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Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments. Microbiol Spectr 2022; 10:e0035222. [PMID: 35647693 PMCID: PMC9241837 DOI: 10.1128/spectrum.00352-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs. IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.
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102
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Chen X, Sheng Y, Wang G, Guo L, Zhang H, Zhang F, Yang T, Huang D, Han X, Zhou L. Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water. WATER RESEARCH 2022; 215:118277. [PMID: 35305487 DOI: 10.1016/j.watres.2022.118277] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO42-/rCl-), coefficient of sodium and chloride (rNa+/rCl-), and coefficient of magnesium and chloride (rMg2+/rCl-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO3-, Fe3+, and SO42-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.
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Affiliation(s)
- Xianglong Chen
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Yizhi Sheng
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China; Department of Geology and Environmental Earth Science, Miami University, OH 45056, USA.
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China.
| | - Liang Guo
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an 710054, PR China
| | - Hongyu Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Fan Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Tao Yang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Dandan Huang
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang 330013, PR China
| | - Xu Han
- Geology Institute of China Chemical Geology and Mine Bureau, Beijing, PR China
| | - Ling Zhou
- Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
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103
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Gendron A, Allen KD. Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Front Microbiol 2022; 13:867342. [PMID: 35547147 PMCID: PMC9081873 DOI: 10.3389/fmicb.2022.867342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 12/02/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
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Affiliation(s)
- Aleksei Gendron
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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104
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Lemaire ON, Wagner T. A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea. Biochemistry 2022; 61:805-821. [PMID: 35500274 PMCID: PMC9118554 DOI: 10.1021/acs.biochem.2c00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Microbial anaerobic
oxidation of alkanes intrigues the scientific
community by way of its impact on the global carbon cycle, and its
biotechnological applications. Archaea are proposed to degrade short-
and long-chain alkanes to CO2 by reversing methanogenesis,
a theoretically reversible process. The pathway would start with alkane
activation, an endergonic step catalyzed by methyl-coenzyme M reductase
(MCR) homologues that would generate alkyl-thiols carried by coenzyme
M. While the methane-generating MCR found in methanogens has been
well characterized, the enzymatic activity of the putative alkane-fixing
counterparts has not been validated so far. Such an absence of biochemical
investigations contrasts with the current explosion of metagenomics
data, which draws new potential alkane-oxidizing pathways in various
archaeal phyla. Therefore, validating the physiological function of
these putative alkane-fixing machines and investigating how their
structures, catalytic mechanisms, and cofactors vary depending on
the targeted alkane have become urgent needs. The first structural
insights into the methane- and ethane-capturing MCRs highlighted unsuspected
differences and proposed some explanations for their substrate specificity.
This Perspective reviews the current physiological, biochemical, and
structural knowledge of alkyl-CoM reductases and offers fresh ideas
about the expected mechanistic and chemical differences among members
of this broad family. We conclude with the challenges of the investigation
of these particular enzymes, which might one day generate biofuels
for our modern society.
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Affiliation(s)
- Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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105
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Chen Y, Xu C, Wu N, Sun Z, Liu C, Zhen Y, Xin Y, Zhang X, Geng W, Cao H, Zhai B, Li J, Qin S, Zhou Y. Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough. Front Microbiol 2022; 13:819187. [PMID: 35495656 PMCID: PMC9048799 DOI: 10.3389/fmicb.2022.819187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Active cold seeps in the Okinawa Trough (OT) have been widely identified, but the sediment microbial communities associated with these sites are still poorly understood. Here, we investigated the distribution and biomass of the microbial communities, particularly those associated with the anaerobic oxidation of methane (AOM), in sediments from an active cold seep in the mid-Okinawa Trough. Methane-oxidizing archaea, including ANME-1a, ANME-1b, ANME-2a/b, ANME-2c, and ANME-3, were detected in the OT cold seep sediments. Vertical stratification of anaerobic methanotrophic archaea (ANME) communities was observed in the following order: ANME-3, ANME-1a, and ANME-1b. In addition, the abundance of methyl coenzyme M reductase A (mcrA) genes corresponded to high levels of dissolved iron, suggesting that methane-metabolizing archaea might participate in iron reduction coupled to methane oxidation (Fe-AOM) in the OT cold seep. Furthermore, the relative abundance of ANME-1a was strongly related to the concentration of dissolved iron, indicating that ANME-1a is a key microbial player for Fe-AOM in the OT cold seep sediments. Co-occurrence analysis revealed that methane-metabolizing microbial communities were mainly associated with heterotrophic microorganisms, such as JS1, Bathy-1, and Bathy-15.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Cuiling Xu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- *Correspondence: Nengyou Wu,
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Zhilei Sun,
| | - Changling Liu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Youzhi Xin
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xilin Zhang
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wei Geng
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hong Cao
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bin Zhai
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jing Li
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuangshuang Qin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Yucheng Zhou
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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106
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Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. THE ISME JOURNAL 2022; 16:915-926. [PMID: 34689183 PMCID: PMC8941128 DOI: 10.1038/s41396-021-01139-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
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107
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Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. Proc Natl Acad Sci U S A 2022; 119:2106628119. [PMID: 35165204 PMCID: PMC8892325 DOI: 10.1073/pnas.2106628119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 11/18/2022] Open
Abstract
Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m-2 ⋅ d-1 Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.
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108
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Hester ER, Vaksmaa A, Valè G, Monaco S, Jetten MSM, Lüke C. Effect of water management on microbial diversity and composition in an Italian rice field system. FEMS Microbiol Ecol 2022; 98:6529233. [PMID: 35170720 PMCID: PMC8924702 DOI: 10.1093/femsec/fiac018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.
