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Hou A, Fu H, Liu L, Su X, Zhang S, Lai J, Sun F. Exploring the distribution and co-occurrence of rpf-like genes and nitrogen-cycling genes in water reservoir sediments. Front Microbiol 2024; 15:1433046. [PMID: 39104579 PMCID: PMC11298755 DOI: 10.3389/fmicb.2024.1433046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/12/2024] [Indexed: 08/07/2024] Open
Abstract
Water reservoir sediments represent a distinct habitat that harbors diverse microbial resources crucial for nitrogen cycling processes. The discovery of resuscitation promoting factor (Rpf) has been recognized as a crucial development in understanding the potential of microbial populations. However, our understanding of the relationship between microorganisms containing rpf-like genes and nitrogen-cycling functional populations remains limited. The present study explored the distribution patterns of rpf-like genes and nitrogen-cycling genes in various water reservoir sediments, along with their correlation with environmental factors. Additionally, the co-occurrence of rpf-like genes with genes associated with the nitrogen cycle and viable but non-culturable (VBNC) formation was investigated. The findings indicated the ubiquitous occurrence of Rpf-like domains and their related genes in the examined reservoir sediments. Notably, rpf-like genes were predominantly associated with Bradyrhizobium, Nitrospira, and Anaeromyxobacter, with pH emerging as the primary influencing factor for their distribution. Genera such as Nitrospira, Bradyrhizobium, Anaeromyxobacter, and Dechloromonas harbor the majority of nitrogen-cycling functional genes, particularly denitrification genes. The distribution of nitrogen-cycling microbial communities in the reservoir sediments was mainly influenced by pH and NH4 +. Notably, correlation network analysis revealed close connections between microorganisms containing rpf-like genes and nitrogen-cycling functional populations, as well as VBNC bacteria. These findings offer new insights into the prevalence of rpf-like genes in the water reservoir sediments and their correlation with nitrogen-cycling microbial communities, enhancing our understanding of the significant potential of microbial nitrogen cycling.
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Affiliation(s)
- Aiqin Hou
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
| | - Huayi Fu
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
| | - Leilei Liu
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
| | - Shusheng Zhang
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou, China
| | - Jiahou Lai
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [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: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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Feng L, Hu P. Changing temporal and spatial patterns of methane emission from rivers by reservoir dams: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27716-5. [PMID: 37219780 DOI: 10.1007/s11356-023-27716-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 05/13/2023] [Indexed: 05/24/2023]
Abstract
Dams built on rivers can bring economic benefits to local production and are considered to be environmentally friendly. However, in recent years, many researchers found that the establishment of dams has created excellent conditions for the production of methane (CH4) in rivers, making it change from a "weak source" of rivers to a "strong source" of dams. In particular, reservoir dams have a great impact on CH4 emission in rivers within their regions in terms of time and space. Spatially, the sedimentary layer and water level fluctuation zone of reservoirs are the main direct and indirect causes of CH4 production. Temporally, the synergetic effect between water level adjustment of the reservoir dam and environmental factors leads to large changes in the substances of the water body, impacts on the production and transport of CH4. Finally, the generated CH4 is emitted into the atmosphere through several important emission modes: molecular diffusion, bubbling, and degassing. The contribution of CH4 emitted from reservoir dams to the global greenhouse effect cannot be ignored.
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Affiliation(s)
- Lan Feng
- College of Civil Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- Ecological Complexity and Modeling Laboratory, Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
- College of Environment and Biology, Nanjing Forestry University, Nanjing, 210037, China.
| | - Pan Hu
- College of Civil Engineering, Nanjing Forestry University, Nanjing, 210037, China
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Yue Y, Wang F, Pan J, Chen XP, Tang Y, Yang Z, Ma J, Li M, Yang M. Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load. FEMS Microbiol Ecol 2022; 98:6701916. [PMID: 36111740 DOI: 10.1093/femsec/fiac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023] Open
Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
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Affiliation(s)
- Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xue-Ping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Yi Tang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Zhihong Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
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Parida PK, Behera BK, Dehury B, Rout AK, Sarkar DJ, Rai A, Das BK, Mohapatra T. Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:71311-71325. [PMID: 35596862 DOI: 10.1007/s11356-022-20766-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.
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Affiliation(s)
- Pranaya Kumar Parida
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India.
| | - Budheswar Dehury
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
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Shen H, Ye L, Cai Q, Tan L. Longitudinal Variations in Physiochemical Conditions and Their Consequent Effect on Phytoplankton Functional Diversity Within a Subtropical System of Cascade Reservoirs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.914623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The social and environmental impacts of large dams are quantifiable and have been well documented, while small dams have often been presumed to be less environmentally damaging than large dams. The purpose of this study was to analyze longitudinal gradients in environmental, hydrodynamic variables and their impact on phytoplankton function, within a cascade of four reservoirs (XuanMiaoGuan, XMG; TianFuMiao, TFM; XiBeiKou, XBK; ShangJiaHe, SJH) and one reservoir bay (Huangbohe Bay, HBH), located from upstream to downstream in the Huangbo River, Hubei Province, China. Our results showed that water temperature, total nitrogen, and soluble silicate increased along the cascade reservoir system, while the concentration of dissolved oxygen and total phosphorus decreased. We identified 16 phytoplankton functional groups, and the predominant groups, including D (Synedra and Stephanodiscus hantzschii), E (Dinobryon divergens), Lo (Dinoflagellate: Peridinium bipes and Peridiniopsis), X2 (Chroomona), and Y (Cryptomonas), changed longitudinally from up to down in the cascade reservoirs. The number of dominant functional groups increased along the longitudinal gradient, indicating that the function of the phytoplankton community was more stable. Functional group D was the dominant phytoplankton functional group among the four reservoirs, and Lo group was dominant except SJH. The phytoplankton functional groups in the HBH have been completely changed due to the backwater jacking of the main stream of the Yangtze River. Euphotic depth, suspended solids, and nutrients were apparently the key factors driving variations in phytoplankton functional groups among the reservoirs. Notably, the patterns we observed were not all consistent with the cascading reservoir continuum concept (CRCC) that typically characterizes large rivers. Thus, our findings contribute to the further theoretical development of the CRCC, which may not apply widely to all cascade systems.
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