021.113152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) comprises a series of biochemical reactions, with methane as one of the target products. Amino acids (AAs) are important molecular and primary intermediate products when protein is the main component of organic waste/wastewater. The L (levorotatory, left-handed)-configuration is natural for AAs, while D (dextrorotatory, right-handed) -AAs also widely exist in the natural environment and can be generated by racemization. However, the effects and underlying mechanisms of natural AAs and their enantiomers on the methane yield and the underlying mechanisms remain unclear. In this study, the effects of certain widespread L-AAs and their enantiomers on two-stage AD and the mechanisms therein were investigated. The AAs enantiomers showed variable or even opposite effects on different processes. The methane yield from a model monosaccharide (glucose) decreased by 57% with D-leucine addition. The butyrate generation and the methane yield from propionate were sensitive to the AA configuration and were inhibited by D-leucine by 80% and 61.8%, respectively, with D-leucine addition, while the volatile fatty acids concentration was slightly increased with the addition of L-leucine. The related mechanisms were further investigated in terms of key enzymes and microbial communities. The addition of D-Leucine decreased acetic acid production from homoacetogens by 30.2% due to the inhibition of key enzymes involved in hydrogen generation and consumption. The transform of butyryl CoA to butyryl phosphate was the rate-limiting step, with the related enzyme (phosphotransbutylase) was inhibited by D-leucine. Furthermore, the bacteria related to butyric acid generation and organic matter degradation were inhibited by D-leucine, while the methanogenic archaea remained stable irrespective of leucine addition. The effect of D-AAs on microorganisms is related to the type of sludge. In this study, the methanogenetic seed sludge was granular and did not dissociate after treatment; however, the D-AAs could trigger biofilm disassembly and reduce the stability of the sludge floc. The study provides a novel method for regulating AD by adding specific AAs with L or D configuration.
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Affiliation(s)
- Hui Liu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China.
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Jianfeng Ye
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China.
| | - Huiting Xu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China
| | - Zhihao Zhu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China
| | - Tianchen Xu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China
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Gallardo-Altamirano MJ, Maza-Márquez P, Montemurro N, Pérez S, Rodelas B, Osorio F, Pozo C. Insights into the removal of pharmaceutically active compounds from sewage sludge by two-stage mesophilic anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147869. [PMID: 34051504 DOI: 10.1016/j.scitotenv.2021.147869] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/22/2021] [Accepted: 05/14/2021] [Indexed: 05/23/2023]
Abstract
The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two antihypertensives/diuretics, three lipid regulators and four psychiatric drugs) were evaluated in a pilot-scale two-stage mesophilic anaerobic digestion (MAD) system treating thickened sewage sludge from a pilot-scale A2O™ wastewater treatment plant (WWTP) which was fed with wastewater from the pre-treatment of the full-scale WWTP Murcia Este (Murcia, Spain). The MAD system was long-term operated using two different sets of sludge retention times (SRTs) for the acidogenic (AcD) and methanogenic (MD) digesters (phase I, 2 and 12 days; and phase II, 5 and 24 days, in AcD and MD, respectively). Quantitative PCR (qPCR) and Illumina MiSeq sequencing were used to estimate the absolute abundance of Bacteria, Archaea, and Fungi and investigate the structure, diversity and population dynamics of their communities in the AcD and MD effluents. The extension of the SRT from 12 (phase I) to 24 days (phase II) in the MD was significantly linked with an improved removal of carbamazepine, clarithromycin, codeine, gemfibrozil, ibuprofen, lorazepam, and propranolol. The absolute abundances of total Bacteria and Archaea were higher in the MD regardless of the phase, while the diversity of bacterial and archaeal communities was lower in phase II, in both digesters. Non-metric multidimensional scaling (MDS) plots showed strong negative correlations among phyla Proteobacteria and Firmicutes and between genera Methanosaeta and Methanosarcina throughout the full experimental period. Strong positive correlations were revealed between the relative abundances of Methanospirillum and Methanoculleus and the methanogenesis performance parameters (volatile solids removal, CH4 recovery rate and %CH4 in the biogas), which were also related to longer SRT. The REs of several PhACs (naproxen, ketoprofen, ofloxacin, fenofibrate, trimethoprim, and atenolol) correlated positively (r > 0.75) with the relative abundances of specific bacterial and archaeal groups, suggesting their participation in biodegradation/biotransformation pathways.