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Affiliation(s)
- Eric R Hester
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Giampiero Valè
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy.,DiSIT-Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Stefano Monaco
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
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109
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Gavrilov SN, Potapov EG, Prokof’eva MI, Klyukina AA, Merkel AY, Maslov AA, Zavarzina DG. Diversity of Novel Uncultured Prokaryotes in Microbial Communities of the Yessentukskoye Underground Mineral Water Deposit. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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110
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Dang W, Li M, Fu W, Zhu K, Liu H, Yuan J, Gao W, Chen G, Wang Z. Effects of different N-acyl-serine lactone signaling molecules on the performance of anaerobic granular sludge. RSC Adv 2022; 12:5439-5446. [PMID: 35425575 PMCID: PMC8981730 DOI: 10.1039/d1ra07885b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/01/2022] [Indexed: 12/30/2022] Open
Abstract
Exogenous addition of acyl-homoserine lactone (AHL) signaling molecules can improve or inhibit the methane production performance of anaerobic granular sludge (AnGS) by quorum sensing (QS). To explore the specific effect of AHLs on AnGS, 2 μM of signal molecules were added to the reactor and we analyzed their effects on AnGS biodiversity, extracellular polymeric substance (EPS), specific methanogenic activity (SMA) and chemical oxygen demand (COD) removal rate of AnGS. The results indicated that the four types of AHLs improve the COD removal rate, SMA and organic composition of AnGS. The addition of N-(β-ketocaproyl)-dl-homoserine lactone (3O-C6-HSL) yielded the greatest increase in methanogenic activity, reaching a maximum of 30.83%. The four types of AHLs stimulate the secretion of EPS in AnGS by group sensing regulation. The addition of N-hexanoyl-l-homoserine lactone (C6-HSL), N-octanoyl-dl-lactone (C8-HSL) and 3O-C6-HSL induced the enrichment of Actinobacteria. Thus, the process of hydrolysis and acidification of AnGS is accelerated. The addition of N-butyryl-dl-homoserine lactone (C4-HSL), C6-HSL and 3O-C6-HSL promote the potential methanogenic metabolic pathway of AnGS. The addition of all AHLs directly or indirectly enhanced the methane metabolism pathway of sludge and improved the specific methane generation activity of AnGS. These results are expected to provide preliminary research data for enhancing the methane production efficiency of reactors and enriching the biological activity of AnGS. Adding trace signal molecule (AHLs) to the reactor can promote the growth of methanogens and increase the microbial abundance of AnGS. This technology may be applied to enhance methanogenesis of AnGS or restore microbial activity of calcified anaerobic granular sludge.![]()
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Affiliation(s)
- Wenhao Dang
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China
| | - Meiling Li
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China
| | - Wencai Fu
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China
| | - Kaili Zhu
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China
| | - Hui Liu
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China
| | - Jinxia Yuan
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China .,College of Environmental Science and Forestry, State University of New York Syracuse USA
| | - Wenhua Gao
- School of Light Industry and Engineering, South China University of Technology Guangzhou 510006 China
| | - Guoning Chen
- Guangxi Bossco Environmental Protection Technology Co., Ltd Nanning 530007 China
| | - Zhiwei Wang
- Key Laboratory of Clean Pulp & Papermaking and Pollution Control of Guangxi Province, College of Light Industry and Food Engineering, Guangxi University Nanning 530004 China .,Guangxi Bossco Environmental Protection Technology Co., Ltd Nanning 530007 China
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111
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Khan A, Akbar S, Okonkwo V, Smith C, Khan S, Ali Shah A, Adnan F, Zeeshan Ijaz U, Ahmed S, Badshah M. Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor. BIORESOURCE TECHNOLOGY 2022; 345:126219. [PMID: 34813923 DOI: 10.1016/j.biortech.2021.126219] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
During in situ biogas up-gradation by supplying hydrogen from an external source and enrichment of hydrogenotrophic methanogens, high pressure of H2 negatively affects hydrolytic and fermentative activities. To overcome this problem, the present study aimed to enrich the hydrogenotrophic methanogens by optimization of various parameters associated with gas recirculation along-with hydrogen supply from the external source. Due to recirculation of gases and supplied hydrogen, methane generation was two-fold higher in the optimal condition than in conventional anaerobic digestion, with the highest methane content of 99%. Additionally, the hydrogenotrophic methanogens were enriched, with a decrease in acetoclastic methanogens and an increase in Bathyarchaeia population, which utilizes H2 and CO2 to produce acetate and lactate as end products. The study concludes that recirculation increases methane production by converting H2 and CO2 into methane and enhances the degradation of organic matter left over undigested in the hydrolytic reactor.
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Affiliation(s)
- Alam Khan
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sedrah Akbar
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Valentine Okonkwo
- Water Engineering Group, School of Engineering, The University of Glasgow, Glasgow, United Kingdom
| | - Cindy Smith
- Water Engineering Group, School of Engineering, The University of Glasgow, Glasgow, United Kingdom; Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Samiullah Khan
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Aamer Ali Shah
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Umer Zeeshan Ijaz
- Water Engineering Group, School of Engineering, The University of Glasgow, Glasgow, United Kingdom
| | - Safia Ahmed
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Malik Badshah
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Qian L, Yu X, Zhou J, Gu H, Ding J, Peng Y, He Q, Tian Y, Liu J, Wang S, Wang C, Shu L, Yan Q, He J, Liu G, Tu Q, He Z. MCycDB: a curated database for comprehensively profiling methane cycling processes of environmental microbiomes. Mol Ecol Resour 2022; 22:1803-1823. [DOI: 10.1111/1755-0998.13589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/24/2021] [Accepted: 01/17/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Jiayin Zhou
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Hang Gu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Jijuan Ding
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering the University of Tennessee Knoxville TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems School of Life Sciences Xiamen University Xiamen 361005 China
| | - Jihua Liu
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Jianguo He
- School of Life Science Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Guangli Liu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou 510006 China
- College of Agronomy Hunan Agricultural University Changsha 410128 China
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113
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Inoue M, Omae K, Nakamoto I, Kamikawa R, Yoshida T, Sako Y. Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases. Extremophiles 2022; 26:9. [PMID: 35059858 PMCID: PMC8776680 DOI: 10.1007/s00792-022-01259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
Abstract
Ni-containing carbon monoxide dehydrogenase (Ni-CODH) plays an important role in the CO/CO2-based carbon and energy metabolism of microbiomes. Ni-CODH is classified into distinct phylogenetic clades, A–G, with possibly distinct cellular roles. However, the types of Ni-CODH clade used by organisms in different microbiomes are unknown. Here, we conducted a metagenomic survey of a protein database to determine the relationship between the phylogeny and biome distribution of Ni-CODHs. Clustering and phylogenetic analyses showed that the metagenome assembly-derived Ni-CODH sequences were distributed in ~ 60% Ni-CODH clusters and in all Ni-CODH clades. We also identified a novel Ni-CODH clade, clade H. Biome mapping on the Ni-CODH phylogenetic tree revealed that Ni-CODHs of almost all the clades were found in natural aquatic environmental and engineered samples, whereas those of specific subclades were found only in host-associated samples. These results are comparable with our finding that the diversity in the phylum-level taxonomy of host-associated Ni-CODH owners is statistically different from those of the other biomes. Our findings suggest that while Ni-CODH is a ubiquitous enzyme produced across diverse microbiomes, its distribution in each clade is biased and mainly affected by the distinct composition of microbiomes.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
- R-GIRO, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Kimiho Omae
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Issei Nakamoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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114
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Braga Nan L, Trably E, Santa-Catalina G, Bernet N, Delgenes JP, Escudie R. Microbial community redundance in biomethanation systems lead to faster recovery of methane production rates after starvation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150073. [PMID: 34517312 DOI: 10.1016/j.scitotenv.2021.150073] [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: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
The Power-to-Gas concept corresponds to the use of the electric energy surplus to produce H2 by water electrolysis, that can be further converted to methane by biomethanation. However, the fluctuant production of renewable energy sources can lead to discontinuous H2 injections into the reactors, that may interfere with the adaptation of the microbial community to high H2 partial pressures. In this study, the response of the microbial community to H2 and organic feed starvation was evaluated in in-situ and ex-situ biomethanation. The fed-batch reactors were fed with acetate or glucose and H2, and one or four weeks of starvation periods were investigated. Methane productivity was mostly affected by the four-week starvation period. However, both in-situ and ex-situ biomethanation reactors recovered their methane production rate after starvation within approximately one-week of normal operation, while the anaerobic digestion (AD) reactors did not recover their performances even after 3 weeks of normal operation. The recovery failure of the AD reactors was probably related to a slow growth of the syntrophic and methanogen microorganisms, that led to a VFA accumulation. On the contrary, the faster recovery of both biomethanation reactors was related to the replacement of Methanoculleus sp. by Methanobacterium sp., restoring the methane production in the in-situ and ex-situ biomethanation reactors. This study has shown that biomethanation processes can respond favourably to the intermittent H2 addition without compromising their CH4 production performance.
