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Zhang Y, Chen J, Du M, Ruan Y, Wang Y, Guo J, Yang Q, Shao R, Wang H. Metagenomic insights into microbial variation and carbon cycling function in crop rotation systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174529. [PMID: 38986711 DOI: 10.1016/j.scitotenv.2024.174529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
The decomposition and utilization of plant-derived carbon by microorganisms and carbon fixation are crucial pathways for enhancing soil organic carbon (SOC) storage. However, a gap remains in our understanding of the impact of microorganisms on the decomposition of plant-derived carbon and their capacity for carbon fixation in crop rotation systems. Based on a 12-year experiment with wheat-maize (WM), wheat-cotton (WC), and wheat-soybean (WS) rotations, the microbial communities and carbon cycle function were investigated. The results indicated that WS rotation significantly increased SOC content compared to WM and WC. In addition, a significant increase was observed in microbially available carbon and microbial biomass carbon in the WS soil compared with those in the others. Further analysis of the microbial community factors that influenced SOC content revealed that WS rotation, in contrast to WM rotation, enhanced the diversity and richness of bacteria and fungi. Analysis of microbial carbon decomposition functions revealed an increase in starch, lignin, and hemicellulose decomposition genes in the WS soil compared to the others. The changes in carbon decomposition genes were primarily attributed to six bacterial genera, namely Nocardioides, Agromyces, Microvirga, Skermanella, Anaeromyxobacter, and Arthrobacter, as well as four fungal genera, namely Dendryphion, Staphylotrichum, Apiotrichum, and Abortiporus, which were significantly influenced by the crop rotation systems. In addition, microbial carbon fixation-related genes such as ACAT, IDH1, GAPDH, rpiA, and rbcS were significantly enriched in WS. Species annotation of differential carbon fixation genes identified 18 genera that play a role in soil carbon fixation variation within the crop rotation systems. This study highlights the impact of crop rotation systems on SOC content and alterations in specific microbial communities on carbon cycle function.
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Affiliation(s)
- Yinglei Zhang
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China
| | - Jinping Chen
- Shangqiu Station of National Field Agroecosystem Experimental Network, Shangqiu 476000, Henan, PR China
| | - Mingxue Du
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China
| | - Yihao Ruan
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China
| | - Yongchao Wang
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China; Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Zhengzhou 450046, Henan, PR China
| | - Jiameng Guo
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China; Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Zhengzhou 450046, Henan, PR China
| | - Qinghua Yang
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China; Engineering Research Center for Crop Chemical Regulation, Zhengzhou 450046, Henan, PR China.
| | - Ruixin Shao
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China; Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Zhengzhou 450046, Henan, PR China
| | - Hao Wang
- College of Agronomy, Henan Agriculture University, Zhengzhou 450046, Henan, PR China; Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Zhengzhou 450046, Henan, PR China.
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Qiu Y, Zhang J, Tong YW, He Y. Reverse electron transfer: Novel anaerobic methanogenesis pathway regulated through exogenous CO 2 synergized with biochar. BIORESOURCE TECHNOLOGY 2024; 401:130741. [PMID: 38670292 DOI: 10.1016/j.biortech.2024.130741] [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: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/24/2024] [Indexed: 04/28/2024]
Abstract
Acid accumulation and carbon emission are two major challenges in anaerobic digestion. Syntrophic consortia can employ reverse electron transfer (RET) to facilitate thermodynamically unfavorable redox reactions during acetogenesis. However, the potential mechanisms and regulatory methods of RET remain unclear. This study examines the regulatory mechanisms by which exogenous CO2 affects RET and demonstrates that biochar maximizes CO2 solubility at 25.8 mmol/L to enhance effects further. CO2 synergized with biochar significantly increases cumulative methane production and propionate degradation rate. From the bioenergetic perspective, CO2 decreases energy level to a maximum of -87 kJ/mol, strengthening the thermodynamic viability. The underlying mechanism can be attributed to RET promotion, as indicated by increased formate dehydrogenase and enrichment of H2/formate-producing bacteria with their partner Methanospirillum hungatei. Moreover, the 5 % 13CH4 and methane contribution result show that CO2 accomplishes directed methanogenesis. Overall, this investigation riches the roles of CO2 and biochar in AD surrounding RET.
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Affiliation(s)
- Yang Qiu
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingxin Zhang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Yen Wah Tong
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore
| | - Yiliang He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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Ruan Y, Ling N, Jiang S, Jing X, He JS, Shen Q, Nan Z. Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment. eLife 2024; 12:RP89392. [PMID: 38647539 PMCID: PMC11034942 DOI: 10.7554/elife.89392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the 18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members in Solirubrobacter and Pseudonocardia genera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors.