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Affiliation(s)
- M J Gallardo-Altamirano
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Civil Engineering, University of Granada, Granada, Spain
| | - P Maza-Márquez
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
| | - N Montemurro
- Water, Environmental and Food Chemistry (ENFOCHEM), Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - S Pérez
- Water, Environmental and Food Chemistry (ENFOCHEM), Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - B Rodelas
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain.
| | - F Osorio
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Civil Engineering, University of Granada, Granada, Spain
| | - C Pozo
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
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Ramírez GA, Mara P, Sehein T, Wegener G, Chambers CR, Joye SB, Peterson RN, Philippe A, Burgaud G, Edgcomb VP, Teske AP. Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California. PLoS One 2021; 16:e0256321. [PMID: 34495995 PMCID: PMC8425543 DOI: 10.1371/journal.pone.0256321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/03/2021] [Indexed: 01/04/2023] Open
Abstract
The flanking regions of Guaymas Basin, a young marginal rift basin located in the Gulf of California, are covered with thick sediment layers that are hydrothermally altered due to magmatic intrusions. To explore environmental controls on microbial community structure in this complex environment, we analyzed site- and depth-related patterns of microbial community composition (bacteria, archaea, and fungi) in hydrothermally influenced sediments with different thermal conditions, geochemical regimes, and extent of microbial mats. We compared communities in hot hydrothermal sediments (75-100°C at ~40 cm depth) covered by orange-pigmented Beggiatoaceae mats in the Cathedral Hill area, temperate sediments (25-30°C at ~40 cm depth) covered by yellow sulfur precipitates and filamentous sulfur oxidizers at the Aceto Balsamico location, hot sediments (>115°C at ~40 cm depth) with orange-pigmented mats surrounded by yellow and white mats at the Marker 14 location, and background, non-hydrothermal sediments (3.8°C at ~45 cm depth) overlain with ambient seawater. Whereas bacterial and archaeal communities are clearly structured by site-specific in-situ thermal gradients and geochemical conditions, fungal communities are generally structured by sediment depth. Unexpectedly, chytrid sequence biosignatures are ubiquitous in surficial sediments whereas deeper sediments contain diverse yeasts and filamentous fungi. In correlation analyses across different sites and sediment depths, fungal phylotypes correlate to each other to a much greater degree than Bacteria and Archaea do to each other or to fungi, further substantiating that site-specific in-situ thermal gradients and geochemical conditions that control bacteria and archaea do not extend to fungi.
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Affiliation(s)
- Gustavo A. Ramírez
- Department of Marine Sciences, University of North Carolina at Chapel Hill, NC, United States of America
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States of America
- * E-mail:
| | - Paraskevi Mara
- Geology and Geophysics Dept., Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Taylor Sehein
- Geology and Geophysics Dept., Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Germany
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Christopher R. Chambers
- Department of Marine Sciences, University of North Carolina at Chapel Hill, NC, United States of America
| | - Samantha B. Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - Richard N. Peterson
- School of Coastal and Marine Systems Science, Coastal Carolina University, Conway, SC, United States of America
| | - Aurélie Philippe
- Univ. Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Gaëtan Burgaud
- Univ. Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Virginia P. Edgcomb
- Geology and Geophysics Dept., Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Andreas P. Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, NC, United States of America
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Pal S, Dutta A, Sarkar J, Roy A, Sar P, Kazy SK. Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50074-50093. [PMID: 33945094 DOI: 10.1007/s11356-021-13744-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.