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Affiliation(s)
- L Braga Nan
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - E Trably
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - G Santa-Catalina
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - N Bernet
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - J-P Delgenes
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France
| | - R Escudie
- INRAE, Univ. Montpellier, LBE, 102 AV. des Etangs, 11100 Narbonne, France.
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115
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Deconstructing Methanosarcina acetivorans into an acetogenic archaeon. Proc Natl Acad Sci U S A 2022; 119:2113853119. [PMID: 34992140 PMCID: PMC8764690 DOI: 10.1073/pnas.2113853119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 12/02/2022] Open
Abstract
The reductive acetyl-coenzyme A (acetyl-CoA) pathway is the only carbon fixation pathway that can also be used for energy conservation like it is known for acetogenic bacteria. In methanogenic archaea, this pathway is extended with one route toward acetyl-CoA formation for anabolism and another route toward methane formation for catabolism. Which of these traits is ancestral in evolution has not been resolved. By diverging virtually all substrate carbon from methanogenesis to flow through acetyl-CoA, Methanosarcina acetivorans can be converted to an acetogenic organism. Being able to deconstruct methanogenic into the seemingly simpler acetogenic energy metabolism provides compelling evidence that methanogens are not nearly as metabolically limited as previously thought and suggests that methanogenesis might have evolved from the acetyl-CoA pathway. The reductive acetyl-coenzyme A (acetyl-CoA) pathway, whereby carbon dioxide is sequentially reduced to acetyl-CoA via coenzyme-bound C1 intermediates, is the only autotrophic pathway that can at the same time be the means for energy conservation. A conceptually similar metabolism and a key process in the global carbon cycle is methanogenesis, the biogenic formation of methane. All known methanogenic archaea depend on methanogenesis to sustain growth and use the reductive acetyl-CoA pathway for autotrophic carbon fixation. Here, we converted a methanogen into an acetogen and show that Methanosarcina acetivorans can dispense with methanogenesis for energy conservation completely. By targeted disruption of the methanogenic pathway, followed by adaptive evolution, a strain was created that sustained growth via carbon monoxide–dependent acetogenesis. A minute flux (less than 0.2% of the carbon monoxide consumed) through the methane-liberating reaction remained essential, indicating that currently living methanogens utilize metabolites of this reaction also for anabolic purposes. These results suggest that the metabolic flexibility of methanogenic archaea might be much greater than currently known. Also, our ability to deconstruct a methanogen into an acetogen by merely removing cellular functions provides experimental support for the notion that methanogenesis could have evolved from the reductive acetyl-coenzyme A pathway.
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116
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Adam PS, Bornemann TLV, Probst AJ. Progress and Challenges in Studying the Ecophysiology of Archaea. Methods Mol Biol 2022; 2522:469-486. [PMID: 36125771 DOI: 10.1007/978-1-0716-2445-6_32] [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] [Indexed: 06/15/2023]
Abstract
It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.
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Affiliation(s)
- Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany.
| | - Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany.
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117
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Xie Z, Cao Q, Chen Y, Luo Y, Liu X, Li D. The biological and abiotic effects of powdered activated carbon on the anaerobic digestion performance of cornstalk. BIORESOURCE TECHNOLOGY 2022; 343:126072. [PMID: 34626759 DOI: 10.1016/j.biortech.2021.126072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
To comprehensively evaluate the biological and abiotic influence of powdered activated carbon (PAC) on the anaerobic digestion of cornstalk, mesophilic and thermophilic digestion were conducted. Adding PAC (10 g/L) under thermophilic system obtained the maximum cellulose degradation rate and methane yield (MY), which were 57.47% and 128.19 L/kg VS. However, adding same dose of PAC at mesophilic system decreased the MY by 8.16% while increased the cellulose degradation rate and methane production rate by 6.48% and 17.92%. Under mesophilic conditions, the enhancement of PAC was owing to the enrichment of cellulolytic microorganisms, improvement of the syntrophic process and direct interspecies electron transfer. The lower methane yield was attributed to the adsorption of carbon source by PAC and CH4 consumption by Norank_c_Bathyarchaeia. The good performance of thermophilic system was owing to the lower adsorption capability of PAC, absence of Norank_c_Bathyarchaeia, and concentrated carbon flow to methane.
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Affiliation(s)
- Zhijie Xie
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qin Cao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yichao Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yiping Luo
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, PR China
| | - Xiaofeng Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Dong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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118
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Xu RZ, Fang S, Zhang L, Huang W, Shao Q, Fang F, Feng Q, Cao J, Luo J. Distribution patterns of functional microbial community in anaerobic digesters under different operational circumstances: A review. BIORESOURCE TECHNOLOGY 2021; 341:125823. [PMID: 34454239 DOI: 10.1016/j.biortech.2021.125823] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) processes are promising to effectively recover resources from organic wastes or wastewater. As a microbial-driven process, the functional anaerobic species played critical roles in AD. However, the lack of effective understanding of the correlations of varying microbial communities with different operational factors hinders the microbial regulation to improve the AD performance. In this paper, the main anaerobic functional microorganisms involved in different stages of AD processes were first demonstrated. Then, the response of anaerobic microbial community to different operating parameters, exogenous interfering substances and digestion substrates, as well as the digestion efficiency, were discussed. Finally, the research gaps and future directions on the understanding of functional microorganisms in AD were proposed. This review provides insightful knowledge of distribution patterns of functional microbial community in anaerobic digesters, and gives critical guidance to regulate and enrich specific functional microorganisms to accumulate certain AD products.
