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Zhang R, Xu Q, Song Z, Wu J, Chen H, Bai X, Wang N, Chen Y, Huang D. Manipulating soil microbial community assembly by the cooperation of exogenous bacteria and biochar for establishing an efficient and healthy CH 4 biofiltration system. CHEMOSPHERE 2024; 352:141319. [PMID: 38286313 DOI: 10.1016/j.chemosphere.2024.141319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/05/2024] [Accepted: 01/27/2024] [Indexed: 01/31/2024]
Abstract
Manipulating the methanotroph (MOB) composition and microbial diversity is a promising strategy to optimize the methane (CH4) biofiltration efficiency of an engineered landfill cover soil (LCS) system. Inoculating soil with exogenous MOB-rich bacteria and amending soil with biochar show strong manipulating potential, but how the two stimuli interactively shape the microbial community structure and diversity has not been clarified. Therefore, three types of soils with active CH4 activities, including paddy soil, river wetland soil, and LCS were selected for enriching MOB-dominated communities (abbreviated as B_PS, B_RWS, and B_LCS, respectively). They were then inoculated to LCS which was amended with two distinct biochar. Besides the aerobic CH4 oxidation efficiencies, the evolution of the three microbial communities during the MOB enrichment processes and their colonization in two-biochar amended LCS were obtained. During the MOB enriching, a lag phase in CH4 consumption was observed merely for B_LCS. Type II MOB Methylocystis was the primary MOB for both B_PS and B_LCS; while type I MOB dominated for B_RWS and the major species were altered by gas concentrations. Compared to biochar, a more critical role was demonstrated for the bacteria inoculation in determining the community diversity and function of LCS. Instead, biochar modified the community structures by mainly stimulating the dominant MOB but could induce stochastic processes in community assembly, possibly related to its inorganic nutrients. Particularly, combined with biochar advantages, the paddy soil-derived bacteria consortiums with diverse MOB species demonstrated the potent adaption to LCS niches, not only retaining the high CH4-oxidizing capacities but also shaping a community structure with more diverse soil function. The results provided new insights into the optimization of an engineered CH4-mitigation soil system by manipulating the soil microbiomes with the cooperation of exogenous bacteria and biochar.
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Affiliation(s)
- Rujie Zhang
- Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, China
| | - Qiyong Xu
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, China
| | - Zilong Song
- Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, China
| | - Jiang Wu
- Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, China
| | - Huaihai Chen
- Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, China
| | - Xinyue Bai
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, China
| | - Ning Wang
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, China
| | - Yuke Chen
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, China
| | - Dandan Huang
- Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, China.
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Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps. mSystems 2022; 7:e0032022. [PMID: 35938718 PMCID: PMC9426478 DOI: 10.1128/msystems.00320-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.
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Zhao F, Zhou Y, Xu H, Zhu G, Zhan X, Zou W, Zhu M, Kang L, Zhao X. Oxic urban rivers as a potential source of atmospheric methane. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 297:118769. [PMID: 34973384 DOI: 10.1016/j.envpol.2021.118769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/20/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Urban rivers play a vital role in global methane (CH4) emissions. Previous studies have mainly focused on CH4 concentrations in urban rivers with a large amount of organic sediment. However, to date, the CH4 concentration in gravel-bed urban rivers with very little organic sediment has not been well documented. Here, we collected water samples from an oxic urban river (Xin'an River, China; annual mean dissolved oxygen concentration was 9.91 ± 1.99 mg L-1) with a stony riverbed containing very little organic sediment. Dissolved CH4 concentrations were measured using a membrane inlet mass spectrometer to investigate whether such rivers potentially act as an important source of atmospheric CH4 and the corresponding potential drivers. The results showed that CH4 was supersaturated at all sampling sites in the five sampling months. The mean CH4 saturation ratio (ratio of river dissolved CH4 concentration to the corresponding CH4 concentration that is in equilibrium with the atmosphere) across all sampling sites in the five sampling months was 204 ± 257, suggesting that the Xin'an River had a large CH4 emission potential. The CH4 concentration was significantly higher in the downstream river than in the upstream river (p < 0.05), which suggested that human activities along the river greatly impacted the CH4 level. Statistical analyses and incubation experiments indicated that algae can produce CH4 under oxic conditions, which may contribute to the significantly higher CH4 concentration in August 2020 (p < 0.001) when a severe algal bloom occurred. Furthermore, other factors, such as heavy rainfall events, dissolved organic carbon concentration, and water temperature, may also be vital factors affecting CH4 concentration. Our study enhances the understanding of dissolved CH4 dynamics in oxic urban rivers with very little organic sediment and further proposes feasible measures to control the CH4 concentration in urban rivers.
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Affiliation(s)
- Feng Zhao
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China; School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Yongqiang Zhou
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Hai Xu
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Guangwei Zhu
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Xu Zhan
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Wei Zou
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Mengyuan Zhu
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Lijuan Kang
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Xingchen Zhao
- State Key Laboratory of Lake and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
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