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Kim S, Lee C, Kim J, Young Kim J. Feasibility of thermal hydrolysis pretreatment to reduce hydraulic retention time of anaerobic digestion of cattle manure. BIORESOURCE TECHNOLOGY 2023:129308. [PMID: 37311528 DOI: 10.1016/j.biortech.2023.129308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023]
Abstract
In this study, we investigated the potential of thermal hydrolysis pretreatment (THP) to reduce the hydraulic retention times (HRTs) in the anaerobic digestion (AD) of cattle manure (CM). The AD with THP (THP AD) outperformed the control AD by over 1.4 times in terms of methane yield and volatile solid removal, even under the same HRT conditions. Remarkably, even when the THP AD was operated with an HRT of 13.2 d, it performed better than the control AD operated with an HRT of 36.0 d. In THP AD, there was a shift in the dominant archaeal genus responsible for methane generation from Methanogranum (at HRT of 36.0 - 13.2 d) to Methanosaeta (at HRT of 8.0 d). However, decreasing HRT, and applying THP resulted in reduced stability, accompanied by increased inhibitory compounds, and changes in the microbial community. Further confirmation is required to assess the long-term stability of THP AD.
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Affiliation(s)
- Seunghwan Kim
- Department of Civil & Environmental Engineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Changmin Lee
- Department of Civil & Environmental Engineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Junhyeon Kim
- Department of Civil & Environmental Engineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jae Young Kim
- Department of Civil & Environmental Engineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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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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Li B, Wang H, Lai A, Xue J, Wu Q, Yu C, Xie K, Mao Z, Li H, Xing P, Wu QL. Hydrogenotrophic pathway dominates methanogenesis along the river-estuary continuum of the Yangtze River. WATER RESEARCH 2023; 240:120096. [PMID: 37229838 DOI: 10.1016/j.watres.2023.120096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
Rivers are considered as an important source of methane (CH4) to the atmosphere, but our understanding for the methanogenic pathway in rivers and its linkage with CH4 emission is very limited. Here, we investigated the diffusive flux of CH4 and its stable carbon isotope signature (δ13C-CH4) along the river-estuary continuum of the Yangtze River. The diffusive CH4 flux was estimated to 27.9 ± 11.4 μmol/m2/d and 36.5 ± 24.4 μmol/m2/d in wet season and dry season, respectively. The δ13C-CH4 values were generally lower than -60‰, with the fractionation factor (αc) higher than 1.055 and the isotope separation factor (εc) ranged from 55 to 100. In situ microbial composition showed that hydrogenotrophic methanogens accounts for over 70% of the total reads. Moreover, the incubation test showed that the headspace CH4 concentration by adding CO2/H2 to the sediment was orders of magnitude higher than that by adding trimethylamine and sodium acetate. These results jointly verified the river-estuary continuum is a minor CH4 source and dominated by hydrogenotrophic pathway. Based on the methanogenic pathway here and previous reported data in the same region, the historical variation of diffusive CH4 flux was calculated and results showed that CH4 emission has reduced 82.5% since the construction of Three Gorges Dam (TGD). Our study verified the dominant methanogenic pathway in river ecosystems and clarified the effect and mechanism of dam construction on riverine CH4 emission.
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Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hongwei Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Anxing Lai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jingya Xue
- School of Geographical Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qiong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Yu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ke Xie
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China.
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54
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Frolov EN, Elcheninov AG, Gololobova AV, Toshchakov SV, Novikov AA, Lebedinsky AV, Kublanov IV. Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium. Front Microbiol 2023; 14:1185739. [PMID: 37250036 PMCID: PMC10213532 DOI: 10.3389/fmicb.2023.1185739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
One of the important current issues of bioenergetics is the establishment of the thermodynamic limits of life. There is still no final understanding of what is the minimum value of the energy yield of a reaction that is sufficient to be used by an organism (the so-called "biological quantum of energy"). A reasonable model for determination of the minimal energy yield would be microorganisms capable of living on low-energy substrates, such as acetogenic prokaryotes. The most prominent metabolic feature of acetogens is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates, which is hardly competitive in environments. Most probably, that is why only facultative autotrophic acetogens have been known so far. Here, we describe the first obligately autotrophic acetogenic bacterium Aceticella autotrophica gen. nov., sp. nov., strain 3443-3AcT. Phylogenetically, the new genus falls into a monophyletic group of heterotrophic bacteria of the genera Thermoanaerobacterium, Thermoanaerobacter, and Caldanaerobacter (hereinafter referred to as TTC group), where the sole acetogenic representative has so far been the facultatively autotrophic Thermoanaerobacter kivui. A. autotrophica and T. kivui both are acetogens employing energy-converting hydrogenase (Ech-acetogens) that are likely to have inherited the acetogenesis capacity vertically from common ancestor. However, their acetogenic machineries have undergone different adjustments by gene replacements due to horizontal gene transfers from different donors. Obligate autotrophy of A. autotrophica is associated with the lack of many sugar transport systems and carbohydrate catabolism enzymes that are present in other TTC group representatives, including T. kivui.