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Affiliation(s)
- Yang Ruan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Shengjing Jiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
| | - Jin-Sheng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking UniversityBeijingChina
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
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Wang S, Yuan X, Li T, Yang J, Zhao L, Yuan D, Guo Z, Liu C, Duan C. Changes in soil microbe-mediated carbon, nitrogen and phosphorus cycling during spontaneous succession in abandoned PbZn mining areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:171018. [PMID: 38378054 DOI: 10.1016/j.scitotenv.2024.171018] [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: 12/23/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
The mechanism through which soil microorganisms mediate carbon and nutrient cycling during mine wasteland restoration remained unknown. Using soil metagenome sequencing, we investigated the dynamic changes in soil microbial potential metabolic functions during the transition from biological soil crusts (BSC) to mixed broad-conifer forest (MBF) in a typical PbZn mine. The results showed soil microorganisms favored carbon sequestration through anaerobic and microaerobic pathways, predominantly using efficient, low-energy pathways during succession. Genes governing carbon degradation and aerobic respiration increased by 19.56 % and 24.79 %, respectively, reflecting change toward more efficient and intensive soil carbon utilization in late succession. Nitrogen-cycling genes mediated by soil microorganisms met their maximum influence during early succession (sparse grassland, SGL), leading to a respective increase of 75.29 % and 76.81 % in the net potential nitrification rate and total nitrogen content. Mantel and correlation analyses indicated that TOC, TN, Zn and Cd contents were the main factors affecting the soil carbon and phosphorus cycles. Soil AP content emerged as the primary influencer of genes associated with the nitrogen cycle. These results shed light on the dynamic shifts in microbial metabolic activities during succession, providing a genetic insight into biogeochemical cycling mechanisms and underscoring crucial factors influencing soil biogeochemical processes in mining regions.
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Affiliation(s)
- Sichen Wang
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Xinqi Yuan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Ting Li
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Jie Yang
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Luoqi Zhao
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Duanyang Yuan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Zhaolai Guo
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Chang'e Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China
| | - Changqun Duan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming 650091, China.
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Liu C, Liu H, Liu X, Li G, Zhang Y, Zhang M, Li Z. Metagenomic analysis insights into the influence of 3,4-dimethylpyrazole phosphate application on nitrous oxide mitigation efficiency across different climate zones in Eastern China. ENVIRONMENTAL RESEARCH 2023; 236:116761. [PMID: 37516265 DOI: 10.1016/j.envres.2023.116761] [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: 06/05/2023] [Revised: 07/13/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Excessive nitrogen (N) fertilization in agroecological systems increases nitrous oxide (N2O) emissions. 3,4-dimethylpyrazole phosphate (DMPP) is used to mitigate N2O losses. The influence of DMPP efficiency on N2O mitigation was clearly affected by spatiotemporal heterogeneity. Using field and incubation experiments combined with metagenomic sequencing, we aimed to investigate DMPP efficiency and the underlying microbial mechanisms in dark-brown (Siping, SP), fluvo-aquic (Cangzhou, CZ; Xinxiang, XX), and red soil (Wenzhou, WZ) from diverse climatic zones. In the field experiments, the DMPP efficiency in N2O mitigation ranged from 51.6% to 89.9%, in the order of XX, CZ, SP, and WZ. The DMPP efficiency in the incubation experiments ranged from 58.3% to 93.9%, and the order of efficiency from the highest to lowest was the same as that of the field experiments. Soil organic matter, total N, pH, texture, and taxonomic and functional α-diversity were important soil environment and microbial factors for DMPP efficiency. DMPP significantly enriched ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB), which promoted N-cycling with low N2O emissions. Random forest (RF) and regression analyses found that an AOA (Nitrosocosmicus) and NOB (Nitrospina) demonstrated important and positive correlation with DMPP efficiency. Moreover, genes associated with carbohydrate metabolism were important for DMPP efficiency and could influenced N-cycling and DMPP metabolism. The similar DMPP efficiency indicated that the variation in DMPP efficiency was significantly due to soil physicochemical and microbial variations. In conclusion, filling the knowledge gap regarding the response of DMPP efficiency to abiotic and biotic factors could be beneficial in DMPP applications, and in adapting more efficient strategies to improve DMPP efficiency and mitigate N2O emissions in multiple regions.
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Affiliation(s)
- Churong Liu
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China; College of Natural Resources and Environment, Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou, 10642, China
| | - Hongrun Liu
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueqing Liu
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Gang Li
- Key Laboratory of Northeast Crop Physiology Ecology and Cultivation, Ministry of Agriculture in People's Republic of China, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Yushi Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Mingcai Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Li M, Wang K, Zheng W, Maddela NR, Xiao Y, Li Z, Tawfik A, Chen Y, Zhou Z. Metagenomics and network analysis decipher profiles and co-occurrence patterns of bacterial taxa in soils amended with biogas slurry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162911. [PMID: 36933736 DOI: 10.1016/j.scitotenv.2023.162911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Microbial community and interaction play crucial roles in ecological functions of soil including nutrient cycling carbon storage, and water maintenance etc. Numerous studies have shown that the application of fertilizers alters bacterial diversity; However, it remains unknown whether and how the continuous application of biogas slurry from anaerobic digestion affects the spatiotemporal heterogeneity of soil layers, complexity and stability of microbial networks, and functions related to C and N cycling. Here, we investigated the bacterial taxa of purple soils treated with swine biogas slurry for four different periods (0, 1, 3 and 8 years) and five different soil depths (20, 40, 60, 80 and 100 cm). The results showed that the application period of biogas slurry and soil depth were two powerful drivers of bacterial diversity and communities. Biogas slurry input resulted in marked changes in the bacterial diversity and composition at the soil depths of 0-60 cm. The relative abundances of Acidobacteriota, Myxococcot, and Nitrospirota decreased, while Actinobacteria, Chloroflexi, and Gemmatimonadota increased with repeated biogas slurry input. The decreasing complexity and stability of the bacterial network with decreasing nodes, links, robustness, and cohesions were found with increasing years of biogas slurry application, suggesting that the bacterial network of soils treated by the biogas slurry became more vulnerability compared with the control. Also, the linkages between the keystone taxa and soil properties were weakened after biogas slurry input, leading to the cooccurrence patterns being less affected by the keystones in the high level of nutrients. Metagenomic analysis confirmed that biogas slurry input increased the relative abundance of liable-C degradation and denitrification genes, which could highly impact the network properties. Overall, our study could give comprehensive understandings on the impacts of biogas slurry amendment on soils, which could be useful for maintaining sustainable agriculture and soil health with liquid fertilization.
