The key role of Geobacter in regulating emissions and biogeochemical cycling of soil-derived greenhouse gases

Li, Tian; Zhou, Qixing

doi:10.1016/j.envpol.2020.115135

Cited by 37 publications

(13 citation statements)

References 132 publications

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“…The most important biomarkers were almost aerobic, including bacteria for nitrifying or nitrosifying ( Rhodopseudomonas and Nitrosomonas ), aerobic organic matter degradation ( Acinetobacter , Cellulomonas , Luteolibacter ), , tolerance to oxidative stress ( Ramlibacter ), and Cu binding ( Psudomonas and Sphingomonas ), in regard to the bacterial community. The most important biomarkers responding to the control without the oxygen nanobubble amendment were strictly or facultatively anaerobic, including bacteria for N 2 fixation ( Azospira, Devosia , and Paenibacillus ), anaerobic organic matter degradation ( Lautropia , Terrisporobacter , Rhodopseudomonas and Muribaculaceae ), , sulfur oxidation ( Thiobacillus ), and methanogensis and denitrification ( Geobacter ) . The most important biomarkers responding to the ONBC treatment in the fungal community include organic matter mineralization ( Aspergillus , Botryotrichum , Thermomyces , and Mortierella ) − and Cu binding ( Acremonium , Pichia , Sakaguchia , and Penicillium ). − The most important biomarkers responding to the control without the oxygen nanobubble amendment include beneficial endophytes ( Porostereum , Serendipita , and Schizothecium ), phytopathogens ( Myrmecridium , Mycosphaerella , and Stemphylium ), , and biocontrol against phytopathogens ( Fusicolla and Periconia ). , The different microbial biomarkers between the ONBC treatments and control implied that the fungi and aerobic bacteria that are beneficial for Cu binding and organic matter mineralization contributed more in response to the ONBC treatments, which could further affect Cu sequestration and nutrients availability in soil.…”

Section: Resultsmentioning

confidence: 99%

“…The ONBC amendment inhibited bacterial N metabolism via these pathways. The enzymes involved in N dissimilation, assimilation, denitrification, and N 2 fixation generally require an anaerobic environment. , Therefore, their metabolism may suffer negative effects from increased DO. The flooding hypoxia in paddy soils is favorable for azotobacter to fix N 2 from the atmosphere. , The increased DO might have inhibited N 2 fixation and impeded the soil ammonium availability.…”

Section: Resultsmentioning

confidence: 99%

“…The most important biomarkers responding to the control without the oxygen nanobubble amendment were strictly or facultatively anaerobic, including bacteria for N 2 fixation (Azospira, Devosia, and Paenibacillus), 43 anaerobic organic matter degradation (Lautropia, Terrisporobacter, Rhodopseudomonas and Muribaculaceae), 44,45 sulfur oxidation (Thiobacillus), 46 and methanogensis and denitrification (Geobacter). 47 The most important biomarkers responding to the ONBC treatment in the fungal community include organic matter mineralization (Aspergillus, Botryotrichum, Thermomyces, and Mortierella) 48−50 and Cu binding (Acremonium, Pichia, Sakaguchia, and Penicillium). 51−53 The most important biomarkers responding to the control without the oxygen nanobubble amendment include beneficial endophytes (Porostereum, Serendipita, and Schizothecium), 54 phytopathogens (Myrmecridium, Mycosphaerella, and Stemphylium), 55,56 and biocontrol against phytopathogens (Fusicolla and Periconia).…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Oxygen Nanobubble-Loaded Biochars Mitigate Copper Transfer from Copper-Contaminated Soil to Rice and Improve Rice Growth

Chu

Sha

Feng

et al. 2023

ACS Sustainable Chem. Eng.

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Copper (Cu)-contaminated paddy soil has caused substantial concerns for human health through biomagnification in the soil–rice–human chain. In this study, oxygen nanobubble-loaded biochars (ONBC), including pyrochars (NPC) and hydrochars (NHC), were used to amend Cu-contaminated paddy soils and reduce rice Cu toxicity. The ONBC amendment improved the rhizospheric redox potential and dissolved oxygen concentration via slow, continuous oxygen release, promoting root iron plaque formation and effectively inhibiting root Cu influx. Moreover, the ONBC amendment improved soil microbial diversity. The abundance of bacterial genes involved in cytosolic Cu complexation and Cu export to the periplasm space for Cu stabilization markedly improved. The sequestered Cu in root iron plaque and soil bacteria inhibited Cu influx into the shoots to avoid Cu overaccumulation in the edible parts. This was reflected by the Cu content decreasing by 1.91-fold and 2.38-fold in shoots under NPC and NHC treatments, respectively. Furthermore, the improved oxygen-enriched rhizosphere environment via the ONBC amendment promoted root activity and the abundance of bacterial genes involved in nutrients mineralization, further promoting shoot biomass by 1.46-fold and 2.29-fold under NPC and NHC treatments, respectively. This study proposes an environmentally friendly strategy to mitigate Cu transfer from soil to crops and improve crop productivity.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Oxygen Nanobubble-Loaded Biochars Mitigate Copper Transfer from Copper-Contaminated Soil to Rice and Improve Rice Growth