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Affiliation(s)
- Evgenii N. Frolov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G. Elcheninov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra V. Gololobova
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Andrei A. Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, Moscow, Russia
| | - Alexander V. Lebedinsky
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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55
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Liu X, Lee C, Kim JY. Comparison of mesophilic and thermophilic anaerobic digestions of thermal hydrolysis pretreated swine manure: Process performance, microbial communities and energy balance. J Environ Sci (China) 2023; 126:222-233. [PMID: 36503751 DOI: 10.1016/j.jes.2022.03.032] [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: 12/22/2021] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/17/2023]
Abstract
Anaerobic digestion (AD) of swine manure (SM) commonly shows low biogas output and unsatisfactory economic performance. In this study, thermophilic AD (TAD, 50 ± 1 °C) was combined with thermal hydrolysis pretreatment (THP, 170 °C/10 bar), to investigate its potential for maximizing biogas yield, securing successful digestion and microbial diversity, as well as improving energy balance. Four lab-scale continuously stirred tank reactors were operated for 300 days and compared with each other, i.e., reactor 1 (raw SM fed in mesophilic AD: RSM-MAD), reactor 2 (THP-treated SM fed in MAD: TSM-MAD), reactor 3 (RSM-TAD), and reactor 4 (TSM-TAD). The results showed that THP was efficient to increase methane production of SM, TSM-TAD mode led to the highest methane yield (129.8 ± 40.5 mL-CH4/g-VS/day) among the tests (p < 0.05). Although TAD was more likely to induce free ammonia (> 700 mg/L) or volatile fatty acids (> 6000 mg/L) accumulation compared with MAD in start-up phase, TSM-TAD treatment mode behaved a sustainable digestion process in a long-term operation. For TSM-TAD scenario, higher Shannon-Weaver (3.873) and lower Simpson index (0.061) indicated this mode ensured and enlarged the diversity of bacteria communities. Phylum Bathyarchaeota was dominant (59.3%-90.0%) in archaea community, followed by Euryarchaeota in the four reactors. RSM-MAD treatment mode achieved the highest energy output (4.65 GJ/day), TSM-TAD was less effective (-17.38 GJ/day) due to increased energy demands. Thus improving the energetic efficiency of THP units is recommended for the development of TSM-TAD treatment mode.
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Affiliation(s)
- Xiaohui Liu
- Department of Civil and Environmental Engineering, Seoul National University, Seoul 08826, Korea
| | - Changmin Lee
- Department of Civil and Environmental Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Kim
- Department of Civil and Environmental Engineering, Seoul National University, Seoul 08826, Korea.
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56
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Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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57
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Kim C, Staver LW, Chen X, Bulseco A, Cornwell JC, Malkin SY. Microbial Community Succession Along a Chronosequence in Constructed Salt Marsh Soils. MICROBIAL ECOLOGY 2023; 85:931-950. [PMID: 36764950 DOI: 10.1007/s00248-023-02189-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/02/2023] [Indexed: 05/04/2023]
Abstract
In this study, we examined the succession of soil microbial communities across a chronosequence of newly constructed salt marshes constructed primarily of fine-grained dredge material, using 16S rRNA amplicon sequences. Alpha diversity in the subsurface horizons was initially low and increased to reference levels within 3 years of marsh construction, while alpha diversity in the newly accumulating organic matter-rich surface soils was initially high and remained unchanged. Microbial community succession was fastest in the surface horizon (~ 24 years to reference equivalency) and became progressively slower with depth in the subsurface horizons (~ 30-67 years). Random forest linear regression analysis was used to identify important taxa driving the trajectories toward reference conditions. In the parent material, putative sulfate-reducers (Desulfobacterota), methanogens (Crenarchaeota, especially Methanosaeta), and fermenters (Chloroflexi and Clostridia) increased over time, suggesting an enrichment of these metabolisms over time, similar to natural marshes. Concurrently in the surface soils, the relative abundances of putative methane-, methyl-, and sulfide oxidizers, especially among Gammaproteobacteria, increased over time, suggesting the co-development of sulfide and methane removal metabolisms in marsh soils. Finally, we observed that the surface soil communities at one of the marshes did not follow the trajectory of the others, exhibiting a greater relative abundance of anaerobic taxa. Uniquely in this dataset, this marsh was developing signs of excessive inundation stress in terms of vegetation coverage and soil geochemistry. Therefore, we suggest that soil microbial community structure may be effective bioindicators of salt marsh inundation and are worthy of further targeted investigation.
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Affiliation(s)
- Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Lorie W Staver
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Xuan Chen
- Department of Biology, Salisbury University, Salisbury, MD, USA
| | | | - Jeffrey C Cornwell
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA.
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Dang Q, Zhao X, Li Y, Xi B. Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain. ENVIRONMENTAL RESEARCH 2023; 222:115185. [PMID: 36586711 DOI: 10.1016/j.envres.2022.115185] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Landfill is the third highest contributor to anthropogenic methane (CH4) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH4 production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH4+ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.
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Affiliation(s)
- Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yanping Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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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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60
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Seidel L, Sachpazidou V, Ketzer M, Hylander S, Forsman A, Dopson M. Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments. Front Microbiol 2023; 14:1099445. [PMID: 37065140 PMCID: PMC10090409 DOI: 10.3389/fmicb.2023.1099445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.
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Cummings S, Ardor Bellucci LM, Seabrook S, Raineault NA, McPhail KL, Thurber AR. Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific. PeerJ 2023; 11:e15119. [PMID: 37009161 PMCID: PMC10064993 DOI: 10.7717/peerj.15119] [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: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.
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Affiliation(s)
- Susie Cummings
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States of America
| | - Lila M. Ardor Bellucci
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Sarah Seabrook
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | | | - Kerry L. McPhail
- College of Pharmacy, Oregon State University, Corvallis, OR, United States of America
| | - Andrew R. Thurber
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States of America
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States of America
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García-Maldonado JQ, Latisnere-Barragán H, Escobar-Zepeda A, Cadena S, Ramírez-Arenas PJ, Vázquez-Juárez R, Rojas-Contreras M, López-Cortés A. Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities. Microorganisms 2023; 11:microorganisms11030812. [PMID: 36985385 PMCID: PMC10059902 DOI: 10.3390/microorganisms11030812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023] Open
Abstract
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.