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Affiliation(s)
- Mengjie Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China
| | - Kangting Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China
| | - Wei Zheng
- College of Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Naga Raju Maddela
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Salud, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador
| | - Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Zhaolei Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ahmed Tawfik
- National Research Centre, Water Pollution Research Department, Dokki,Giza 12622, Egypt
| | - Yucheng Chen
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China.
| | - Zhongbo Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China.
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Wei J, Fontaine L, Valiente N, Dörsch P, Hessen DO, Eiler A. Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat. Nat Commun 2023; 14:3234. [PMID: 37270637 DOI: 10.1038/s41467-023-38806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/15/2023] [Indexed: 06/05/2023] Open
Abstract
Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.
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Affiliation(s)
- Jing Wei
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Laurent Fontaine
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Nicolas Valiente
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
- Division of Terrestrial Ecosystem Research, Center of Microbiology and Environmental Systems Science, University of Vienna, 1030, Vienna, Austria
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dag O Hessen
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Alexander Eiler
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway.
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Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
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Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
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10
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Ren Z, Ma K, Jia X, Wang Q, Zhang C, Li X. Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area. MICROBIAL ECOLOGY 2023; 85:904-915. [PMID: 35650293 DOI: 10.1007/s00248-022-02053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 05/04/2023]
Abstract
Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.
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Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China.
- School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xuan Jia
- College of Education for the Future, Beijing Normal University, Zhuhai, 519087, China
| | - Qing Wang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
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11
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Zhao L, Fu G, Pang W, Li X, Pan C, Hu Z. A novel autotrophic denitrification and nitrification integrated constructed wetland process for marine aquaculture wastewater treatment. CHEMOSPHERE 2023; 321:138157. [PMID: 36796520 DOI: 10.1016/j.chemosphere.2023.138157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/29/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
We undertook a lab-scale evaluation of a novel autotrophic denitrification and nitrification integrated constructed wetland (ADNI-CW) for improved carbon (C), nitrogen (N), and sulfur (S) cycling to treat mariculture wastewater. The process involved an up-flow autotrophic denitrification constructed wetland unit (AD-CW) for sulfate reduction and autotrophic denitrification, and an autotrophic nitrification constructed wetland unit (AN-CW) for nitrification. The 400-day experiment investigated the performance of the AD-CW, AN-CW, and entire ADNI-CW processes under various hydraulic retention times (HRTs), nitrate concentrations, dissolved oxygen levels, and recirculation ratios. Under various HRTs, the AN-CW achieved a nitrification performance exceeding 92%. Correlation analysis of the chemical oxygen demand (COD) revealed that, on average, approximately 96% of COD was removed by sulfate reduction. Under different HRTs, increases in influent NO3--N concentrations caused the amount of sulfide to gradually decrease from sufficient to deficient, and the autotrophic denitrification rate also decreased from 62.18 to 40.93%. In addition, when the NO3--N load rate was above 21.53 g N/m2·d, the transformation of organic N by mangrove roots may have increased NO3--N in the top effluent of the AD-CW. The coupling of N and S metabolic processes mediated by various functional microorganisms (Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and unclassified_d__Bacteria) enhanced N removal. We intensively explored the effects of changing inputs as culture species developed on the physical, chemical, and microbial changes of CW to ensure a consistent and effective management of C, N, and S. This study lays the foundation for green and sustainable mariculture development.
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Affiliation(s)
- Lin Zhao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China; Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518055, China
| | - Guiping Fu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Weicheng Pang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xiaxin Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chao Pan
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China; Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518055, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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12
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Ma W, Du W, Gu K, Xu M, Yin Y, Sun Y, Wu J, Zhu J, Guo H. Elevated CO 2 exacerbates effects of TiO 2 nanoparticles on rice (Oryza sativa L.) leaf transcriptome and soil bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159689. [PMID: 36302435 DOI: 10.1016/j.scitotenv.2022.159689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/16/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Elevated CO2 affects the plant rhizosphere and can therefore affect the fate and toxicity of soil contaminants. However, little is known about how the effects of nanoparticles on plants and soil bacteria will change under future CO2 levels. A free-air CO2 enrichment system with two CO2 levels (ambient, 390 μmol mol-1; elevated, 590 μmol mol-1) was used to investigate the responses of rice (Oryza sativa L.) and soil bacteria to titanium dioxide nanoparticles (nano-TiO2, 0 and 200 mg kg-1). Results showed that nano-TiO2 alone did not significantly affect rice growth but affected soil bacteria involved in the carbon and sulfur cycles. Elevated CO2 alone increased rice plant biomass and up-regulated genes related to ribosomes, but its combination with nano-TiO2 down-regulated genes related to photosynthesis and photosynthetic antennae. Elevated CO2 also exacerbated the disturbance by nano-TiO2 to soil bacteria involved in carbon and nitrogen cycles, and consequently inhibited the rice growth. These findings provide a reference for the comprehensive evaluation for the risk of soil pollution.