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Affiliation(s)
- Run-Ze Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Shiyu Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Le Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Wenxuan Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Qianqi Shao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Fang Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Qian Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
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119
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Seasonal Dynamics of Bathyarchaeota-Dominated Benthic Archaeal Communities Associated with Seagrass (Zostera japonica) Meadows. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9111304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Little is known about the seasonal dynamic of archaeal communities and their potential ecological functions in temperate seagrass ecosystems. In this study, seasonal changes in diversity, community structure, and potential metabolic functions of benthic archaea in surface sediments of two seagrass meadows along the northern Bohai Sea in China were investigated using Miseq sequencing of the 16S rRNA gene and Tax4Fun2 functional prediction. Overall, Crenarchaeota (mainly Bathy-15, Bathy-8, and Bathy-6) dominated, followed by Thermoplasmatota, Asgardarchaeota, and Halobacterota, in terms of alpha diversities and relative abundance. Significant seasonal changes in the entire archaeal community structure were observed. The major phyla Methanobacteria, Nitrosopumilales, and genus Methanolobus had higher proportions in spring, while MBG-D and Bathyarchaeota were more abundant in summer and autumn, respectively. Alpha diversities (Shannon and Simpson) were the highest in summer and the lowest in autumn (ANOVA test, p < 0.05). Salinity, total organic carbon, and total organic nitrogen were the most significant factors influencing the entire archaeal community. Higher cellulose and hemicellulose degradation potentials occurred in summer, while methane metabolism potentials were higher in winter. This study indicated that season had strong effects in modulating benthic archaeal diversity and functional potentials in the temperate seagrass ecosystems.
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Tenelanda-Osorio LI, Parra JL, Cuartas-Restrepo P, Zuluaga JI. Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass. Life (Basel) 2021; 11:1182. [PMID: 34833058 PMCID: PMC8624164 DOI: 10.3390/life11111182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Enceladus is a potential target for future astrobiological missions. NASA's Cassini spacecraft demonstrated that the Saturnian moon harbors a salty ocean beneath its icy crust and the existence and analysis of the plume suggest water-rock reactions, consistent with the possible presence of hydrothermal vents. Particularly, the plume analysis revealed the presence of molecular hydrogen, which may be used as an energy source by microorganisms ( e.g., methanogens). This could support the possibility that populations of methanogens could establish in such environments if they exist on Enceladus. We took a macroscale approximation using ecological niche modeling to evaluate whether conditions suitable for methanogenic archaea on Earth are expected in Enceladus. In addition, we employed a new approach for computing the biomass using the Monod growth model. The response curves for the environmental variables performed well statistically, indicating that simple correlative models may be used to approximate large-scale distributions of these genera on Earth. We found that the potential hydrothermal conditions on Enceladus fit within the macroscale conditions identified as suitable for methanogens on Earth, and estimated a concentration of 1010-1011 cells/cm3.
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Affiliation(s)
- Laura I. Tenelanda-Osorio
- Grupo de Estudios en Astrobiología AMEBA, Planetario de Medellín, Medellín 050010, Colombia;
- Grupo de Ecología y Evolución de Vertebrados, Instituto de Biología-FCEN, Universidad de Antioquia, Medellín 050010, Colombia;
- Solar, Earth and Planetary Physics—SEAP, Instituto de Física-FCEN, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados, Instituto de Biología-FCEN, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Pablo Cuartas-Restrepo
- Solar, Earth and Planetary Physics—SEAP, Instituto de Física-FCEN, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Jorge I. Zuluaga
- Grupo de Estudios en Astrobiología AMEBA, Planetario de Medellín, Medellín 050010, Colombia;
- Solar, Earth and Planetary Physics—SEAP, Instituto de Física-FCEN, Universidad de Antioquia, Medellín 050010, Colombia;
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121
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Singh NK, Choudhary S. Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58819-58836. [PMID: 33410029 DOI: 10.1007/s11356-020-11705-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.
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Affiliation(s)
- Nishi Kumari Singh
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India.
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Wang B, Zheng X, Zhang H, Yu X, Lian Y, Yang X, Yu H, Hu R, He Z, Xiao F, Yan Q. Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:405-415. [PMID: 37073260 PMCID: PMC10077182 DOI: 10.1007/s42995-021-00100-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling. However, their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood. Here, we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants (i.e., Vallisneria natans). A large number of functional genes involved in carbon (C), nitrogen (N) and sulfur (S) cycling were detected in the wetland sediments. However, most functional genes showed higher abundance in sediments with submerged plants than in those without plants. Based on the comparison of annotated functional genes in the N and S cycling databases (i.e., NCycDB and SCycDB), we found that genes involved in nitrogen fixation (e.g., nifD/H/K/W), assimilatory nitrate reduction (e.g., nasA and nirA), denitrification (e.g., nirK/S and nosZ), assimilatory sulfate reduction (e.g., cysD/H/J/N/Q and sir), and sulfur oxidation (e.g., glpE, soeA, sqr and sseA) were significantly higher (corrected p < 0.05) in vegetated vs. unvegetated sediments. This could be mainly driven by environmental factors including total phosphorus, total nitrogen, and C:N ratio. The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis, which are crucial to the wetland methane budget and carbon cycling. This study opens a new avenue for linking submerged plants with microbial functions, and has further implications for understanding global carbon, nitrogen and sulfur cycling in wetland ecosystems. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00100-3.
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Affiliation(s)
- Binhao Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
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123
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Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH, Ley RE. Vertebrate host phylogeny influences gut archaeal diversity. Nat Microbiol 2021; 6:1443-1454. [PMID: 34702978 PMCID: PMC8556154 DOI: 10.1038/s41564-021-00980-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 09/16/2021] [Indexed: 01/04/2023]
Abstract
Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Silke Dauser
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sophie Maisch
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chris Walzer
- Wildlife Conservation Society, Bronx, NY, USA.,Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria.,Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, Krems an der Donau, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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124
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Nagoya M, Kouzuma A, Watanabe K. Codh/Acs-Deficient Methanogens Are Prevalent in Anaerobic Digesters. Microorganisms 2021; 9:microorganisms9112248. [PMID: 34835373 PMCID: PMC8621161 DOI: 10.3390/microorganisms9112248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types-namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO2 and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood-Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology.