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Affiliation(s)
- José Q García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida 97310, Yucatán, Mexico
| | - Hever Latisnere-Barragán
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | | | - Santiago Cadena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Patricia J Ramírez-Arenas
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Maurilia Rojas-Contreras
- Departamento de Agronomía, Universidad Autónoma de Baja California Sur, La Paz 23080, Baja California Sur, Mexico
| | - Alejandro López-Cortés
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
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Lynes MM, Krukenberg V, Jay ZJ, Kohtz AJ, Gobrogge CA, Spietz RL, Hatzenpichler R. Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments. ISME COMMUNICATIONS 2023; 3:22. [PMID: 36949220 PMCID: PMC10033731 DOI: 10.1038/s43705-023-00225-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Abstract
Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.
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Affiliation(s)
- Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | | | - Rachel L Spietz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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64
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Acetoclastic archaea adaptation under increasing temperature in lake sediments and wetland soils from Alaska. Polar Biol 2023. [DOI: 10.1007/s00300-023-03120-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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65
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Shekarriz E, Chen J, Xu Z, Liu H. Disentangling the Functional Role of Fungi in Cold Seep Sediment. Microbiol Spectr 2023; 11:e0197822. [PMID: 36912690 PMCID: PMC10100914 DOI: 10.1128/spectrum.01978-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/22/2022] [Indexed: 03/14/2023] Open
Abstract
Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.
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Affiliation(s)
- Erfan Shekarriz
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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66
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Zhang C, Fang YX, Yin X, Lai H, Kuang Z, Zhang T, Xu XP, Wegener G, Wang JH, Dong X. The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules. MICROBIOME 2023; 11:37. [PMID: 36864529 PMCID: PMC9979476 DOI: 10.1186/s40168-023-01482-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization. RESULTS Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons. CONCLUSIONS These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yun-Xin Fang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hongfei Lai
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Zenggui Kuang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Tianxueyu Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xiang-Po Xu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Qu YN, Rao YZ, Qi YL, Li YX, Li A, Palmer M, Hedlund BP, Shu WS, Evans PN, Nie GX, Hua ZS, Li WJ. Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum. Cell Rep 2023; 42:112158. [PMID: 36827180 DOI: 10.1016/j.celrep.2023.112158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/27/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.
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Affiliation(s)
- Yan-Ni Qu
- 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, PR China
| | - Yang-Zhi Rao
- 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, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, 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-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - 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, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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Liu H, Cai X, Luo K, Chen S, Su M, Lu J. Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology. Microbiol Spectr 2023; 11:e0421022. [PMID: 36802161 PMCID: PMC10100816 DOI: 10.1128/spectrum.04210-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xueyu Cai
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Kunwen Luo
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Sihan Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou Guangdong, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou Guangdong, China
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China
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de la Garza Varela A, Aguirre-Macedo ML, García-Maldonado JQ. Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area. Microorganisms 2023; 11:microorganisms11020494. [PMID: 36838457 PMCID: PMC9963909 DOI: 10.3390/microorganisms11020494] [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: 01/25/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented.
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Gómez-Acata ES, Teutli C, Falcón LI, García-Maldonado JQ, Prieto-Davó A, Yanez-Montalvo A, Cadena S, Chiappa-Carrara X, Herrera-Silveira JA. Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico. PeerJ 2023; 11:e14587. [PMID: 36785710 PMCID: PMC9921989 DOI: 10.7717/peerj.14587] [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: 10/20/2021] [Accepted: 11/28/2022] [Indexed: 02/11/2023] Open
Abstract
Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.
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Affiliation(s)
| | - Claudia Teutli
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México
| | | | - José Q. García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | | | | | - Santiago Cadena
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Xavier Chiappa-Carrara
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Unidad Multidisciplinaria de Docencia e Investigación, Unidad Sisal, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Jorge A. Herrera-Silveira
- Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México,Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
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71
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Yu G, Chen J, Wang G, Chen H, Huang J, Li Y, Wang W, Song F, Ma Y, Wang Q, Wang M, Ling T, Shu Z, Sun J, Yu Z. Recent advances in constructed wetlands methane reduction: Mechanisms and methods. Front Microbiol 2023; 14:1106332. [PMID: 36819020 PMCID: PMC9936987 DOI: 10.3389/fmicb.2023.1106332] [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: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Constructed wetlands (CWs) are artificial systems that use natural processes to treat wastewater containing organic pollutants. This approach has been widely applied in both developing and developed countries worldwide, providing a cost-effective method for industrial wastewater treatment and the improvement of environmental water quality. However, due to the large organic carbon inputs, CWs is produced in varying amounts of CH4 and have the potential to become an important contributor to global climate change. Subsequently, research on the mitigation of CH4 emissions by CWs is key to achieving sustainable, low-carbon dependency wastewater treatment systems. This review evaluates the current research on CH4 emissions from CWs through bibliometric analysis, summarizing the reported mechanisms of CH4 generation, transfer and oxidation in CWs. Furthermore, the important environmental factors driving CH4 generation in CW systems are summarized, including: temperature, water table position, oxidation reduction potential, and the effects of CW characteristics such as wetland type, plant species composition, substrate type, CW-coupled microbial fuel cell, oxygen supply, available carbon source, and salinity. This review provides guidance and novel perspectives for sustainable and effective CW management, as well as for future studies on CH4 reduction in CWs.