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Affiliation(s)
- Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
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Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment. Commun Biol 2021; 4:1006. [PMID: 34433861 PMCID: PMC8387401 DOI: 10.1038/s42003-021-02507-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below. Lagostina et al. show that relative abundances of Bacteria and Archaea in sediments of Guaymas Basin, Gulf of California, are controlled by temperature, while energy flux explains microbial community structure at the phylum-level and below. Hot diffusion-dominated and energy-depleted sediments are dominated by taxa with relatives in cold subseafloor sediments, while hot sediments with high energy supply from fluid seepage are dominated by taxa also found at hydrothermal vents and in hot springs.
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33
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Coskun ÖK, Vuillemin A, Schubotz F, Klein F, Sichel SE, Eisenreich W, Orsi WD. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. ISME JOURNAL 2021; 16:257-271. [PMID: 34312482 PMCID: PMC8692406 DOI: 10.1038/s41396-021-01066-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frieder Klein
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Susanna E Sichel
- Departamento de Geologia e Geofísica/LAGEMAR-Universidade Federal Fluminense-Brazil, Niterói, RJ, Brazil
| | - Wolfgang Eisenreich
- Department of Chemistry, Bavarian NMR Center-Structural Membrane Biochemistry, Technische Universität München, Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany. .,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.
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34
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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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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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Mu DS, Ouyang Y, Chen GJ, Du ZJ. Strategies for culturing active/dormant marine microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:121-131. [PMID: 37073338 PMCID: PMC10077298 DOI: 10.1007/s42995-020-00053-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/18/2020] [Indexed: 05/03/2023]
Abstract
Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK USA
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
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37
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Rojas CA, De Santiago Torio A, Park S, Bosak T, Klepac-Ceraj V. Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake. Front Microbiol 2021; 12:620424. [PMID: 33967973 PMCID: PMC8103211 DOI: 10.3389/fmicb.2021.620424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
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Affiliation(s)
- Connie A. Rojas
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
- Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, United States
| | - Ana De Santiago Torio
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Serry Park
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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38
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Aromokeye DA, Oni OE, Tebben J, Yin X, Richter-Heitmann T, Wendt J, Nimzyk R, Littmann S, Tienken D, Kulkarni AC, Henkel S, Hinrichs KU, Elvert M, Harder T, Kasten S, Friedrich MW. Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures. THE ISME JOURNAL 2021; 15:965-980. [PMID: 33154547 PMCID: PMC8115662 DOI: 10.1038/s41396-020-00824-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/09/2020] [Accepted: 10/22/2020] [Indexed: 01/29/2023]
Abstract
Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe2+ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.
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Affiliation(s)
- David A. Aromokeye
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Oluwatobi E. Oni
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Jan Tebben
- grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Xiuran Yin
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Sten Littmann
- grid.419529.20000 0004 0491 3210Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daniela Tienken
- grid.419529.20000 0004 0491 3210Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ajinkya C. Kulkarni
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Susann Henkel
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Kai-Uwe Hinrichs
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Tilmann Harder
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sabine Kasten
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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39
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Lewis WH, Tahon G, Geesink P, Sousa DZ, Ettema TJG. Innovations to culturing the uncultured microbial majority. Nat Rev Microbiol 2021; 19:225-240. [PMID: 33093661 DOI: 10.1038/s41579-020-00458-8] [Citation(s) in RCA: 209] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
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Affiliation(s)
- William H Lewis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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40
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Ao T, Xie Z, Zhou P, Liu X, Wan L, Li D. Comparison of microbial community structures between mesophilic and thermophilic anaerobic digestion of vegetable waste. Bioprocess Biosyst Eng 2021; 44:1201-1214. [PMID: 33591430 DOI: 10.1007/s00449-021-02519-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
