Effects of copper on methane emission, methanogens and methanotrophs in the rhizosphere and bulk soil of rice paddy

Mao, Tingting; Yin, Rui; Deng, Huan

doi:10.1016/j.catena.2015.05.024

Cited by 22 publications

(4 citation statements)

References 48 publications

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“…The phylum Euryarchaeota was detected in all profile depths with the proportion varying between 9.7 and 44.6% and mainly composed of Methanobacteria and Methanomicrobia in this study. The proportions in the present study were clearly higher than the proportion (∼15%) in upland soils according to previously reported ( Hu et al, 2013 ), as the representative Euryarchaeota -affiliating class Methanobacteria and Methanomicrobia were commonly detected in anaerobic environments such as aquatic ecosystems, wetlands, and paddy soils and responsible for methanogenesis ( Mao et al, 2015 ; Tong et al, 2015 ). Although the two classes were both detected in all the samples, the ratio of Methanobacteria and Methanomicrobia proportion varied markedly among soils types, ranging from 22.22 in BH soils to 0.23 in TY soils.…”

Section: Discussionsupporting

confidence: 51%

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

et al. 2017

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Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

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Section: Discussionsupporting

confidence: 51%

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

et al. 2017

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“…Cu has long been considered, and proven to have antimicrobial properties (Berg et al, 2005;Gajjar et al, 2009;Wheeldon et al, 2008), and is also found to commonly alter soil microbial communities (Nunes et al, 2016;Smit et al, 1997), which could have impacted the microbial communities involved in aerobic decomposition, resulting in reduced CO2 emissions with 20 increased concentration of Cu. This element is also known to affect anaerobic microbial communities, however the effects of Cu on methanotrophs are greater than their effects on methanogens (Mao et al, 2015), and in environments with high C content, Cu concentrations were also found to favour CH4 emissions (Jiao et al, 2005). Therefore higher Cu concentrations likely significantly impacted CO2 emissions but not CH4 emissions in our study.…”

Section: Higher Nutrient Content In Primary Forest and Their Impact Omentioning

confidence: 49%

Are secondary forests second-rate? Comparing peatland greenhouse gas emissions, chemical and microbial community properties between primary and secondary forests in Peninsular Malaysia

Dhandapani

Ritz

Evers

et al. 2019

Science of The Total Environment

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“…Previous studies have separately discussed methanogens or methanotrophs in the context of their distinct community composition in bulk soil and the rhizosphere (Eller & Frenzel, 2001; Mao et al., 2015), or the differences in community composition among different rice cultivars in the rhizosphere, rhizoplane and endosphere (Liechty et al., 2020). However, limited research has focused on co‐occurrence network evidence for community interactions between methanogens and methanotrophs.…”

Section: Introductionmentioning

confidence: 99%

Methanogen–methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane

Wang,

Guo,

Yang

et al. 2024

Molecular Ecology

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Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high‐throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross‐feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance–decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.

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Effects of copper on methane emission, methanogens and methanotrophs in the rhizosphere and bulk soil of rice paddy

Cited by 22 publications

References 48 publications

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

Are secondary forests second-rate? Comparing peatland greenhouse gas emissions, chemical and microbial community properties between primary and secondary forests in Peninsular Malaysia

Methanogen–methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane

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