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Microorganisms
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Microbial Communities Involved in the Methane Cycle
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Microbial Communities Involved in the Methane Cycle

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 7723

Special Issue Editor

Dr. Alexander Yu Merkel

E-Mail Website
Guest Editor
Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
Interests: microbiology; bioinformatics; ecology; methane cycle

Special Issue Information

Dear Colleagues,

The methane cycle is one of the key components of the global carbon cycle and has a direct impact on the biosphere and climate of Earth. Methane is considered to be the second most important “greenhouse gas”. About 70–80% of methane emission to the atmosphere is of modern biogenic origin. The main agents responsible for biological methane production are methanogenic archaea. They are widely distributed in nature where they usually act as a terminal link in the anaerobic degradation of organic matter. They can also be primary producers of organic matter in ecotopes where substrates for methanogenesis are formed by abiotic reactions, e.g., in geothermal conditions. In recent years, our knowledge of the diversity of methanogens has expanded considerably. This leads to the next task for researchers: assessment of the ecological significance of these newly discovered groups of methanogens. Methanotrophic microorganisms oxidize methane to gain energy under oxic and anoxic conditions using a range of electron acceptors. Recent years have also been characterized by the convincing progress of our understanding of the diversity and physiology of these microorganisms. The evaluation of their global role as a methane sink may be the main focus of their future study. The diversity, ecological role, and physiology of numerous syntrophic partners of methanogenic and methanotrophic prokaryotes also deserve special attention since their activity can be the limiting link in the methane cycle stages. All these tasks can be successfully completed thanks to integrated approaches, including NGS-based molecular methods, bioinformatics, cultivation of new prokaryotes, isotope-based process rate estimation, and statistical approaches.

Dr. Alexander Yu Merkel
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • methane cycle
  • methanotrophic microorganisms
  • methanogenic prokaryotes
  • diversity

Published Papers (5 papers)

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Research

16 pages, 3130 KiB  
Article
Enhancing the Startup Rate of Microbial Methanogenic Systems through the Synergy of β-lactam Antibiotics and Electrolytic Cells
by Yuting Zhe, Huaigang Cheng, Fangqin Cheng, Huiping Song and Zihe Pan
Microorganisms 2024, 12(4), 734; https://doi.org/10.3390/microorganisms12040734 - 3 Apr 2024
Viewed by 630
Abstract
The slow startup and suboptimal efficiency of microbial carbon sequestration and methane-production systems have not been fully resolved despite their contribution to sustainable energy production and the reduction of greenhouse gas emissions. These systems often grapple with persistent hurdles, including interference from miscellaneous [...] Read more.
The slow startup and suboptimal efficiency of microbial carbon sequestration and methane-production systems have not been fully resolved despite their contribution to sustainable energy production and the reduction of greenhouse gas emissions. These systems often grapple with persistent hurdles, including interference from miscellaneous bacteria and the slow enrichment of methanogens. To address these issues, this paper examines the synergistic effect of coupling β-lactam antibiotics with an electrolytic cell on the methanogenic process. The results indicated that β-lactam antibiotics exhibited inhibitory effects on Campylobacteria and Alphaproteobacteria (two types of miscellaneous bacteria), reducing their relative abundance by 53.03% and 87.78%, respectively. Nevertheless, it also resulted in a decrease in hydrogenogens and hindered the CO2 reduction pathway. When coupled with an electrolytic cell, sufficient electrons were supplied for CO2 reduction to compensate for the hydrogen deficiency, effectively mitigating the side effects of antibiotics. Consequently, a substantial improvement in methane production was observed, reaching 0.57 mL·L−1·d−1, exemplifying a remarkable 6.3-fold increase over the control group. This discovery reinforces the efficiency of methanogen enrichment and enhances methane-production levels. Full article
(This article belongs to the Special Issue Microbial Communities Involved in the Methane Cycle)
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15 pages, 5289 KiB  
Article
Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep
by Song Zhong, Jingchun Feng, Jie Kong, Yongji Huang, Xiao Chen and Si Zhang
Microorganisms 2023, 11(12), 3001; https://doi.org/10.3390/microorganisms11123001 - 18 Dec 2023
Cited by 1 | Viewed by 904
Abstract
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We [...] Read more.
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics. Full article
(This article belongs to the Special Issue Microbial Communities Involved in the Methane Cycle)
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17 pages, 5151 KiB  
Article
A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California
by John E. Hinkle, Paraskevi Mara, David J. Beaudoin, Virginia P. Edgcomb and Andreas P. Teske
Microorganisms 2023, 11(12), 2956; https://doi.org/10.3390/microorganisms11122956 - 10 Dec 2023
Cited by 1 | Viewed by 951
Abstract
The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and [...] Read more.
The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin. Full article
(This article belongs to the Special Issue Microbial Communities Involved in the Methane Cycle)
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15 pages, 1794 KiB  
Article
Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria
by Alexander I. Slobodkin, Nataliya M. Ratnikova, Galina B. Slobodkina, Alexandra A. Klyukina, Nikolay A. Chernyh and Alexander Y. Merkel
Microorganisms 2023, 11(3), 555; https://doi.org/10.3390/microorganisms11030555 - 22 Feb 2023
Cited by 4 | Viewed by 2042
Abstract
The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an [...] Read more.
The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood–Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide. Full article
(This article belongs to the Special Issue Microbial Communities Involved in the Methane Cycle)
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22 pages, 5403 KiB  
Article
Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea
by Alexander S. Savvichev, Igor I. Rusanov, Vitaly V. Kadnikov, Alexey V. Beletsky, Elena E. Zakcharova, Olga S. Samylina, Pavel A. Sigalevich, Igor P. Semiletov, Nikolai V. Ravin and Nikolay V. Pimenov
Microorganisms 2023, 11(2), 250; https://doi.org/10.3390/microorganisms11020250 - 19 Jan 2023
Cited by 7 | Viewed by 2264
Abstract
Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol [...] Read more.
Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH4 dm−3. Methane carbon isotopic composition (δ13C-CH4) varied from −98.9 to −77.6‰, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4–5.0 nmol dm−3 day−1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm−3 day−1 at the seep stations. Four lineages of anaerobic methanotrophic archaea (ANME) (1, 2a–2b, 2c, and 3) were found in the deeper sediments at the seep stations along with sulfate-reducing Desulfobacteriota. The ANME-2a-2b clade was predominant among ANME. Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments along with heterotrophic Actinobacteriota and Bacteroidota, and mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae). Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean. Full article
(This article belongs to the Special Issue Microbial Communities Involved in the Methane Cycle)
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