The anaerobic digestion performance correlates with the functional microbial community. Mesophilic and thermophilic digestions of vegetable waste were conducted, and dynamics of the microbial community were investigated. The mesophilic and thermophilic collapsed stages occurred at organic loading rates of 1.5 and 2.0 g VS/(L d) due to the accumulation of volatile fatty acids with final concentrations of 2276 and 6476 mg/L, respectively. A high concentration of volatile fatty acids caused the severe inhibition of methanogens, which finally led to the imbalance between acetogenesis and methanogenesis. The mesophilic digestion exhibited a higher microbial diversity and richness than the thermophilic digestion. Syntrophic acetate-oxidizing coupled with hydrogenotrophic methanogenesis was the dominant pathway in the thermophilic stable system, and acetoclastic methanogenesis in the mesophilic stable system. The dominant acidogens, syntrophus, and methanogens were unclassified_f__Anaerolineaceae (8.68%), Candidatus_Cloacamonas (19.70%), Methanosaeta (6.10%), and Methanosarcina (4.08%) in the mesophilic stable stage, and Anaerobaculum (12.59%), Syntrophaceticus (4.84%), Methanosarcina (30.58%), and Methanothermobacter (3.17%) in thermophilic stable stage. Spirochaetae and Thermotogae phyla were the characteristic microorganisms in the mesophilic and thermophilic collapsed stages, respectively. These findings provided valuable information for the deep understanding of the difference of the microbial community and methane-producing mechanism between mesophilic and thermophilic digestion of vegetable waste.
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Affiliation(s)
- Tianjie Ao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhijie Xie
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Zhou
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaofeng Liu
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Liping Wan
- Jiangxi Zhenghe Ecological Agriculture Co., Ltd, Xinyu, 338008, China.
| | - Dong Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Jiangxi Zhenghe Ecological Agriculture Co., Ltd, Xinyu, 338008, China.
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41
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Teske A, Wegener G, Chanton JP, White D, MacGregor B, Hoer D, de Beer D, Zhuang G, Saxton MA, Joye SB, Lizarralde D, Soule SA, Ruff SE. Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin. Front Microbiol 2021; 12:633649. [PMID: 33643265 PMCID: PMC7906980 DOI: 10.3389/fmicb.2021.633649] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/12/2021] [Indexed: 01/04/2023] Open
Abstract
Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.
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Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gunter Wegener
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jeffrey P Chanton
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, United States
| | - Dylan White
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Barbara MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Earth and Environmental Sciences, University of Minnesota, St. Paul, MI, United States
| | - Daniel Hoer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States.,United States Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Dirk de Beer
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Guangchao Zhuang
- Frontiers Science Centre for Deep Ocean Multispheres and Earth System (FDOMES)/Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Ocean University of China, Qingdao, China.,Department of Marine Sciences, University of Georgia, Athens, GA, United States
| | - Matthew A Saxton
- Department of Marine Sciences, University of Georgia, Athens, GA, United States.,Department of Biological Sciences, Miami University, Oxford, OH, United States
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, United States
| | - Daniel Lizarralde
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - S Adam Soule
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - S Emil Ruff
- Marine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United States.,Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United States
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42
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Zhang T, Xiao X, Chen S, Zhao J, Chen Z, Feng J, Liang Q, Phelps TJ, Zhang C. Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea. Front Microbiol 2021; 11:612135. [PMID: 33391242 PMCID: PMC7772427 DOI: 10.3389/fmicb.2020.612135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.
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Affiliation(s)
- Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Songze Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Jing Zhao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongheng Chen
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Junxi Feng
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China
| | - Qianyong Liang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Tommy J Phelps
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
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43
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van Teeseling MCF, Jogler C. Cultivation of elusive microbes unearthed exciting biology. Nat Commun 2021; 12:75. [PMID: 33398002 PMCID: PMC7782747 DOI: 10.1038/s41467-020-20393-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Many newly-discovered microbial phyla have been studied solely by cultivation-independent techniques such as metagenomics. Much of their biology thus remains elusive, because the organisms have not yet been isolated and grown in the lab. Katayama et al. lift the curtain on some intriguing biology by cultivating and studying bacteria from the elusive OP9 phylum (Atribacterota).
