Journal of Microbiology

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Trophic strategy of diverse methanogens across a river-to-sea gradient: Bingchen Wang , Fanghua Liu , Shiling Zheng , Qinqin Hao; J. Microbiol. 2019;57(6):470-478. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8482-3

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Methanogens are an important biogenic source of methane, especially in estuarine waters across a river-to-sea gradient. However, the diversity and trophic strategy of methanogens in this gradient are not clear. In this study, the diversity and trophic strategy of methanogens in sediments across the Yellow River (YR) to the Bohai Sea (BS) gradient were investigated by high-throughput sequencing based on the 16S rRNA gene. The results showed that the diversity of methanogens in sediments varied from multitrophic communities in YR samples to specific methylotrophic communities in BS samples. The methanogenic community in YR samples was dominated by Methanosarcina, while that of BS samples was dominated by methylotrophic Methanococcoides. The distinct methanogens suggested that the methanogenic community of BS sediments did not originate from YR sediment input. High-throughput sequencing of the mcrA gene revealed that active Methanococcoides dominated in the BS enrichment cultures with trimethylamine as the substrate, and methylotrophic Methanolobus dominated in the YR enrichment cultures, as detected to a limited amount in in situ sediment samples. Methanosarcina were also detected in this gradient sample. Furthermore, the same species of Methanosarcina mazei, which was widely distributed, was isolated from the area across a river-to-sea gradient by the culture-dependent
method
. In summary, our results showed that a distribution of diverse methanogens across a river-to-sea gradient may shed light on adaption strategies and survival mechanisms in methanogens.

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Methanogenic symbionts of anaerobic ciliates are host and habitat specific
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The ISME Journal.2024;[Epub] CrossRef
Methylmercury cycling in the Bohai Sea and Yellow Sea: Reasons for the low system efficiency of methylmercury production
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Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems
Mingwei Cai, Xiuran Yin, Xiaoyu Tang, Cuijing Zhang, Qingfei Zheng, Meng Li
Science of The Total Environment.2022; 802: 149848. CrossRef
Improving soil fertility by driving microbial community changes in saline soils of Yellow River Delta under petroleum pollution
Bingchen Wang, Shaoping Kuang, Hongbo Shao, Fei Cheng, Huihui Wang
Journal of Environmental Management.2022; 304: 114265. CrossRef
Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea
Ye Chen, Yu Zhen, Jili Wan, Xia Yin, Siqi Li, Jiayin Liu, Guodong Zhang, Tiezhu Mi
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Science of The Total Environment.2022; 815: 152645. CrossRef
Complete Genome Sequence of Methanobacterium electrotrophus Strain YSL, Isolated from Coastal Riverine Sediments
Shiling Zheng, Fanghua Liu, Frank J. Stewart
Microbiology Resource Announcements.2021;[Epub] CrossRef
Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps
Haizhou Li, Qunhui Yang, Huaiyang Zhou
Frontiers in Microbiology.2020;[Epub] CrossRef
Exploring Sources and Biogeochemical Dynamics of Dissolved Methane in the Central Bohai Sea in Summer
Yong Zhang, Bing Chen, Wei-dong Zhai
Frontiers in Marine Science.2020;[Epub] CrossRef
Effects of Organic Phosphorus on Methylotrophic Methanogenesis in Coastal Lagoon Sediments With Seagrass (Zostera marina) Colonization
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Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China: Xue Ping Chen , Jing Sun , Yi Wang , Heng Yang Zhang , Chi Quan He , Xiao Yan Liu , Nai Shun Bu , Xi-En Long; J. Microbiol. 2018;56(7):507-515. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8062-y

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Abstract

Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China’s wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.

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Stronger increase of methane emissions from coastal wetlands by non‐native Spartina alterniflora than non‐native Phragmites australis
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PLANTS, PEOPLE, PLANET.2025; 7(1): 62. CrossRef
Predictions of Spartina alterniflora leaf functional traits based on hyperspectral data and machine learning models
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Hailey Erb, Ashley Keiser, Kristen M DeAngelis
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Jian Li, Zhanrui Leng, Taitiya Kenneth Yuguda, Lili Wei, Jiaojiao Xia, Chongyu Zhuo, Ziying Nie, Daolin Du
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Spartina alterniflora Invaded Coastal Wetlands by Raising Soil Sulfur Contents: A Meta-Analysis
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Exogenous nitrogen from riverine exports promotes soil methane production in saltmarshes in China
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Exogenous Nitrogen from Riverine Exports Promotes Soil Methane Production in Saltmarshes in China
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SSRN Electronic Journal .2021;[Epub] CrossRef
Spartina alterniflora raised soil sulfide content by regulating sulfur cycle-associated bacteria in the Jiuduansha Wetland of China
Chiquan He, Liyu Cheng, Daoyuan Wang, Zhenzhen Zhao, Zhengyu Wang, Feifei Wang, Xiaoxi Wang, Pu Zhang, Xueping Chen, Xiaoyan Liu
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Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments: Shiling Zheng , Bingchen Wang , Fanghua Liu , Oumei Wang; J. Microbiol. 2017;55(11):862-870. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7104-1

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Abstract

Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNAbased terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The
results
also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