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Affiliation(s)
- Wenqian Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Wenchao Du
- School of Environment, Nanjing Normal University, Nanjing 210023, China.
| | - Kaihua Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Meiling Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Yuanyuan Sun
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Surficial Geochemistry, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Jichun Wu
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Surficial Geochemistry, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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13
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Han C, Wu H, Sun N, Tang Y, Dai Y, Dai T. Differences in Carbon and Nitrogen Migration and Transformation Driven by Cyanobacteria and Macrophyte Activities in Taihu Lake. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:371. [PMID: 36612693 PMCID: PMC9819403 DOI: 10.3390/ijerph20010371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The metabolic activities of primary producers play an important role in the migration and transformation of carbon (C) and nitrogen (N) in aquatic environments. This study selected two typical areas in Taihu Lake, a cyanobacteria-dominant area (Meiliang Bay) and a macrophyte-dominant area (in the east area of the lake), to study the effects of cyanobacteria and macrophyte activities on C and N migration and transformation in aquatic environments. The results showed that total N and total particulate N concentrations in the water of the cyanobacteria-dominant area were much higher than those in the macrophyte-dominant area, which was mainly due to the assimilated intracellular N in cyanobacteria. Macrophyte activity drove a significantly higher release of dissolved organic C (DOC) in the water than that driven by cyanobacteria activity, and the DOC contents in the water of the macrophyte-dominant area were 2.4~4.6 times the DOC contents in the cyanobacteria-dominant area. In terms of the sediments, organic matter (OM), sediment total N and N species had positive correlations and their contents were higher in the macrophyte-dominant area than in the cyanobacteria-dominant area. Sediment OM contents in the macrophyte-dominant area increased from 4.19% to 9.33% as the sediment deepened (0~10 cm), while the opposite trend was presented in the sediments of the cyanobacteria-dominant area. Sediment OM in the macrophyte-dominant area may contain a relatively high proportion of recalcitrant OC species, while sediment OM in the cyanobacteria-dominant area may contain a relatively high proportion of labile OC species. Compared with the macrophyte-dominant area, there was a relatively high richness and diversity observed in the bacterial community in the sediments in the cyanobacteria-dominant area, which may be related to the high proportion of labile OC in the OM composition in its sediments. The relative abundances of most OC-decomposing bacteria, denitrifying bacteria, Nitrosomonas and Nitrospira were higher in the sediments of the cyanobacteria-dominant area than in the macrophyte-dominant area. These bacteria in the sediments of the cyanobacteria-dominant area potentially accelerated the migration and transformation of C and N, which may supply nutrients to overlying water for the demands of cyanobacteria growth. This study enhances the understanding of the migration and transformation of C and N and the potential effects of bacterial community structures under the different primary producer habitats.
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14
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Chen Y, Li X, Liu T, Li F, Sun W, Young LY, Huang W. Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158068. [PMID: 35987227 DOI: 10.1016/j.scitotenv.2022.158068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO3, and Fe3(PO4)2 as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation. Results showed that the highest rate of Fe(II) oxidation (k = 0.836 mM d-1) was obtained in the FeCO3 tubes, and cells grown in the Fe3(PO4)2 tubes yielded maximum assimilation amounts of 13C-NaHCO3 of 1.74% on Day 15. Amorphous Fe(III) oxides were found in all the cell bands with iron substrates as a result of microbial Fe(II) oxidation. Metagenomics analysis of the enriched microbes targeted genes encoding iron oxidase Cyc2, oxygen-reducing terminal oxidase, and ribulose-bisphosphate carboxylase, with results indicated that the potential Fe(II) oxidizers include nitrate-reducing FeOB (Dechloromonas and Thiobacillus), Curvibacter, and Magnetospirillum. By combining cultivation-dependent and metagenomic approaches, our results found a number of FeOB from paddy soil under microoxic conditions, which provide insight into the complex biogeochemical interactions of iron and carbon within paddy fields. The contribution of the FeOB to the element cycling in rice-growing regions deserves further investigation.
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Affiliation(s)
- Yating Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu 610207, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lily Y Young
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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15
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Chen Y, Gao B, Yang Y, Pan Z, Liu J, Sun K, Xing B. Tracking microplastics biodegradation through CO 2 emission: Role of photoaging and mineral addition. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129615. [PMID: 35870205 DOI: 10.1016/j.jhazmat.2022.129615] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Once microplastics (MPs) enter the terrestrial ecosystem, they may affect the assessment of soil carbon storage and the fluxes of greenhouse gases. This study showed microbial incubation diminished the size and dissolved organic carbon (DOC) content of MPs and introduced more oxygen-containing functional groups to MPs potentially through microbial colonization. The aged MPs generally showed higher carbon mineralization ratio (0.010-0.876 %) than the pristine MPs (0.007-0.189 %), which was supported by their higher enzyme activities and DOC content. Interestingly, four model minerals increased the DOC release and CO2 emission from MPs by altering MPs physicochemical properties and shaping the habitat for microbial growth. The higher enzyme activities in mineral artificial soils, except for montmorillonite, served as a potential valid explanation for their higher mineralization. The high CO2 emission but low enzyme activity in montmorillonite artificial soil was due to most DOC being already mineralized. Aging and minerals altered the microflora and enhanced the expression of some C metabolism- and N-related functional genes, which supplemented the cause of higher CO2 and N2O emissions from the corresponding artificial soils. Overall, the increased biomineralization of MPs carbon by minerals was divergent from the protective role of minerals on soil organic carbon.
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Affiliation(s)
- Yalan Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Bo Gao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yan Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zezhen Pan
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Jie Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ke Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
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16
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Song L, Wang Y, Zhang R, Yang S. Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02056-y. [PMID: 35705745 DOI: 10.1007/s00248-022-02056-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.