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Affiliation(s)
| | - Christian Jogler
- Institute of Microbiology, Department of Microbial Interactions, Friedrich Schiller University Jena, Jena, Germany.
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44
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Isolation of a member of the candidate phylum 'Atribacteria' reveals a unique cell membrane structure. Nat Commun 2020; 11:6381. [PMID: 33318506 PMCID: PMC7736352 DOI: 10.1038/s41467-020-20149-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/04/2020] [Indexed: 11/11/2022] Open
Abstract
A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov. A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, the authors isolate a member of the ubiquitous, yet-to-be-cultivated bacterial phylum ‘Candidatus Atribacteria’ that has an intracytoplasmic membrane apparently surrounding the nucleoid.
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45
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Thomas C, Francke A, Vogel H, Wagner B, Ariztegui D. Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka. Microorganisms 2020; 8:microorganisms8111736. [PMID: 33167482 PMCID: PMC7716225 DOI: 10.3390/microorganisms8111736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 01/05/2023] Open
Abstract
Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid.
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Affiliation(s)
- Camille Thomas
- Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland;
- Correspondence:
| | - Alexander Francke
- Department of Earth Sciences, University of Adelaide, 5005 Adelaide, Australia;
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3012 Bern, Switzerland;
| | - Bernd Wagner
- Institute of Geology and Mineralogy, University of Cologne, 50674 Cologne, Germany;
| | - Daniel Ariztegui
- Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland;
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46
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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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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48
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Abstract
How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum "Candidatus Atribacteria," which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. "Ca. Atribacteria" dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing "Ca. Atribacteria" also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD+ Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor "Ca Atribacteria," as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the "Ca Atribacteria" can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments.IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum "Candidatus Atribacteria" dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that "Ca Atribacteria" can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.
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49
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Theuerl S, Klang J, Hülsemann B, Mächtig T, Hassa J. Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants. Microorganisms 2020; 8:microorganisms8081169. [PMID: 32752188 PMCID: PMC7464807 DOI: 10.3390/microorganisms8081169] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022] Open
Abstract
Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L-1 and 193 mg L-1 or volatile fatty acid concentrations of 0.75 g L-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.
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Affiliation(s)
- Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
- Correspondence: ; Tel.: +49-331-5699-900
| | - Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
| | - Benedikt Hülsemann
- University of Hohenheim, The State Institute of Agricultural Engineering and Bioenergy, 70599 Stuttgart, Germany;
| | - Torsten Mächtig
- Kiel University, Institute of Agricultural Engineering, 24098 Kiel, Germany;
| | - Julia Hassa
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, 33615 Bielefeld, Germany
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50
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Dyksma S, Jansen L, Gallert C. Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste. MICROBIOME 2020; 8:105. [PMID: 32620171 PMCID: PMC7334858 DOI: 10.1186/s40168-020-00862-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate oxidation is an important pathway for methane production, knowledge about the SAOB is still very limited. RESULTS A metabolic reconstruction of metagenome-assembled genomes (MAGs) from a thermophilic solid state biowaste digester covered the basic functions of the biogas microbial community. Firmicutes was the most abundant phylum in the metagenome (53%) harboring species that take place in various functions ranging from the hydrolysis of polymers to syntrophic acetate oxidation. The Wood-Ljungdahl pathway for syntrophic acetate oxidation and corresponding genes for energy conservation were identified in a Dethiobacteraceae MAG that is phylogenetically related to known SAOB. 16S rRNA gene amplicon sequencing and enrichment cultivation consistently identified the uncultured Dethiobacteraceae together with Syntrophaceticus, Tepidanaerobacter, and unclassified Clostridia as members of a potential acetate-oxidizing core community in nine full-scare digesters, whereas acetoclastic methanogens were barely detected. CONCLUSIONS Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.
| | - Lukas Jansen
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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