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Affiliation(s)
- Guanlong Yu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Jundan Chen
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Guoliang Wang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Huifang Chen
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Jiajun Huang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Yifu Li
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Wenming Wang
- Technology Center, Hunan Pilot Yanghu Reclaimed Water Co., Ltd., Changsha, China,*Correspondence: Wenming Wang,
| | - Fengming Song
- Technology Center, Hunan Pilot Yanghu Reclaimed Water Co., Ltd., Changsha, China
| | - Yuanjun Ma
- Technology Department, Hunan Rongantai Ecological Technology Co., Ltd., Changsha, China
| | - Qi Wang
- Technology and Information Department, CCCC-TDC Environmental Engineering Co., Ltd., Tianjin, China
| | - Miaomiao Wang
- Technology and Information Department, CCCC-TDC Environmental Engineering Co., Ltd., Tianjin, China
| | - Tao Ling
- Engineering Department, China Railway Wuju Group the First Engineering Co., Ltd., Changsha, China
| | - Zhilai Shu
- Engineering Department, China Railway Wuju Group the First Engineering Co., Ltd., Changsha, China
| | - Julong Sun
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Zhi Yu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
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72
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Morgan-Lang C, Hallam SJ. A Guide to Gene-Centric Analysis Using TreeSAPP. Curr Protoc 2023; 3:e671. [PMID: 36801973 DOI: 10.1002/cpz1.671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree. Here, we provide a set of protocols that link the various analysis modules in TreeSAPP into a coherent process that both informs and directs the user experience. This workflow, initiated from a collection of candidate reference sequences, progresses through construction and refinement of a reference package to marker identification and normalized relative abundance calculations for homologous sequences in metagenomic and metatranscriptomic datasets. The alpha subunit of methyl-coenzyme M reductase (McrA) involved in biological methane cycling is presented as a use case given its dual role as a phylogenetic and functional marker gene driving an ecologically relevant process. These protocols fill several gaps in prior TreeSAPP documentation and provide best practices for reference package construction and refinement, including manual curation steps from trusted sources in support of reproducible gene-centric analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating reference packages Support Protocol 1: Installing TreeSAPP Support Protocol 2: Annotating traits within a phylogenetic context Basic Protocol 2: Updating reference packages Basic Protocol 3: Calculating relative abundance of genes in metagenomic and metatranscriptomic datasets.
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Affiliation(s)
- Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
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Xiang X, Wang H, Man B, Xu Y, Gong L, Tian W, Yang H. Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China. MICROBIAL ECOLOGY 2023; 85:557-571. [PMID: 35332366 DOI: 10.1007/s00248-022-01990-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.
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Affiliation(s)
- Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Linfeng Gong
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
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74
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Zhao J, Chakrabarti S, Chambers R, Weisenhorn P, Travieso R, Stumpf S, Standen E, Briceno H, Troxler T, Gaiser E, Kominoski J, Dhillon B, Martens-Habbena W. Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159865. [PMID: 36461566 DOI: 10.1016/j.scitotenv.2022.159865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA
| | - Randolph Chambers
- College of William and Mary, W.M. Keck Environmental Field Laboratory, P.O. Box 8795, Williamsburg, VA, USA
| | | | - Rafael Travieso
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Sandro Stumpf
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Emily Standen
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Henry Briceno
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - Tiffany Troxler
- Department of Earth and Environment and Sea Level Solutions Center in the Institute of Environment, Florida International University, Miami, FL, USA
| | - Evelyn Gaiser
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - John Kominoski
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - Braham Dhillon
- Fort Lauderdale Research and Education Center and Department of Plant Pathology, University of Florida, Davie, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA.
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75
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Chen R, Bao Y, Zhang Y. A Review of Biogenic Coalbed Methane Experimental Studies in China. Microorganisms 2023; 11:microorganisms11020304. [PMID: 36838269 PMCID: PMC9959753 DOI: 10.3390/microorganisms11020304] [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: 11/15/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Biogenic coalbed methane (CBM) is an important alternative energy that can help achieve carbon neutrality. Accordingly, its exploration and development have become a research hotspot in the field of fossil energy. In this review, the latest detection technologies for and experimental research on biogenic CBM in China in recent decades are summarized. The factors influencing the generation of biogenic CBM and the identification method of biogenic CBM are systematically analyzed. The technologies to detect biogas and the research methods to study microbial diversity are summarized. The literature shows that biogenic CBM is easily produced in the presence of highly abundant organic matter of low maturity, and the organic matter reaching a certain thickness can compensate for the limitation of biogenic CBM gas production due to the small abundance of organic matter to a certain extent. Biogenic CBM production could be increased in an environment with low salinity, medium alkalinity, and rich Fe2+ and Ni2+ sources. Furthermore, biogenic CBM can be identified by considering three aspects: (1) the presence of gas composition indicators; (2) the content of heavy hydrocarbon; and (3) variation in the abundance of biomarkers. In recent years, research methods to study the microbial community and diversity of CBM-producing environments in China have mainly included 16S rRNA gene library, fluorescence in situ hybridization, and high-throughput sequencing, and the dominant microorganisms have been determined in various basins in China. The results of numerous studies show that the dominant bacterial phyla are commonly Firmicutes and Proteobacteria, while the archaeal fraction mainly includes Methanoculleus, Methanobacterium, Methanocorpusculum, and Methanothrix. This review summarizes and discusses the advances in biogenic CBM production and the associated microbial community in order to promote further development of coal biotransformation and CO2 bio-utilization to meet energy demands under carbon neutrality.
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Affiliation(s)
- Run Chen
- Jiangsu Key Laboratory of Coal-Based Greenhouse Gas Control and Utilization, Carbon Neutrality Institute, CUMT, Xuzhou 221008, China
- Key Laboratory of Coalbed Methane Resource & Reservoir Formation History, Ministry of Education, School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221008, China
- Correspondence: ; Tel.: +86-158-0520-3840
| | - Yunxia Bao
- Jiangsu Key Laboratory of Coal-Based Greenhouse Gas Control and Utilization, Carbon Neutrality Institute, CUMT, Xuzhou 221008, China
- Key Laboratory of Coalbed Methane Resource & Reservoir Formation History, Ministry of Education, School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221008, China
| | - Yajun Zhang
- Jiangsu Key Laboratory of Coal-Based Greenhouse Gas Control and Utilization, Carbon Neutrality Institute, CUMT, Xuzhou 221008, China
- Key Laboratory of Coalbed Methane Resource & Reservoir Formation History, Ministry of Education, School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221008, China
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76
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Jiang F, Li Q, Wang S, Shen T, Wang H, Wang A, Xu D, Yuan L, Lei L, Chen R, Yang B, Deng Y, Fan W. Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing. Front Microbiol 2023; 13:1095497. [PMID: 36699587 PMCID: PMC9869026 DOI: 10.3389/fmicb.2022.1095497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced. Results In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes. Conclusion High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.