Chu

Sha

Feng

et al. 2023

ACS Sustainable Chem. Eng.

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“…Legionella (Vignola et al 2018b)) and soil (i.e. Vicinamibacter (Huber et al 2016), Pseudomonas (Bushnaf et al 2017) and Geobacter (Li and Zhou 2020)).…”

Section: Bacterial Community Compositions Derived From 16s Rrna Gene ...mentioning

confidence: 99%

Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment

Halla

Massawa

Joseph

et al. 2022

Environment International

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“…Both EP and CS, exhibited potentials of bacterial dissimilatory reduction of nitrite to ammonia anaerobically (DNRA, Reaction 9, Figs. 8A and B) (52)(53)(54)(55)(56)(57)59) by organisms such as Campylobacter, Geobacter, Meniscus, Opitutaceae, and Pelotomaculum (70)(71)(72). The anammox, an anaerobic denitri cation process which couples ammonia oxidation with nitrite reduction producing N 2 , seemed to be absent in the stored manure of EP and CS.…”

Section: Characterization Of Nitrogen-transforming Microorganisms In ...mentioning

confidence: 99%

Nitrogen Transformation Processes in Manure Microbiomes of Earthen Pit and Concrete Storages on Commercial Dairy Farms

Khairunisa

Loganathan

Ogejo

et al. 2022

Preprint

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Storing manure is an essential aspect of nutrient management on dairy farms, presenting the opportunity to use it effectively as a fertilizer in crop and pasture production. The storage structures are earthen, concrete, or steel-based constructs. However, this practice presents the potential of losing nitrogen (fertilizer value) and emitting greenhouse gases (environmental stressors) to the atmosphere through microbial and physicochemical processes. We have conducted a study to characterize the relevant microbial processes in two manure storage structures, a clay lined earthen pit and an above-ground concrete storage tank, on commercial dairy farms, to inform the development of mitigation practices to preserve the value of manure. First, we analyzed the 16S rRNA-V4 amplicons generated from manure samples collected from several locations and depths (0.3, 1.2 and 2.1–2.75 meters below the surface) of the storages, identifying a set of OTUs and quantifying their abundances. Then, we inferred the respective metabolic capabilities. These results showed that the manure microbiome composition was more complex and exhibited more location-to-location variation in the earthen pit than in the concrete tank. Further, the inlet and a location with hard surface crust in the earthen pit had unique consortia. The microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to gaseous compounds. However, the microbial conversion of nitrate to emittable N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction seemed possible; minor quantities of nitrate was present in manure, potentially originating from oxidative processes occurring on barn floor. The nitrate-transformation linked OTUs were more prevalent at the near-surface locations and all depths of the inlet. No anammox bacteria and autotrophic nitrifiers, archaeal or bacterial, were detected in both storages. Hydrogenotrophic Methanocorpusculum species were the primary methanogens or methane producers, exhibiting higher abundance in the earthen pit. These findings suggested that microbial activities were not the main drivers for nitrogen loss from manure storage, and commonly reported losses are associated with the physicochemical processes. Finally, the microbiomes of stored manure had the potential to emit greenhouse gases such as NO, N2O, and methane.

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The key role of Geobacter in regulating emissions and biogeochemical cycling of soil-derived greenhouse gases

Cited by 37 publications

References 132 publications

Oxygen Nanobubble-Loaded Biochars Mitigate Copper Transfer from Copper-Contaminated Soil to Rice and Improve Rice Growth

Oxygen Nanobubble-Loaded Biochars Mitigate Copper Transfer from Copper-Contaminated Soil to Rice and Improve Rice Growth

Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment

Nitrogen Transformation Processes in Manure Microbiomes of Earthen Pit and Concrete Storages on Commercial Dairy Farms

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