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125
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Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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126
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Zhang R, Liu WC, Liu Y, Zhang HL, Zhao ZH, Zou LY, Shen YC, Lan WS. Impacts of anthropogenic disturbances on microbial community of coastal waters in Shenzhen, South China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1652-1661. [PMID: 33161467 DOI: 10.1007/s10646-020-02297-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/20/2020] [Indexed: 05/16/2023]
Abstract
During the urbanization, human activities have brought great changes to marine biodiversity and microbial communities of coastal water. Shenzhen is a coastal city that has developed rapidly over the past four decades, but the microbial communities and metabolic potential in offshore water are still not well characterized. Here, 16S rRNA gene V4-V5 sequencing was conducted to determine the microbial components from coastal waters in twenty selected areas of Shenzhen. The results showed a significant difference on the microbial composition between the western and eastern waters. Samples from western coast had more abundant Burkholderiaceae, Sporichthyaceae, Aeromonadaceae, and Methylophilaceae compared to eastern coast, and at the genus level, Candidatus Aquiluna, Aeromonas, Arcobacter, Ottowia and Acidibacter were significantly higher in western waters. There was also a notable difference within the western sample group, suggesting the taxa-compositional heterogeneity. Moreover, analysis of environmental factors and water quality revealed that salinity, pH and dissolved oxygen were relatively decreased in western samples, while total nitrogen, total phosphorus, chemical oxygen demand, and harmful marine vibrio were significantly increased compared to eastern waters. The results suggest the coastal waters pollution is more serious in western Shenzhen than eastern Shenzhen and the microbial communities are altered, which can be associated with anthropogenic disturbances.
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Affiliation(s)
- Rui Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, PR China.
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China.
| | - Wen-Chao Liu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, PR China
- College of Agriculture, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Yu Liu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, PR China
- College of Agriculture, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Hong-Lian Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, PR China
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Zhi-Hui Zhao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, PR China
- College of Agriculture, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Ling-Yun Zou
- Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, PR China
| | - Yu-Chun Shen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Wen-Sheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Science and Technology for Inspection and Quarantine, Technology Center for Animal and Plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518010, PR China.
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127
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Owusu-Agyeman I, Plaza E, Cetecioglu Z. A pilot-scale study of granule-based anaerobic reactors for biogas recovery from municipal wastewater under sub-mesophilic conditions. BIORESOURCE TECHNOLOGY 2021; 337:125431. [PMID: 34198242 DOI: 10.1016/j.biortech.2021.125431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The influence of hydraulic retention time (HRT of 3-5 h) and temperature (20-25 °C) on performance and microbial dynamics of two pilot-scale upflow anaerobic sludge blanket (UASB) reactors with different granule size distribution (UASB1 = 3-4 mm and UASB2 = 1-2 mm) were investigated for 217 days. Increasing the HRT to 5 h even at a lower temperature of 20 °C enhanced COD removal and biogas production with average of 59 ± 16% (up to 85%) and 73 ± 9 L/(m3·d) (up to 102 L/(m3·d)) for UASB1; 63 ± 16% (up to 85%) and 75 ± 9 L/(m3·d) (up to 90 L/(m3·d)) for UASB2, respectively. This is explained by sufficient contact time between microorganisms and substrate. Acetoclastic methanogenic activity was higher in UASB1 because Methanosaetaceae (produces methane from acetate) dominated (64 ± 4%). However, Methanoregulaceae (29 ± 3%) and Methanomicrobiales_unassigned (20 ± 6%) which produce methane from H2/CO2 and formate were significant in UASB2. The extent of change in the microbial dynamics with HRT and temperature was more obvious in the smaller granule reactor.
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Affiliation(s)
- Isaac Owusu-Agyeman
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
| | - Elzbieta Plaza
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
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128
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Tóth E, Toumi M, Farkas R, Takáts K, Somodi C, Ács É. Insight into the hidden bacterial diversity of Lake Balaton, Hungary. Biol Futur 2021; 71:383-391. [PMID: 34554460 DOI: 10.1007/s42977-020-00040-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/17/2020] [Indexed: 11/26/2022]
Abstract
In the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum beta-lactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.
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Affiliation(s)
- E Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary.
| | - M Toumi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - R Farkas
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - K Takáts
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Cs Somodi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - É Ács
- MTA Centre for Ecological Research, Danube Research Institute, Budapest, Hungary
- National University of Public Service, Faculty of Water Sciences, Baja, Hungary
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129
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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130
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Lavergne C, Aguilar-Muñoz P, Calle N, Thalasso F, Astorga-España MS, Sepulveda-Jauregui A, Martinez-Cruz K, Gandois L, Mansilla A, Chamy R, Barret M, Cabrol L. Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems. ENVIRONMENT INTERNATIONAL 2021; 154:106575. [PMID: 33901975 DOI: 10.1016/j.envint.2021.106575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Freshwater ecosystems are responsible for an important part of the methane (CH4) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH4 flux measurements, CH4 production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H2/CO2, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H2/CO2-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H2/CO2 (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H2/CO2-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H2-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.
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Affiliation(s)
- Céline Lavergne
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Valparaíso, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile.
| | - Polette Aguilar-Muñoz
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile
| | - Natalia Calle
- Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Frédéric Thalasso
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, DF, Mexico
| | - Maria Soledad Astorga-España
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile; ENBEELAB, University of Magallanes, Punta Arenas, Chile
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)(2), Santiago, Chile
| | - Karla Martinez-Cruz
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile; ENBEELAB, University of Magallanes, Punta Arenas, Chile
| | - Laure Gandois
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Andrés Mansilla
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Rolando Chamy
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile
| | - Maialen Barret
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Léa Cabrol
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile; Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile.