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Affiliation(s)
- Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China.
| | - Yangqing Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Rui Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Shu Yang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
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17
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Díaz-Torres O, Lugo-Melchor OY, de Anda J, Pacheco A, Yebra-Montes C, Gradilla-Hernández MS, Senés-Guerrero C. Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season. Front Microbiol 2022; 13:832477. [PMID: 35479621 PMCID: PMC9037096 DOI: 10.3389/fmicb.2022.832477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake’s water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH4+, and NO3–. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.
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Affiliation(s)
- Osiris Díaz-Torres
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - Ofelia Yadira Lugo-Melchor
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - José de Anda
- Departamento de Tecnologia Ambiental, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Mexico
| | - Adriana Pacheco
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Monterrey, Mexico
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18
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Effects of Imazethapyr on Soybean Root Growth and Soil Microbial Communities in Sloped Fields. SUSTAINABILITY 2022. [DOI: 10.3390/su14063518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The herbicide imazethapyr was previously recommended for controlling weeds in soybean fields. However, the effects of imazethapyr on soil microbial communities and their relationship with crop root growth in sloped soils remain unclear. In this study, a field experiment was conducted on a sloped field to explore the effects of imazethapyr on crop root growth, microbial communities, microbial co-occurrence networks, and the interactions between microbes and crop root growth. The field experiment included two factors: slope and imazethapyr. The slope factor included three different slope gradients: 5° (S1), 10° (S2), and 15° (S3). The imazethapyr factor included two treatments: with (I1) and without (I0) imazethapyr. Thus, six total combinations of slope and imazethapyr treatments were tested in this study: S1I1, S2I1, S3I1, S1I0, S2I0, and S3I0. The results show that, compared to the I0 treatments, the I1 treatments significantly increased the soybean root length, surface area, and volume by 11.7~26.5 m, 171.7~324.2 cm2, and 1.8~3.1 cm3, respectively, across all the slopes. The Proteobacteria, Actinobacteriota, and Bacteroidota bacterial phyla and Ascomycota and Basidiomycota fungal phyla were found to be the top phyla represented bacterial and fungal communities. These five phyla were scattered in co-occurrence networks of bacterial and fungal communities, suggesting these phyla play critical roles in enhancing the stability of co-occurrence networks. Compared to the I0 treatments, the I1 treatments increased nodes from Proteobacteria, Actinobacteriota, and Bacteroidota phyla by 6.4%, 9.1%, and 11.2%, respectively, in the bacterial co-occurrence network. Similarly, in the fungal co-occurrence network, the I1 treatments improved nodes from Ascomycota and Basidiomycota phyla by 1.8% and 5.8%, respectively. Compared to the I0 treatments, the I1 treatments increased positive relations by 8.3% and 3.2%, respectively, in the bacterial and fungal co-occurrence networks. Moreover, the I1 treatments increased the relative abundance of root-promoting biomarkers and suppressed root-limiting biomarkers. However, the application of imazethapyr reduced the diversity and richness of bacterial and fungal communities in general. Furthermore, the nodes and links of bacterial co-occurrence networks in the I0 treatments were 9.2% and 78.8% higher than these in the I1 treatments. Similarly, the I1 treatments also decreased 17.9% of fungal community links compared to the I0 treatments. Our data also show that compared to the I0 treatments, the I1 treatments decreased almost all gene families encoding nitrogen and carbon cycling pathways. In conclusion, the application of imazethapyr increased soybean root growth by increasing root-promoting biomarkers and improved the stability and cooperation of co-occurrence networks of bacterial and fungal communities. However, the application of imazethapyr had some negative impacts on microbial communities, such as reducing the diversity of bacterial and fungal communities and nitrogen and carbon cycling pathways.
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Zhang H, Yang L, Li Y, Wang C, Zhang W, Wang L, Niu L. Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114380. [PMID: 34995945 DOI: 10.1016/j.jenvman.2021.114380] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/30/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.
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Affiliation(s)
- Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Liu Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Chao Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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Liu C, Zhang Y, Liu H, Liu X, Ren D, Wang L, Guan D, Li Z, Zhang M. Fertilizer stabilizers reduce nitrous oxide emissions from agricultural soil by targeting microbial nitrogen transformations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151225. [PMID: 34715210 DOI: 10.1016/j.scitotenv.2021.151225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Nitrous oxide (N2O) is a pollutant released from agriculture soils following N fertilizer application. N stabilizers, such as N-(n-butyl) thiophosphoric triamide (NBPT) and 3,4-dimethylpyrazole phosphate (DMPP) could mitigate these N2O emissions when applied with fertilizer. Here, field experiments were conducted to investigate the microbial mechanisms by which NBPT and DMPP mitigate N2O emissions following urea application. We determined dynamic N2O emissions and inorganic N concentrations for two wheat seasons and combined this with metagenomic sequencing. Application of NBPT, DMPP, and both NBPT and DMPP together with urea decreased mean N2O accumulative emissions by 77.8, 91.4 and 90.7%, respectively, compared with urea application alone, mainly via repressing the increase in NO2- concentration after N fertilization. Sequencing results indicated that urea application enriched microorganisms that were positively correlated with N2O production, whereas N stabilizers enriched microorganisms that were negatively correlated with N2O production. Furthermore, compared to urea application alone, NBPT with urea reduced the abundances of genes related to denitrification, including napA/nasA, nirS/nirK, and norBC, resulting in a higher soil NO3- pool. Conversely, DMPP application, either alone or together with NBPT, decreased the abundance of genes involved in ammonia oxidation and denitrification, including amoCAB, hao, napA/nasA, nirS/nirK, and norBC, and maintained a greater soil NH4+ pool. Both N stabilizers resulted in similar abundances of nirABD-which is related to NO2- reducers-as when no N fertilizer was applied, which could prevent NO2- accumulation, consequently mitigating N2O emissions. These findings suggest that the high effectiveness of N stabilizers on mitigating N2O emissions could be attributed to changes to soil microbial communities and N-cycling functional genes to control the by-product or intermediate products of microbial N-cycling processes in agricultural soils.