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Affiliation(s)
- Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Qiang Li
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Ting Shen
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Rong Chen
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yu Deng
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China,*Correspondence: Yu Deng, ; Wei Fan,
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China,*Correspondence: Yu Deng, ; Wei Fan,
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77
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Roth F, Broman E, Sun X, Bonaglia S, Nascimento F, Prytherch J, Brüchert V, Lundevall Zara M, Brunberg M, Geibel MC, Humborg C, Norkko A. Methane emissions offset atmospheric carbon dioxide uptake in coastal macroalgae, mixed vegetation and sediment ecosystems. Nat Commun 2023; 14:42. [PMID: 36596795 PMCID: PMC9810657 DOI: 10.1038/s41467-022-35673-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Abstract
Coastal ecosystems can efficiently remove carbon dioxide (CO2) from the atmosphere and are thus promoted for nature-based climate change mitigation. Natural methane (CH4) emissions from these ecosystems may counterbalance atmospheric CO2 uptake. Still, knowledge of mechanisms sustaining such CH4 emissions and their contribution to net radiative forcing remains scarce for globally prevalent macroalgae, mixed vegetation, and surrounding depositional sediment habitats. Here we show that these habitats emit CH4 in the range of 0.1 - 2.9 mg CH4 m-2 d-1 to the atmosphere, revealing in situ CH4 emissions from macroalgae that were sustained by divergent methanogenic archaea in anoxic microsites. Over an annual cycle, CO2-equivalent CH4 emissions offset 28 and 35% of the carbon sink capacity attributed to atmospheric CO2 uptake in the macroalgae and mixed vegetation habitats, respectively, and augment net CO2 release of unvegetated sediments by 57%. Accounting for CH4 alongside CO2 sea-air fluxes and identifying the mechanisms controlling these emissions is crucial to constrain the potential of coastal ecosystems as net atmospheric carbon sinks and develop informed climate mitigation strategies.
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Affiliation(s)
- Florian Roth
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden. .,Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland.
| | - Elias Broman
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Xiaole Sun
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Francisco Nascimento
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - John Prytherch
- Department of Meteorology, Stockholm University, Stockholm, Sweden
| | - Volker Brüchert
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden.,Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | | | - Märta Brunberg
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland
| | - Marc C Geibel
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Christoph Humborg
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland
| | - Alf Norkko
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland
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78
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Chen C, Chen S, Wang B. A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples. Front Microbiol 2023; 14:1035944. [PMID: 37125200 PMCID: PMC10140447 DOI: 10.3389/fmicb.2023.1035944] [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: 10/12/2022] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.
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Affiliation(s)
- Chuizhe Chen
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shu Chen
- Medical Laboratory Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Bo Wang
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Bo Wang,
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79
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Karavaeva V, Sousa FL. Modular structure of complex II: An evolutionary perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148916. [PMID: 36084748 DOI: 10.1016/j.bbabio.2022.148916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022]
Abstract
Succinate dehydrogenases (SDHs) and fumarate reductases (FRDs) catalyse the interconversion of succinate and fumarate, a reaction highly conserved in all domains of life. The current classification of SDH/FRDs is based on the structure of the membrane anchor subunits and their cofactors. It is, however, unknown whether this classification would hold in the context of evolution. In this work, a large-scale comparative genomic analysis of complex II addresses the questions of its taxonomic distribution and phylogeny. Our findings report that for types C, D, and F, structural classification and phylogeny go hand in hand, while for types A, B and E the situation is more complex, highlighting the possibility for their classification into subgroups. Based on these findings, we proposed a revised version of the evolutionary scenario for these enzymes in which a primordial soluble module, corresponding to the cytoplasmatic subunits, would give rise to the current diversity via several independent membrane anchor attachment events.
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Affiliation(s)
- Val Karavaeva
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Filipa L Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
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80
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Boyd ES, Spietz RL, Kour M, Colman DR. A naturalist perspective of microbiology: Examples from methanogenic archaea. Environ Microbiol 2023; 25:184-198. [PMID: 36367391 DOI: 10.1111/1462-2920.16285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Manjinder Kour
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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81
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Tadrent N, Dedeine F, Hervé V. SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes. F1000Res 2022; 11:1522. [PMID: 36875992 PMCID: PMC9978240 DOI: 10.12688/f1000research.128091.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.
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Affiliation(s)
- Nachida Tadrent
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Tours, 37200, France
| | - Franck Dedeine
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Tours, 37200, France
| | - Vincent Hervé
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Tours, 37200, France
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, 91120, France
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82
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Tadrent N, Dedeine F, Hervé V. SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes. F1000Res 2022; 11:1522. [PMID: 36875992 PMCID: PMC9978240 DOI: 10.12688/f1000research.128091.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2022] [Indexed: 01/05/2024] Open
Abstract
Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.
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Affiliation(s)
- Nachida Tadrent
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Tours, 37200, France
| | - Franck Dedeine
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Tours, 37200, France
| | - Vincent Hervé
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Tours, 37200, France
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, 91120, France
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83
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Zhang X, Zhang C, Liu Y, Zhang R, Li M. Non-negligible roles of archaea in coastal carbon biogeochemical cycling. Trends Microbiol 2022; 31:586-600. [PMID: 36567186 DOI: 10.1016/j.tim.2022.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022]
Abstract
Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.
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Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Rui Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.