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131
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Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs. J Bacteriol 2021; 203:e0011721. [PMID: 34124941 PMCID: PMC8351635 DOI: 10.1128/jb.00117-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Archaeal methanogens, methanotrophs, and alkanotrophs have a high demand for iron (Fe) and sulfur (S); however, little is known of how they acquire, traffic, deploy, and store these elements. Here, we examined the distribution of homologs of proteins mediating key steps in Fe/S metabolism in model microorganisms, including iron(II) sensing/uptake (FeoAB), sulfide extraction from cysteine (SufS), and the biosynthesis of iron-sulfur [Fe-S] clusters (SufBCDE), siroheme (Pch2 dehydrogenase), protoheme (AhbABCD), cytochrome c (Cyt c) (CcmCF), and iron storage/detoxification (Bfr, FtrA, and IssA), among 326 publicly available, complete or metagenome-assembled genomes of archaeal methanogens/methanotrophs/alkanotrophs. The results indicate several prevalent but nonuniversal features, including FeoB, SufBC, and the biosynthetic apparatus for the basic tetrapyrrole scaffold, as well as its siroheme (and F430) derivatives. However, several early-diverging genomes lacked SufS and pathways to synthesize and deploy heme. Genomes encoding complete versus incomplete heme biosynthetic pathways exhibited equivalent prevalences of [Fe-S] cluster binding proteins, suggesting an expansion of catalytic capabilities rather than substitution of heme for [Fe-S] in the former group. Several strains with heme binding proteins lacked heme biosynthesis capabilities, while other strains with siroheme biosynthesis capability lacked homologs of known siroheme binding proteins, indicating heme auxotrophy and unknown siroheme biochemistry, respectively. While ferritin proteins involved in ferric oxide storage were widespread, those involved in storing Fe as thioferrate were unevenly distributed. Collectively, the results suggest that differences in the mechanisms of Fe and S acquisition, deployment, and storage have accompanied the diversification of methanogens/methanotrophs/alkanotrophs, possibly in response to differential availability of these elements as these organisms evolved. IMPORTANCE Archaeal methanogens, methanotrophs, and alkanotrophs, argued to be among the most ancient forms of life, have a high demand for iron (Fe) and sulfur (S) for cofactor biosynthesis, among other uses. Here, using comparative bioinformatic approaches applied to 326 genomes, we show that major differences in Fe/S acquisition, trafficking, deployment, and storage exist in this group. Variation in these characters was generally congruent with the phylogenetic placement of these genomes, indicating that variation in Fe/S usage and deployment has contributed to the diversification and ecology of these organisms. However, incongruency was observed among the distribution of cofactor biosynthesis pathways and known protein destinations for those cofactors, suggesting auxotrophy or yet-to-be-discovered pathways for cofactor biosynthesis.
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St James AR, Lin J, Richardson RE. Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA. MICROBIAL ECOLOGY 2021; 82:429-441. [PMID: 33410936 DOI: 10.1007/s00248-020-01651-1] [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: 06/25/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.
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Affiliation(s)
- Andrew R St James
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Janni Lin
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
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133
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Li C, Hambright KD, Bowen HG, Trammell MA, Grossart HP, Burford MA, Hamilton DP, Jiang H, Latour D, Meyer EI, Padisák J, Zamor RM, Krumholz LR. Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates. Environ Microbiol 2021; 23:6503-6519. [PMID: 34327792 DOI: 10.1111/1462-2920.15691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.
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Affiliation(s)
- Chuang Li
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, The University of Oklahoma, Norman, Ok, USA
| | - K David Hambright
- Plankton Ecology and Limnology Laboratory, Program in Ecology and Evolutionary Biology, and the Geographical Ecology Group, Department of Biology, The University of Oklahoma, Norman, OK, USA
| | - Hannah G Bowen
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Majoi A Trammell
- Biomedical Research Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Stechlin, and Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Michele A Burford
- Australian Rivers Institute and School of Environment and Science, Griffith University, Nathan, Qld, Australia
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Delphine Latour
- Université Clermont Auvergne CNRS, LMGE, Aubière Cedex, France
| | - Elisabeth I Meyer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Judit Padisák
- Research Group of Limnology, Centre of Natural Sciences, University of Pannonia, Veszprém, Hungary
| | | | - Lee R Krumholz
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, The University of Oklahoma, Norman, Ok, USA
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134
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Feldewert C, Lang K, Brune A. The hydrogen threshold of obligately methyl-reducing methanogens. FEMS Microbiol Lett 2021; 367:5895324. [PMID: 32821944 PMCID: PMC7485788 DOI: 10.1093/femsle/fnaa137] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.
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Affiliation(s)
- Christopher Feldewert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina Lang
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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135
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Kong Y, Lei H, Zhang Z, Cheng W, Wang B, Pan F, Huang F, Huang F, Li W. Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146233. [PMID: 34030248 DOI: 10.1016/j.scitotenv.2021.146233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4 m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.
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Affiliation(s)
- Yuan Kong
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Huaiyan Lei
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China.
| | - Zilian Zhang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Weidong Cheng
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Bin Wang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fulong Pan
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanfan Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanli Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Wenqing Li
- Key Laboratory of Mineral Resources Evaluation in Northeast China, Ministry of Land and Resources, Changchun 130061, PR China
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136
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Glodowska M, Schneider M, Eiche E, Kontny A, Neumann T, Straub D, Berg M, Prommer H, Bostick BC, Nghiem AA, Kleindienst S, Kappler A. Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146501. [PMID: 34030262 DOI: 10.1016/j.scitotenv.2021.146501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/24/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them. We conducted a high spatial resolution geomicrobiological study in combination with analysis of sediment chemistry and mineralogy in an alluvial aquifer system affected by geogenic As in the Red River delta in Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46 m deep core showed a diversity of Fe minerals including poorly crystalline Fe (II/III) and Fe(III) (oxyhydr)oxides such as goethite, hematite, and magnetite, but also the presence of Fe(II)-bearing carbonates and sulfides which likely formed as a result of microbially driven organic carbon (OC) degradation. A potential important role of methane (CH4) as electron donor for reductive Fe mineral (trans)formation was supported by the high abundance of Candidatus Methanoperedens, a known Fe(III)-reducing methanotroph. Overall, these results imply that OC turnover including fermentation, methanogenesis and CH4 oxidation are important mechanisms leading to Fe mineral (trans)formation, dissolution and precipitation, and thus indirectly affecting As mobility by changing the Fe-mineral inventory.