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Affiliation(s)
- Churong Liu
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Yushi Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Hongrun Liu
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Xueqing Liu
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Danyang Ren
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Ligang Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dahai Guan
- Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, China Agricultural University, Beijing 100193, China.
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He J, Zhang N, Muhammad A, Shen X, Sun C, Li Q, Hu Y, Shao Y. From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150395. [PMID: 34818768 DOI: 10.1016/j.scitotenv.2021.150395] [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: 06/24/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 05/11/2023]
Abstract
Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.
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Affiliation(s)
- Jintao He
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Nan Zhang
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Abrar Muhammad
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoqiang Shen
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Li
- Laboratory of Cultural Relics Conservation Materials, Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Yulan Hu
- School of Art and Archaeology, Zhejiang University, Hangzhou, China
| | - Yongqi Shao
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China; Key Laboratory for Molecular Animal Nutrition, Ministry of Education, China.
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22
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Kim Y, Oh S. Machine-learning insights into nitrate-reducing communities in a full-scale municipal wastewater treatment plant. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 300:113795. [PMID: 34560468 DOI: 10.1016/j.jenvman.2021.113795] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
This study carried out machine-learning (ML) modeling using activated sludge microbiome data to predict the operational characteristics of biological unit processes (i.e., anaerobic, anoxic, and aerobic) in a full-scale municipal wastewater treatment plant. An ML application pipeline with optimization strategies (e.g., model selection, input data preprocessing, and hyperparameter tuning) could significantly improve prediction performance. Comparative analysis of the ML prediction performance suggested that linear models (support vector machine and logistic regression) had a high prediction performance (93% accuracy), comparable to that of non-linear models such as random forest. Feature importance analysis using the linear ML models identified the microbial taxa that were specifically associated with anoxic processes, many of which (e.g., Ferruginibacter) were found to have ecologically important genomic and phenotypic characteristics (e.g., for nitrate reduction). Time-series microbial community dynamics demonstrated that the taxa identified using ML were frequently occurring and dominating in the anoxic process over time, thus representing the core nitrate-reducing community. Despite the general dominance of the core community over time, the analysis further revealed successional seasonal patterns of distinct sub-groups, indicating differences in the functional contribution of sub-groups by season to the overall nitrate-reducing potential of the system. Overall, the results of this study suggest that ML modeling holds great promise for the predictive identification and understanding of key microbial players governing the functioning and stability of biological wastewater systems.
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Affiliation(s)
- Youngjun Kim
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea.
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23
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Li S, Pang Y, Ji G. Increase of N 2O production during nitrate reduction after long-term sulfide addition in lake sediment microcosms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118231. [PMID: 34571071 DOI: 10.1016/j.envpol.2021.118231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Microbial denitrification is a main source of nitrous oxide (N2O) emissions which have strong greenhouse effect and destroy stratospheric ozone. Though the importance of sulfide driven chemoautotrophic denitrification has been recognized, its contribution to N2O emissions in nature remains elusive. We built up long-term sulfide-added microcosms with sediments from two freshwater lakes. Chemistry analysis confirmed sulfide could drive nitrate respiration in long term. N2O accumulated to over 1.5% of nitrate load in both microcosms after long-term sulfide addition, which was up to 12.9 times higher than N2O accumulation without sulfide addition. Metagenomes were extracted and sequenced during microcosm incubations. 16 S rRNA genes of Thiobacillus and Defluviimonas were gradually enriched. The nitric oxide reductase with c-type cytochromes as electron donors (cNorB) increased in abundance, while the nitric oxide reductase receiving electrons from quinols (qNorB) decreased in abundance. cnorB genes similar to Thiobacillus were enriched in both microcosms. In parallel, enrichment was observed for enzymes involved in sulfur oxidation, which supplied electrons to nitrate respiration, and enzymes involved in Calvin Cycle, which sustained autotrophic cell growth, implying the coupling relationship between carbon, nitrogen and sulfur cycling processes. Our results suggested sulfur pollution considerably increased N2O emissions in natural environments.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Yunmeng Pang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China; Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing, 100084, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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Zhao B, Li X, Wang Y, Tan X, Qi W, Li H, Wei J, You Y, Shi W, Zhang Q. Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68155-68173. [PMID: 34264489 DOI: 10.1007/s11356-021-15197-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO3-, NH4+, DOC/NO3-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.
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Affiliation(s)
- Binjie Zhao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinshuai Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Tan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wenhua Qi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongran Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junwei Wei
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, China
- College of Science, Tibet University, Lhasa, 850000, China
| | - Yong You
- College of Land and Resources, China West Normal University, Nanchong, 637009, China
| | - Wenjun Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Menéndez-Serra M, Triadó-Margarit X, Casamayor EO. Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain). MICROBIAL ECOLOGY 2021; 82:885-896. [PMID: 33725151 DOI: 10.1007/s00248-021-01732-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/08/2021] [Indexed: 05/20/2023]
Abstract
We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.