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84
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Ross DE, Lipus D, Gulliver D. Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms. Environ Microbiol 2022; 24:5984-5997. [PMID: 36251278 DOI: 10.1111/1462-2920.16251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/13/2022] [Indexed: 01/12/2023]
Abstract
Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.
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Affiliation(s)
- Daniel E Ross
- Research and Innovation Center, National Energy Technology Laboratory, Pittsburgh, Pennsylvania, USA.,Leidos Research Support Team (LRST), NETL Support Contractor, Pittsburgh, Pennsylvania, USA
| | - Daniel Lipus
- Research and Innovation Center, National Energy Technology Laboratory, Pittsburgh, Pennsylvania, USA.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, United States.,Section Geomicrobiology, GFZ Geoforschungszentrum Potsdam, Potsdam, Brandenburg, Germany
| | - Djuna Gulliver
- Research and Innovation Center, National Energy Technology Laboratory, Pittsburgh, Pennsylvania, USA
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85
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Zhu Y, Chen X, Yang Y, Xie S. Impacts of cyanobacterial biomass and nitrate nitrogen on methanogens in eutrophic lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157570. [PMID: 35905968 DOI: 10.1016/j.scitotenv.2022.157570] [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: 03/13/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Methanogenesis is a key process in carbon cycling in lacustrine ecosystems. Knowledge of the methanogenic pathway is important for creating mechanistic models as well as predicting methane emissions. Due to low concentrations of methyl substrates in freshwater lakes, the proportion of methylotrophic methanogenesis is believed to be negligible in such environments. However, the high abundance of methylotrophic methanogens previously detected in Dianchi Lake suggests that methylotrophic methanogenesis may be underestimated in eutrophic lakes, whereas their influencing factors and mechanisms are not yet clear. In this study, the effects of cyanobacteria biomass (CB) or/and nitrate nitrogen on methanogenesis, especially methylotrophic pathway, in eutrophic lakes were investigated using microcosm simulation experiments combined with chemical analysis and high-throughput sequencing techniques. The results showed that either CB or nitrate nitrogen had significant effects on methane flux, the archaeal diversity and community structure of methanogens. Functional prediction, together with the result of chemical analysis, revealed that CB could promote methylotrophic methanogenesis by providing methyl organic substrates, while nitrate nitrogen increased the relative abundance of obligate methylotrophic methanogens by competitively inhibiting the other two methanogenic pathways. In eutrophic lake where both CB and nitrate present at a high concentration, methylotrophic methanogenesis could play a much more important role than previously believed.
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Affiliation(s)
- Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510535, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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86
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Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ. Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling. SCIENCE ADVANCES 2022; 8:eabm9651. [PMID: 36332026 PMCID: PMC9635834 DOI: 10.1126/sciadv.abm9651] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/19/2022] [Indexed: 05/19/2023]
Abstract
Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.
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Affiliation(s)
- Panagiotis S. Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Corresponding author.
| | - George E. Kolyfetis
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Research Center One Health Ruhr, Research Alliance Ruhr, Environmental Metagenomics, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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87
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Sorokin DY, Merkel AY, Abbas B. Ecology of Methanonatronarchaeia. Environ Microbiol 2022; 24:5217-5229. [PMID: 35726892 PMCID: PMC9796771 DOI: 10.1111/1462-2920.16108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda lakes, while the knowledge about the latter is limited to a few mixed cultures with anaerobic haloarchaea. To get more insight into the distribution and ecophysiology of this enigmatic group of extremophilic methanogens, potential activity tests and enrichment cultivation with different substrates and at different conditions were performed with anaerobic sediment slurries from various hypersaline lakes in Russia. Methanonatronarchaeum proliferated exclusively in hypersaline soda lake samples mostly at elevated temperature, while at mesophilic conditions it coexisted with the extremely salt-tolerant methylotroph Methanosalsum natronophilum. Methanonatronarchaeum was also able to serve as a methylotrophic or hydrogenotrophic partner in several thermophilic enrichment cultures with fermentative bacteria. Ca. Methanohalarchaeum did not proliferate at mesophilic conditions and at thermophilic conditions it competed with extremely halophilic and moderately thermophilic methylotroph Methanohalobium, which it outcompeted at a combination of elevated temperature and methyl-reducing conditions. Overall, the results demonstrated that Methanonatronarchaeia are specialized extremophiles specifically proliferating in conditions of elevated temperature coupled with extreme salinity and simultaneous availability of a wide range of C1 -methylated compounds and H2 /formate.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of BiotechnologyRussian Academy of SciencesMoscowRussia,Department of BiotechnologyDelft University of BiotechnologyDelftThe Netherlands
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Centre of BiotechnologyRussian Academy of SciencesMoscowRussia
| | - Ben Abbas
- Department of BiotechnologyDelft University of BiotechnologyDelftThe Netherlands
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88
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Zou D, Li H, Du P, Wang B, Lin H, Liu H, Chen J, Li M. Distinct Features of Sedimentary Archaeal Communities in Hypoxia and Non-Hypoxia Regions off the Changjiang River Estuary. Microbiol Spectr 2022; 10:e0194722. [PMID: 36066619 PMCID: PMC9602602 DOI: 10.1128/spectrum.01947-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
Water hypoxia (DO < 2 mg/L) is a growing global environmental concern that has the potential to significantly influence not only the aquatic ecosystem but also the benthic sedimentary ecosystem. The Changjiang River Estuary hypoxia, classified as one of the world's largest seasonal hypoxic water basins, has been reported to be expanding rapidly in recent decades. However, the microbial community dynamics and responses to this water hypoxia are still unclear. In this study, we examined the abundance, community composition, and distribution of sedimentary archaea, one important component of microbial communities in the Changjiang River Estuary and the East China Sea (ECS). Our results indicated that Thaumarchaeota and Bathyarchaeota were predominant archaeal groups in these research areas, with their 16S rRNA gene abundance ranged from 8.55 × 106 to 7.51 × 108 and 3.18 × 105 to 1.11 × 108 copies/g, respectively. The sedimentary archaeal community was mainly influenced by DO, together with the concentration of ammonium, nitrate, and sulfide. In addition, distinct differences in the archaeal community's composition, abundance, and driving factors were discovered between samples from hypoxia and non-hypoxia stations. Furtherly, microbial networks suggest various microbes leading the different activities in hypoxic and normoxic environments. Bathyarchaeota and Thermoprofundales were "key stone" archaeal members of the low-DO network, whereas Thaumarchaeota constituted a significant component of the high-DO network. Our results provide a clear picture of the sedimentary archaeal community in coastal hypoxia zones and indicates potential distinctions of archaea in hypoxia and non-hypoxia environments, including ecological niches and metabolic functions. IMPORTANCE In this study, the sedimentary archaeal community composition and abundance were detailed revealed and quantified based on 16S rRNA genes off the Changjiang River Estuary. We found that the community composition was distinct between hypoxia and non-hypoxia regions, while Thaumarchaeota and Bathyarchaeota dominated in non-hypoxia and hypoxia samples, respectively. In hypoxia regions, the sedimentary archaea were mainly affected by salinity, ammonium, and nitrate, whereas total organic carbon, total nitrogen, and sulfide were major influencing factors in non-hypoxia regions. The distinct microbial network may suggest the niche difference of archaeal community under various oxygen level.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Bin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hua Lin