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Chemosphere.2022; 300: 134656. CrossRef
Complete Genome Sequence of Methanobacterium electrotrophus Strain YSL, Isolated from Coastal Riverine Sediments
Shiling Zheng, Fanghua Liu, Frank J. Stewart
Microbiology Resource Announcements.2021;[Epub] CrossRef
The differences in the corrosion product compositions of Methanogen-induced microbiologically influenced corrosion (Mi-MIC) between static and dynamic growth conditions
Biwen Annie An, Eric Deland, Oded Sobol, Jizheng Yao, Torben Lund Skovhus, Andrea Koerdt
Corrosion Science.2021; 180: 109179. CrossRef
Organic matter stabilized Fe in drinking water treatment residue with implications for environmental remediation
Changhui Wang, Zhanling Wang, Huacheng Xu, Leilei Bai, Cheng Liu, Helong Jiang, Peixin Cui
Water Research.2021; 189: 116688. CrossRef
Methanobacterium Capable of Direct Interspecies Electron Transfer
Shiling Zheng, Fanghua Liu, Bingchen Wang, Yuechao Zhang, Derek R. Lovley
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Formation of Zerovalent Iron in Iron-Reducing Cultures of Methanosarcina barkeri
Haitao Shang, Mirna Daye, Orit Sivan, Caue S. Borlina, Nobumichi Tamura, Benjamin P. Weiss, Tanja Bosak
Environmental Science & Technology.2020; 54(12): 7354. CrossRef
Tackling antibiotic inhibition in anaerobic digestion: The roles of Fe3+ and Fe3O4 on process performance and volatile fatty acids utilization pattern
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A potential contribution of a Fe(III)-rich red clay horizon to methane release: Biogenetic magnetite-mediated methanogenesis
Leilei Xiao, Wenchao Wei, Min Luo, Hengduo Xu, Dawei Feng, Jiafeng Yu, Jiafang Huang, Fanghua Liu
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Li Zhuang, Ziyang Tang, Zhen Yu, Jian Li, Jia Tang
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A new insight into the strategy for methane production affected by conductive carbon cloth in wetland soil: Beneficial to acetoclastic methanogenesis instead of CO2 reduction
Jiajia Li, Leilei Xiao, Shiling Zheng, Yuechao Zhang, Min Luo, Chuan Tong, Hengduo Xu, Yang Tan, Juan Liu, Oumei Wang, Fanghua Liu
Science of The Total Environment.2018; 643: 1024. CrossRef

Research Support, Non-U.S. Gov'ts

Methyl Coenzyme M Reductase (mcrA) Gene Based Phylogenetic Analysis of Methanogens Population in Murrah Buffaloes (Bubalus bubalis): Prem Prashant Chaudhary , Sunil Kumar Sirohi , Dheer Singh , Jyoti Saxena; J. Microbiol. 2011;49(4):558-561. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-1052-y

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Abstract: The aim of the present study was to decipher the diversity of methanogens in rumen of Murrah buffaloes so that effective strategies can be made in order to mitigate methane emission from these methanogens. In the present study diversity of rumen methanogens in Murrah buffaloes (Bubalus bubalis) from North India was evaluated by using mcr-A gene library obtained from the pooled PCR product from four animals and by using MEGA4 software. A total of 104 clones were examined, revealing 26 different mcr-A gene sequences or phylotypes. Of the 26 phylotypes, 16 (64 of 104 clones) were less than 97% similar to any of the cultured strain of methanogens. Seven clone sequences were clustered with Methanomicrobium mobile and three clone sequences were clustered with Methanobrevibacter gottschalkii during the phylogenetic analysis. Uncultured group of methanogens comes out to be the major component of the methanogens community structure in Murrah buffaloes. Methanomicrobium phylotype comes out to be major phylotype among cultured methanogens followed by Methanobrevibacter phylotype. These results help in making effective strategies to check the growth of dominant methanogenic communities in the rumen of this animal which in turn help in the reduction of methane emission in the environment and ultimately helps us in fighting with the problem of global warming.

Diversity of Bovine Rumen Methanogens In Vitro in the Presence of Condensed Tannins, as Determined by Sequence Analysis of 16S rRNA Gene Library: Hui Yin Tan , Chin Chin Sieo , Chin Mei Lee , Norhani Abdullah , Juan Boo Liang , Yin Wan Ho; J. Microbiol. 2011;49(3):492-498. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0319-7

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Abstract: Molecular diversity of rumen archaeal populations from bovine rumen fluid incubated with or without condensed tannins was investigated using 16S rRNA gene libraries. The predominant order of rumen archaea in the 16S rRNA gene libraries of the control and condensed tannins treatment was found to belong to a novel group of rumen archaea that is distantly related to the order Thermoplasmatales, with 59.5% (15 phylotypes) and 81.43% (21 phylotypes) of the total clones from the control and treatment clone libraries, respectively. The 16S rRNA gene library of the control was found to have higher proportions of methanogens from the orders Methanomicrobiales (32%) and Methanobacteriales (8.5%) as compared to those found in the condensed tannins treatment clone library in both orders (16.88% and 1.68% respectively). The phylotype distributed in the order Methanosarcinales was only found in the control clone library. The study indicated that condensed tannins could alter the diversity of bovine rumen methanogens.

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