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Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain.
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Nitrate Removal from Actual Wastewater by Coupling Sulfur-Based Autotrophic and Heterotrophic Denitrification under Different Influent Concentrations. WATER 2021. [DOI: 10.3390/w13202913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Contamination of wastewater with organic-limited nitrates has become an urgent problem in wastewater treatment. The cooperating heterotrophic with sulfur autotrophic denitrification is an alternative process and the efficiency has been assessed in many studies treating simulated wastewater under different operating conditions. However, due to the complex and diverse nature of actual wastewater, more studies treating actual wastewater are still needed to evaluate the feasibility of collaborative denitrification. In this study, lab-scale experiments were performed with actual nitrate polluted water of two different concentrations, with glucose and sodium thiosulfate introduced as mixed electron donors in the coupling sulfur-based autotrophic and heterotrophic denitrification. Results showed that the optimum denitrification performance was exhibited when the influent substrate mass ratio of C/N/S was 1.3/1/1.9, with a maximum denitrification rate of 3.52 kg NO3−-N/(m3 day) and nitrate removal efficiency of 93% in the coupled systems. Illumina high-throughput sequencing analysis revealed that autotrophic, facultative, and heterotrophic bacteria jointly contributed to high nitrogen removal efficiency. The autotrophic denitrification maintained as the predominant process, while the second most prevalent denitrification process gradually changed from heterotrophic to facultative with the increase of influent concentration at optimum C/N/S ratio conditions. Furthermore, the initiation of dissimilatory nitrate reduction to ammonium (DNRA) was very pivotal in promoting the entire denitrification process. These results suggested that sulfur-based autotrophic coupled with heterotrophic denitrifying process is an alternative and promising method to treat nitrate containing wastewater.
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Zhu HZ, Jiang MZ, Zhou N, Jiang CY, Liu SJ. Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system. Appl Microbiol Biotechnol 2021; 105:7517-7528. [PMID: 34519857 DOI: 10.1007/s00253-021-11565-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022]
Abstract
Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.
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Affiliation(s)
- Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China.,State Key Laboratory of Microbial Technology, Shandong University, Tsingdao, 266237, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Tsingdao, 266237, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Xue CX, Lin H, Zhu XY, Liu J, Zhang Y, Rowley G, Todd JD, Li M, Zhang XH. DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. Front Microbiol 2021; 12:698286. [PMID: 34408730 PMCID: PMC8367434 DOI: 10.3389/fmicb.2021.698286] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Heyu Lin
- School of Earth Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Xiao-Yu Zhu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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29
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Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. THE ISME JOURNAL 2021; 15:2351-2365. [PMID: 33649556 PMCID: PMC8319295 DOI: 10.1038/s41396-021-00931-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 02/08/2021] [Indexed: 02/03/2023]
Abstract
Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean's interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine-seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.
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30
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Rojas CA, De Santiago Torio A, Park S, Bosak T, Klepac-Ceraj V. Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake. Front Microbiol 2021; 12:620424. [PMID: 33967973 PMCID: PMC8103211 DOI: 10.3389/fmicb.2021.620424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
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Affiliation(s)
- Connie A. Rojas
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
- Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, United States
| | - Ana De Santiago Torio
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Serry Park
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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31
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Wang Q, Han Y, Lan S, Hu C. Metagenomic Insight Into Patterns and Mechanism of Nitrogen Cycle During Biocrust Succession. Front Microbiol 2021; 12:633428. [PMID: 33815315 PMCID: PMC8009985 DOI: 10.3389/fmicb.2021.633428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
The successional ecology of nitrogen cycling in biocrusts and the linkages to ecosystem processes remains unclear. To explore this, four successional stages of natural biocrust with five batches of repeated sampling and three developmental stages of simulated biocrust were studied using relative and absolute quantified multi-omics methods. A consistent pattern across all biocrust was found where ammonium assimilation, mineralization, dissimilatory nitrite to ammonium (DNiRA), and assimilatory nitrate to ammonium were abundant, while denitrification medium, N-fixation, and ammonia oxidation were low. Mathematic analysis showed that the nitrogen cycle in natural biocrust was driven by dissolved organic N and NO3–. pH and SO42– were the strongest variables affecting denitrification, while C:(N:P) was the strongest variable affecting N-fixation, DNiRA, nitrite oxidation, and dissimilatory nitrate to nitrite. Furthermore, N-fixation and DNiRA were closely related to elemental stoichiometry and redox balance, while assimilatory nitrite to ammonium (ANiRA) and mineralization were related to hydrological cycles. Together with the absolute quantification and network models, our results suggest that responsive ANiRA and mineralization decreased during biocrust succession; whereas central respiratory DNiRA, the final step of denitrification, and the complexity and interaction of the whole nitrogen cycle network increased. Therefore, our study stresses the changing environmental functions in the biocrust N-cycle, which are succession-dependent.