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Affiliation(s)
- Martyna Glodowska
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Germany; Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Germany; Department of Microbiology, IWWR, Radboud University, the Netherlands.
| | - Magnus Schneider
- Karlsruhe Institute of Technology, Institute of Applied Geosciences, Germany
| | - Elisabeth Eiche
- Karlsruhe Institute of Technology, Institute of Applied Geosciences, Germany
| | - Agnes Kontny
- Karlsruhe Institute of Technology, Institute of Applied Geosciences, Germany
| | - Thomas Neumann
- Technical University of Berlin, Institute for Applied Geosciences, Berlin, Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Germany; Quantitative Biology Center (QBiC), University of Tübingen, Germany
| | - Michael Berg
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Henning Prommer
- School of Earth Sciences, University of Western Australia, Perth, WA, Australia; CSIRO Land and Water, Floreat, WA, Australia
| | | | | | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Germany
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137
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Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in " Candidatus Bathyarchaeia". mSystems 2021; 6:e0025221. [PMID: 34282939 PMCID: PMC8407382 DOI: 10.1128/msystems.00252-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of Ca. Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of Ca. Bathyarchaeia in thermal environments. IMPORTANCE Ca. Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of Ca. Bathyarchaeia in hot springs and give a comprehensive comparative analysis between thermal and nonthermal habitats to reveal the thermal adaptability of Ca. Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca. Bathyarchaeia, since it appears to be the first archaea beyond Euryarchaeota which contains the mcrABG genes. The reclassification of Ca. Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.
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138
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Font-Verdera F, Liébana R, Aldeguer-Riquelme B, Gangloff V, Santos F, Viver T, Rosselló-Móra R. Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns. Syst Appl Microbiol 2021; 44:126231. [PMID: 34332366 DOI: 10.1016/j.syapm.2021.126231] [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: 03/31/2021] [Revised: 06/01/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022]
Abstract
The anaerobic hypersaline sediments of an ephemeral pond from the S'Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.
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Affiliation(s)
- Francisca Font-Verdera
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain.
| | - Raquel Liébana
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Borja Aldeguer-Riquelme
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Valentin Gangloff
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
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139
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High concentrations of dissolved biogenic methane associated with cyanobacterial blooms in East African lake surface water. Commun Biol 2021; 4:845. [PMID: 34234272 PMCID: PMC8263762 DOI: 10.1038/s42003-021-02365-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022] Open
Abstract
The contribution of oxic methane production to greenhouse gas emissions from lakes is globally relevant, yet uncertainties remain about the levels up to which methanogenesis can counterbalance methanotrophy by leading to CH4 oversaturation in productive surface waters. Here, we explored the biogeochemical and microbial community variation patterns in a meromictic soda lake, in the East African Rift Valley (Kenya), showing an extraordinarily high concentration of methane in oxic waters (up to 156 µmol L−1). Vertical profiles of dissolved gases and their isotopic signature indicated a biogenic origin of CH4. A bloom of Oxyphotobacteria co-occurred with abundant hydrogenotrophic and acetoclastic methanogens, mostly found within suspended aggregates promoting the interactions between Bacteria, Cyanobacteria, and Archaea. Moreover, aggregate sedimentation appeared critical in connecting the lake compartments through biomass and organic matter transfer. Our findings provide insights into understanding how hydrogeochemical features of a meromictic soda lake, the origin of carbon sources, and the microbial community profiles, could promote methane oversaturation and production up to exceptionally high rates. Fazi et al. report on an extraordinarily high biogenic methane concentration detected in the surface water of Lake Sonachi, Kenya. Using gas chromatography and microbiome profiling, they determine that these high concentrations are associated with cyanobacterial blooms and help provide insight to methanogenesis in meromictic soda lakes.
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140
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Lu Y, Yuan H, Zuo X, Chang Y, Li X. Biomethane Yield, Physicochemical Structures, and Microbial Community Characteristics of Corn Stover Pretreated by Urea Combined with Mild Temperature Hydrotherm. Polymers (Basel) 2021; 13:polym13132207. [PMID: 34279351 PMCID: PMC8272243 DOI: 10.3390/polym13132207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 12/21/2022] Open
Abstract
The corn stover (CS)’s compact structure makes it challenging for microorganisms to use in anaerobic digestion (AD). Therefore, improving CS biodegradability has become a key focus in AD studies. Methods are being targeted at the pretreatment of CS, combining advanced urea with mild temperature hydrotherm pretreatment to study its effect on promoting the AD process of CS. The biomethane yield, physicochemical structure, and microbial community characteristics were investigated. CS samples were assigned into groups differed by a range of pretreatment times (from 24 to 96 h) and set at a temperature of 50 °C with a 2% urea addition. Results revealed that the 72-h group obtained the highest biomethane yield of 205 mL/g VS−1, volatile solid (VS) and total solid (TS) removal rates of 69.3% and 47.7%, which were 36.7%, 25.3% and 27.5% higher than those of untreated one, respectively. After conducting several analyses, results confirmed the pretreatment as a method for altering CS microstructures benefits biomethane production. The most resounding differences between pretreated and untreated groups were observed within a microbial community, an integral factor for improved AD performance. This study serves to confirm that this specific pretreatment is an effective method for enhancing biomethane production in CS.
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Affiliation(s)
- Yao Lu
- Beijing Engineering Center for Pollution Control and Resource Recovery, Beijing University of Chemical Technology, Beijing 100029, China; (Y.L.); (H.Y.); (X.Z.)
| | - Hairong Yuan
- Beijing Engineering Center for Pollution Control and Resource Recovery, Beijing University of Chemical Technology, Beijing 100029, China; (Y.L.); (H.Y.); (X.Z.)
| | - Xiaoyu Zuo
- Beijing Engineering Center for Pollution Control and Resource Recovery, Beijing University of Chemical Technology, Beijing 100029, China; (Y.L.); (H.Y.); (X.Z.)
| | - Yanqing Chang
- WELLE Environmental Group Co., Ltd., Changzhou 213125, China;
| | - Xiujin Li
- Beijing Engineering Center for Pollution Control and Resource Recovery, Beijing University of Chemical Technology, Beijing 100029, China; (Y.L.); (H.Y.); (X.Z.)
- Correspondence:
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141
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Tian C, Zhang Y, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabj1453. [PMID: 34215592 PMCID: PMC11057702 DOI: 10.1126/sciadv.abj1453] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Tian
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - 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, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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142
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Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proc Natl Acad Sci U S A 2021; 118:2006857118. [PMID: 34161255 PMCID: PMC8237665 DOI: 10.1073/pnas.2006857118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Methane is a strong greenhouse gas that plays a key role in Earth’s climate. At methane seeps, large amounts of methane move upward through the seafloor, where microbial communities consume much of it. A full accounting of methane’s sources and sinks has evaded researchers—in part, perhaps, because key habitats including carbonate rock mounds have been largely neglected. We sampled seven methane seeps representing four geological settings and found that all sites had rock-hosted microbes capable of consuming methane; in lab-based incubations, some did so at the highest rates reported to date. We demonstrate several factors that help determine a sample’s methane-consuming potential and propose that carbonate rocks at methane seeps may represent a methane sink of far-reaching importance. At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample’s methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.