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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89
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Lv Z, Ding J, Wang H, Wan J, Chen Y, Liang L, Yu T, Wang Y, Wang F. Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria. BIOLOGY 2022; 11:biology11101514. [PMID: 36290418 PMCID: PMC9598358 DOI: 10.3390/biology11101514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
Abstract
Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we isolated, pure cultured, and completely sequenced a single methanogen strain DL9LZB001, from a hot spring at Tengchong in Southwest China. DL9LZB001 is a thermophilic and hydrogenotrophic methanogen with an optimum growth temperature of 65 °C. It is a putative novel species, which has been named Methanothermobacter tengchongensis-a Class I methanogen belonging to the class Methanobacteria. Comparative genomic and ancestral analyses indicate that the class Methanobacteria originated in a hyperthermal environment and then evolved to adapt to ambient temperatures. This study extends the understanding of methanogens living in geothermal niches, as well as the origin and evolutionary history of these organisms in ecosystems with different temperatures.
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Affiliation(s)
- Zhenbo Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaxin Ding
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Heng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaxin Wan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence:
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
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90
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Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. THE ISME JOURNAL 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
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Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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91
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Sun Q, Zhao C, Qiu Q, Guo S, Zhang Y, Mu H. Oyster shell waste as potential co-substrate for enhancing methanogenesis of starch wastewater at low inoculation ratio. BIORESOURCE TECHNOLOGY 2022; 361:127689. [PMID: 35901863 DOI: 10.1016/j.biortech.2022.127689] [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: 05/11/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the effect of oyster shells on the methanogenesis of starch wastewater subjected to over-acidification (pH < 4.5) at low inoculum/substrate ratios, and revealed that oyster shells could be used as co-substrates for methane production. The methane yield was improved by approximate 86-folds with optimal dose when compared with that in control. Oyster shells conditioning synchronously improved the acidogenesis and hydrogenotrophic methanogenesis steps, resulting in high methane production. These improvements were attributed to the fact that the oyster shells served as the neutralizing reagent and buffered the sharp pH drop. Carbon dioxide was also released during this process, which was subsequently converted into methane and contributed 17% of the total methane yield. Furthermore, some spheroid and rod microcolonies were observed on the surfaces of the oyster shells. Along with the remarkable enrichment of acetotrophic and methylotrophic methanogens, these microbes benefitted the successful methanogenesis of starch wastewater.
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Affiliation(s)
- Qingyu Sun
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Chunhui Zhao
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Qi Qiu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Shouxing Guo
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Yongfang Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Hui Mu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China.
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92
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Kohtz AJ, Jay ZJ, Lynes MM, Krukenberg V, Hatzenpichler R. Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME COMMUNICATIONS 2022; 2:86. [PMID: 37938354 PMCID: PMC9723716 DOI: 10.1038/s43705-022-00175-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2023]
Abstract
Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.
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Affiliation(s)
- Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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93
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Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle. Arch Microbiol 2022; 204:608. [PMID: 36075991 DOI: 10.1007/s00203-022-03187-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/02/2022]
Abstract
Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.
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94
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Chen W, Yu X, Huang J, Zhao W, Ju J, Ye J, Qin H, Long Y. The synergy of Fe(III) and NO 2- drives the anaerobic oxidation of methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155766. [PMID: 35533860 DOI: 10.1016/j.scitotenv.2022.155766] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/06/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
The anaerobic oxidation of methane (AOM) driven by NO2- or Fe(III) alone was limited by slow electron delivery and ineffective enrichment of microbes. The flexible coupling between Fe(III) and NO2- potentially cooperated to accelerate AOM. One negative control was fed CH4 and NO2-, and four treatment reactors were supplemented with CH4, NO2- and ferric citrate (FC)/ferric chloride (FCH)/ chelate iron (FCI)/ferric hydroxide (FH) and were anaerobically operated for 1200 days to verify the synergy and promicrobial roles of Fe(III) and NO2- in improving AOM. The changes in gas and ion profiles were observed in the reactors, and microbial development was studied using 16S rRNA gene sequencing with the Illumina platform. The results indicated that the combined Fe(III) and NO2- treatment improved AOM, and their synergy followed the order of FC > FCI > FCH > FH. The biochemical reaction of Fe3+ with NO2- and its secondary process accelerated electron transfer to microbial cells and subsequently enhanced AOM in the reactors. The total organic carbon (TOC) content, NH4+ content, NO3- content, and pH value altered the dominant bacteria the most in the FC reactor, FCI, FCH, and FH groups, respectively. Several dominant bacterial species were enriched, whereas only two archaea were highly concentrated in the FC and FCI groups. Only bacteria were detected in the FCH group, and archaea contributed substantially to the FH group. These findings contribute to an improved understanding of the interactions among nitrogen, iron and CH4 that are paramount to accelerating the process of AOM for engineering applications.
