Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments

Chen, Jing; Dick, Richard P.; Lin, Jih‐Gaw; Gu, Ji Dong

doi:10.1007/s00253-016-7853-5

Cited by 23 publications

(4 citation statements)

References 74 publications

(6 reference statements)

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“…The catalyzed reporter deposition-FISH method was used to detect NC10 bacteria in the sediments of Lake Biwa, which marks the first application of the FISH method in environmental samples. However, for the purpose of environmental detection, the FISH method is considered less sensitive compared with the PCR approach and could be limited if the abundance of the target microorganism is low in the environment (Chen et al, 2016).…”

Section: Amo Reactions With Different Eacceptorsmentioning

confidence: 99%

The denitrifying anaerobic methane oxidation process and microorganisms in the environments: A review

Wei

Wang

et al. 2022

Front. Mar. Sci.

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Methane (CH4) is an important greenhouse gas with a global warming potential 28 – 34 times that of CO2 over the 100-year horizon. Denitrifying anaerobic methane oxidation (DAMO) is a recently discovered process that potentially represents an important CH4 sink globally. This process involves two possible pathways: the nitrite-dependent DAMO mediated by NC10 bacteria and the nitrate-dependent DAMO by ANME-2d archaea. Both are widely detected in freshwater and coastal habitats using molecular tools. However, the distributions of these two processes and the functional microorganisms and their interactions with other N cycling pathways are far from clear. In this review, we conducted a scientometric analysis on a co-citation network consisting of 835 references derived from 354 citing articles closely related to the distribution of DAMO in the environment. Through this analysis, we found that current studies focus more on freshwater systems than coastal systems, and ANME-2d archaea are generally under-studied compared to NC10 bacteria. The emerging research topics in this area include AMO processes coupled to alternative electron acceptors and their role as CH4 sinks. We further reviewed papers focusing on DAMO distribution in freshwater and coastal environments guided by the result of the scientometric analysis. Finally, we identified several areas that require further research and proposed future research including comparisons of DAMO with other N cycling pathways and environmental conditions in the context of the river-estuary-sea continuum.

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Section: Amo Reactions With Different Eacceptorsmentioning

confidence: 99%

The denitrifying anaerobic methane oxidation process and microorganisms in the environments: A review

Wei

Wang

et al. 2022

Front. Mar. Sci.

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“…The metabolism of Ca. M. oxyfera is also complex and unusual, because despite being considered an anaerobic microorganism, it is able to oxidize CH 4 using enzymes found in aerobic methanotrophs (Ettwig et al, 2010) such as the particulate methane-monooxygenase (pMMO), encoded in the pmoA gene, which has been used as a biomarker of N-damo bacteria in marine systems (e.g., Chen et al, 2016;Padilla et al, 2016). Metagenomic evidence suggests that Ca.…”

Section: Nitrate/nitrite-dependent Anaerobic Methane Oxidation (N-damo)mentioning

confidence: 99%

Processes and Microorganisms Involved in the Marine Nitrogen Cycle: Knowledge and Gaps

2019

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Nitrogen (N) is a key element for life in the oceans. It controls primary productivity in many parts of the global ocean, consequently playing a crucial role in the uptake of atmospheric carbon dioxide. The marine N cycle is driven by multiple biogeochemical transformations mediated by microorganisms, including processes contributing to the marine fixed N pool (N 2 fixation) and retained N pool (nitrification, assimilation, and dissimilatory nitrate reduction to ammonia), as well as processes contributing to the fixed N loss (denitrification, anaerobic ammonium oxidation and nitrite-dependent anaerobic methane oxidation). The N cycle maintains the functioning of marine ecosystems and will be a crucial component in how the ocean responds to global environmental change. In this review, we summarize the current understanding of the marine microbial N cycle, the ecology and distribution of the main functional players involved, and the main impacts of anthropogenic activities on the marine N cycle.

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“…DAMO bacteria, belonging to the NC10 phylum ( Ettwig et al, 2010 ), is one of the major functional microorganisms participating in DAMO process. Up to now, five phylogenetically distinct subgroups of DAMO bacteria (Groups A–E) have been verified ( Chen et al, 2016 ), among which Group A and Group B were widely distributed in freshwater ecosystem. For example, Group B was more abundant than Group A in the Qiantang River ( Shen et al, 2014 ), while the dominant subgroups were found to be distinct in different reaches in the Wuxijiang River ( Cheng et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process

Wang

Zhu

et al. 2022

Front. Microbiol.

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Denitrifying anaerobic methane-oxidizing bacteria (DAMO bacteria) plays an important role in reducing methane emissions from river ecosystems. However, the assembly process of their communities underlying different hydrologic seasons remains unclarified. In this study, the dynamics of DAMO bacterial communities in river networks of the Taihu Basin were investigated by amplicon sequencing across wet, normal, and dry seasons followed by multiple statistical analyses. Phylogenetic analysis showed that Group B was the major subgroup of DAMO bacteria and significant dynamics for their communities were observed across different seasons (constrained principal coordinate analysis, p = 0.001). Furthermore, the neutral community model and normalized stochasticity ratio model were applied to reveal the underlying assembly process. Stochastic process and deterministic process dominated the assembly process in wet season and normal season, respectively and similar contributions of deterministic and stochastic processes were observed in dry season. Meanwhile, abundant (relative abundance >0.1%) and rare (relative abundance <0.01%) DAMO bacterial communities were found to be shaped via distinct assembly processes. Deterministic and stochastic processes played a considerable role in shaping abundant DAMO bacterial communities, while deterministic process mainly shaped rare DAMO bacterial communities. Results of this study revealed the dynamics of DAMO bacterial communities in river networks and provided a theoretical basis for further understanding of the assembly process.

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Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments

Cited by 23 publications

References 74 publications

The denitrifying anaerobic methane oxidation process and microorganisms in the environments: A review

The denitrifying anaerobic methane oxidation process and microorganisms in the environments: A review

Processes and Microorganisms Involved in the Marine Nitrogen Cycle: Knowledge and Gaps

Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process

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