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143
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Zemskaya TI, Bukin SV, Lomakina AV, Pavlova ON. Microorganisms in the Sediments of Lake Baikal, the Deepest and Oldest Lake in the World. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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144
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [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: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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145
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Chen X, Zhou W, Li G, Song Q, Ismail M, Wang Y, Ren L, Cheng C. Anaerobic biodegradation of soybean-process wastewater: Operation strategy and sludge bed characteristics of a high-performance Spiral Symmetric Stream Anaerobic Bioreactor. WATER RESEARCH 2021; 197:117095. [PMID: 33862392 DOI: 10.1016/j.watres.2021.117095] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
A 300m3/d demonstration project of soybean-process wastewater has been established recently with a Spiral Symmetric Stream Anaerobic Bioreactor (SSSAB) as the core. In order to obtain the optimal operation strategy for a full-scale SSSAB and to make it run efficiently and stably in a demonstration project, a Pilot-scale SSSAB (P-SSSAB, effective volume 100 L) was performed for the treatment of soybean-process wastewater over 216 days. The volumetric load rate (VLR) range of the P-SSSAB was 0.32~27.17 kg COD/(m3·d), where the highest VLR [27.17 kg COD/(m3·d)] was 2.01 times to the highest value [13.5 kg COD/(m3·d)] reported. The pH and VFA/ALK of the effluent from the P-SSSAB were in the range of 6.9 up to 9.2 and 0.03 up to 0.17, respectively. The methane yield of the P-SSSAB increased from 0.03 m3/kg COD to 0.47 m3/kg COD, which was 3.36 times to the maximum value (0.14 m3/kg COD) reported. To meet the influent requirement of the aerobic biological treatment in demonstration project (influent COD ≤ 1.5 g/L), the maximum VLR of SSSAB was optimal at about 22 kg COD/(m3·d). By analyzing the sludge bed characteristics of the P-SSSAB, it was obvious that zone I (the bottom of the bed) was the major contributor of the COD removal, while zone III (the upper part of the bed) was the major contributor for the NH4+-N increase. The anaerobic granular sludge (AGS) in the bed showed a good granulation. The average MLVSS/MLSS value in sludge bed was about 0.7, and PN/PS in TB-EPS (zone I, II and III) increased to 6.830, 4.257, and 3.747, respectively. SMA and coenzyme F420 values of zone III were the maximum [666.35 ml CH4/(g VSS·d) and 0.690 mol/g VSS, respectively]. According to the analysis obtained from the 16S rRNA high-throughput sequencing, the microbial community in the AGS had been more specific to the soybean-process wastewater since the bacteria Firmicutes were increased. The relative abundance of microbe which perform direct interspecies electron transfer (DIET) for the syntrophic degradation of VFAs and production of the methane has been increased significantly, such as the bacteria Syntrophomonas and archaea Methanosaeta.
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Affiliation(s)
- Xiaoguang Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China.
| | - Weizhu Zhou
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Gongsong Li
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Qi Song
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Muhammad Ismail
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yiqi Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Luotong Ren
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Chen Cheng
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
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146
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Li Y, Zhao J, Zhang Z. Implementing metatranscriptomics to unveil the mechanism of bioaugmentation adopted in a continuous anaerobic process treating cow manure. BIORESOURCE TECHNOLOGY 2021; 330:124962. [PMID: 33740585 DOI: 10.1016/j.biortech.2021.124962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the effect of bioaugmentation on microbial community and function in a continuous anaerobic process treating lignocellulosic cow manure. One reactor (Rb) received bioaugmentation dosage for a certain period (d100-d170) and stopped afterward (d170-d220), while the same applied to the control (Rc) except sterilized bioaugmentation dosage was introduced. Samples were taken on day130, 170 and 220 from both reactors for metatranscriptomic analysis. The results underlined the promotive effect of bioaugmentation on indigenous microorganisms regarding hydrolysis and methanogenesis. Bioaugmentation contributed to the enrichment of Clostridium, Cellvibrio, Cellulomonas, Bacillus, Fibrobacter, resulting in enhanced cellulase activity (Rb: 0.917-1.081; Rc: 0.551-0.677). Moreover, bioaugmentation brought Rb the prosperity of uncultured_ Bathyarchaeia, a prominent archaeal group responsible for the improved methyl-coenzyme M reductase activity, thus accelerated methanogenesis. Unique metabolic pathways (autotrophic carbon fixation and methanogenesis) in uncultured_ Bathyarchaeia broadened the horizon of its fundamental role as acetogens and methanogens in anaerobic digestion.
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Affiliation(s)
- Yu Li
- Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Jing Zhao
- Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Zhenhua Zhang
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
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147
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Detman A, Bucha M, Treu L, Chojnacka A, Pleśniak Ł, Salamon A, Łupikasza E, Gromadka R, Gawor J, Gromadka A, Drzewicki W, Jakubiak M, Janiga M, Matyasik I, Błaszczyk MK, Jędrysek MO, Campanaro S, Sikora A. Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:125. [PMID: 34051845 PMCID: PMC8164749 DOI: 10.1186/s13068-021-01968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/06/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. RESULTS Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. CONCLUSIONS In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.
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Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Michał Bucha
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Laura Treu
- Department of Biology, University of Padova, Padova, Italy
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | - Łukasz Pleśniak
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | | | - Ewa Łupikasza
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Robert Gromadka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | | | - Wojciech Drzewicki
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marta Jakubiak
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marek Janiga
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Irena Matyasik
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Mieczysław K Błaszczyk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | | | | | - Anna Sikora
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.
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148
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Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
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Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
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149
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Ghezzi D, Filippini M, Cappelletti M, Firrincieli A, Zannoni D, Gargini A, Fedi S. Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23017-23035. [PMID: 33438126 DOI: 10.1007/s11356-020-12236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Laboratory of NanoBiotechnology, IRCSS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Maria Filippini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Alessandro Gargini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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150
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Two Metagenome-Assembled Genomes of Hydrogen-Dependent Methanomassiliicoccales Methanogens from the Zoige Wetland of the Tibetan Plateau. Microbiol Resour Announc 2021; 10:10/17/e00021-21. [PMID: 33927027 PMCID: PMC8086201 DOI: 10.1128/mra.00021-21] [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] [Indexed: 11/20/2022] Open
Abstract
Wetlands in the Tibetan Plateau play a crucial role in global carbon cycling. Here, we report the metagenome-assembled genomes (MAGs) of two hydrogen-dependent methanogens from the Zoige wetland of the Tibetan Plateau. The novel species belong to Methanomassiliicoccales, the seventh euryarchaeal methanogenic order.
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