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Affiliation(s)
- Weiqi Chen
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xiuling Yu
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Juan Huang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wurong Zhao
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinwei Ju
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huaming Qin
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan Long
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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95
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Venturini AM, Dias NMS, Gontijo JB, Yoshiura CA, Paula FS, Meyer KM, Nakamura FM, da França AG, Borges CD, Barlow J, Berenguer E, Nüsslein K, Rodrigues JLM, Bohannan BJM, Tsai SM. Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. ENVIRONMENTAL RESEARCH 2022; 212:113139. [PMID: 35337832 DOI: 10.1016/j.envres.2022.113139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, 08544, USA.
| | - Naissa M S Dias
- Environmental Biogeochemistry Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, 05508-120, Brazil
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA; Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Fernanda M Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Erika Berenguer
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK; Environmental Change Institute, University of Oxford, Oxford, OX1 3QY, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, 95616, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
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96
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Campbell BC, Greenfield P, Gong S, Barnhart EP, Midgley DJ, Paulsen IT, George SC. Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences. Environ Microbiol 2022; 24:4065-4078. [PMID: 35437913 PMCID: PMC9790511 DOI: 10.1111/1462-2920.16014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/30/2022]
Abstract
The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.
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Affiliation(s)
- Bronwyn C. Campbell
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia,School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Paul Greenfield
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia,School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Se Gong
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia
| | | | - David J. Midgley
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia
| | - Ian T. Paulsen
- School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Simon C. George
- School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
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97
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Alves KJ, Pylro VS, Nakayama CR, Vital VG, Taketani RG, Santos DG, Mazza Rodrigues JL, Mui TS, Andreote FD. Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change. Microbiol Res 2022; 265:127178. [DOI: 10.1016/j.micres.2022.127178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 08/02/2021] [Accepted: 08/24/2022] [Indexed: 10/14/2022]
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98
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Yu W, Li J, Ma X, Lv T, Wang L, Li J, Liu C. Community structure and function of epiphytic bacteria attached to three submerged macrophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155546. [PMID: 35489510 DOI: 10.1016/j.scitotenv.2022.155546] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
In aquatic ecosystems, large amounts of epiphytic bacteria living on the leaf surfaces of submerged macrophytes play important roles in affecting plant growth and biogeochemical cycling. The restoration of different submerged macrophytes has been considered an effective measure to improve eutrophic lakes. However, the community ecology of epiphytic bacteria is far from well understood for different submerged macrophytes. In this study, we used quantitative PCR, 16S rRNA gene high-throughput sequencing and functional prediction analysis to explore the structure and function of epiphytic bacteria in an aquatic ecosystem recovered by three submerged macrophytes (Hydrilla verticillata, Vallisneria natans and Potamogeton maackianus) during two growth periods. The results showed that the community compositions and functions of epiphytic bacterial communities on the submerged macrophyte hosts were different from those of the planktonic bacterial communities in the surrounding water. The alpha diversity of the epiphytic bacterial community was significantly higher in October than in July, and the community compositions and functions differed significantly in July and October. Among the three submerged macrophytes, the structures and functions of the epiphytic bacterial community exhibited obvious differences, and some specific taxa were enriched on the biofilms of the three plants. The alpha diversity and the abundance of functions related to nitrogen and phosphorus transformation were higher in the epiphytic bacteria of P. maackianus. In summary, these results provide clues for understanding the distribution and formation mechanisms of epiphytic bacteria on submerged macrophyte leaves and their roles in freshwater ecosystems.
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Affiliation(s)
- Weicheng Yu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Jiahe Li
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Xiaowen Ma
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Tian Lv
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Ligong Wang
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Jiaru Li
- College of Life Science, Wuhan University, Wuhan, PR China
| | - Chunhua Liu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China.
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99
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The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis. Antonie Van Leeuwenhoek 2022; 115:1229-1244. [PMID: 35947314 PMCID: PMC9534799 DOI: 10.1007/s10482-022-01767-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022]
Abstract
Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable. Here we present the analysis of nineteen draft genomes recovered from a sediment core metagenome of the Polar Fox Lagoon, a thermokarst lake located on the Bykovsky Peninsula in Siberia, Russia, which is connected to the brackish Tiksi Bay. We show that the Bathyarchaeota in this lake are predominantly peptide degraders, producing reduced ferredoxin from the fermentation of peptides, while degradation pathways for plant-derived polymers were found to be incomplete. Several genomes encoded the potential for acetogenesis through the Wood-Ljungdahl pathway, but methanogenesis was determined to be unlikely due to the lack of genes encoding the key enzyme in methanogenesis, methyl-CoM reductase. Many genomes lacked a clear pathway for recycling reduced ferredoxin. Hydrogen metabolism was also hardly found: one type 4e [NiFe] hydrogenase was annotated in a single MAG and no [FeFe] hydrogenases were detected. Little evidence was found for syntrophy through formate or direct interspecies electron transfer, leaving a significant gap in our understanding of the metabolism of these organisms.
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Wegener G, Laso-Pérez R, Orphan VJ, Boetius A. Anaerobic Degradation of Alkanes by Marine Archaea. Annu Rev Microbiol 2022; 76:553-577. [PMID: 35917471 DOI: 10.1146/annurev-micro-111021-045911] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
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