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Affiliation(s)
- Qiong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingchun Han
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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32
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Ma B, Stirling E, Liu Y, Zhao K, Zhou J, Singh BK, Tang C, Dahlgren RA, Xu J. Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network. RESEARCH 2021; 2021:7102769. [PMID: 33796862 PMCID: PMC7978035 DOI: 10.34133/2021/7102769] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/17/2021] [Indexed: 11/06/2022]
Abstract
Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems. However, the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood. Here, we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect (18° N to 48° N) in eastern China. Among environmental and soil factors, soil pH was a sensitive indicator for functional gene composition and diversity. A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron. Our results provide novel evidence for the coupling of soil biogeochemical cycles, identify key regulating microbes, and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.,Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yuanhui Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2750, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, 95616 CA, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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33
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Baker KD, Kellogg CTE, McClelland JW, Dunton KH, Crump BC. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons. Front Microbiol 2021; 12:601901. [PMID: 33643234 PMCID: PMC7906997 DOI: 10.3389/fmicb.2021.601901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
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Affiliation(s)
- Kristina D Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - James W McClelland
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Kenneth H Dunton
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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34
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Housekeeping in the Hydrosphere: Microbial Cooking, Cleaning, and Control under Stress. Life (Basel) 2021; 11:life11020152. [PMID: 33671121 PMCID: PMC7922117 DOI: 10.3390/life11020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022] Open
Abstract
Who’s cooking, who’s cleaning, and who’s got the remote control within the waters blanketing Earth? Anatomically tiny, numerically dominant microbes are the crucial “homemakers” of the watery household. Phytoplankton’s culinary abilities enable them to create food by absorbing sunlight to fix carbon and release oxygen, making microbial autotrophs top-chefs in the aquatic kitchen. However, they are not the only bioengineers that balance this complex household. Ubiquitous heterotrophic microbes including prokaryotic bacteria and archaea (both “bacteria” henceforth), eukaryotic protists, and viruses, recycle organic matter and make inorganic nutrients available to primary producers. Grazing protists compete with viruses for bacterial biomass, whereas mixotrophic protists produce new organic matter as well as consume microbial biomass. When viruses press remote-control buttons, by modifying host genomes or lysing them, the outcome can reverberate throughout the microbial community and beyond. Despite recognition of the vital role of microbes in biosphere housekeeping, impacts of anthropogenic stressors and climate change on their biodiversity, evolution, and ecological function remain poorly understood. How trillions of the smallest organisms in Earth’s largest ecosystem respond will be hugely consequential. By making the study of ecology personal, the “housekeeping” perspective can provide better insights into changing ecosystem structure and function at all scales.
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35
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Gupta D, Guzman MS, Bose A. Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications. ACTA ACUST UNITED AC 2020; 47:863-876. [DOI: 10.1007/s10295-020-02309-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Abstract
Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.
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Affiliation(s)
- Dinesh Gupta
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
| | - Michael S Guzman
- grid.250008.f 0000 0001 2160 9702 Biosciences and Biotechnology Division Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA USA
| | - Arpita Bose
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
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36
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Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands. mSystems 2020; 5:5/3/e00412-20. [PMID: 32518198 PMCID: PMC7289592 DOI: 10.1128/msystems.00412-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vegetation represents probably the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift along with vegetation. In this study, we found that the richness and diversity of soil bacteria increased with vegetation levels and that the community composition was distinctly shifted from bare to vegetative places. The bare land displayed an extremely high abundance of Cyanobacteria as a monospecies genus, while a Gemmatimonadetes genus was predominant as multiple species in all the vegetative wetlands, suggesting their important ecosystem functions and potential mechanisms. Expression of the genes related to photosynthesis was enriched exclusively in bare land. Genes involved in biological organic carbon metabolism and the cycling of main elements (C, N, S, and P) were highly expressed in vegetative wetlands and were mostly included in the metagenome-assembled genome (MAG) of Gemmatimonadetes Some compounds identified from soil metabolomic results also corresponded to pathways involving these key active genes. Cyanobacteria is thus responsible for the carbon sink in early infertile wetlands, and Gemmatimonadetes plays a crucial role in ecosystem functions in vegetative wetlands. Our results highlight that the soil microbial populations execute ecosystem functions for wetlands and that vegetation is the determinant for the population and functional shifts in the coastal estuarine wetland of the Yellow River Delta.IMPORTANCE Vegetation probably represents the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift in pace with the colonization and succession of vegetation. In this study, we found that a Cyanobacteria monospecies genus and a Gemmatimonadetes multispecies genus are fastidiously predominant in the bare and vegetative wetlands of the Yellow River Delta, respectively. Consistently, photosynthesis genes were enriched exclusively in bare land, while genes involved in biological organic carbon metabolism and the cycling of main elements were highly expressed in vegetative wetlands, were mostly included in the MAG of Gemmatimonadetes, and were consistent with soil metabolomic results. Our results provide insight into the adaptive succession of predominant bacterial species and their ecosystem functions in response to the presence of vegetation.
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37
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Llorens-Marès T, Catalan J, Casamayor EO. Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135929. [PMID: 31863999 DOI: 10.1016/j.scitotenv.2019.135929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/15/2019] [Accepted: 12/02/2019] [Indexed: 05/20/2023]
Abstract
High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.
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Affiliation(s)
- Tomas Llorens-Marès
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC, Acc. Cala St Francesc 14, E-17300 Blanes, Catalonia, Spain
| | - Jordi Catalan
- CREAF - CSIC, Campus UAB, Edifici C, 08193 Cerdanyola del Vallès, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC, Acc. Cala St Francesc 14, E-17300 Blanes, Catalonia, Spain.
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38
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Shen M, Li Q, Ren M, Lin Y, Wang J, Chen L, Li T, Zhao J. Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes. Front Microbiol 2019; 10:2560. [PMID: 31787952 PMCID: PMC6853845 DOI: 10.3389/fmicb.2019.02560] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Microbes in various aquatic ecosystems play a key role in global energy fluxes and biogeochemical processes. However, the detailed patterns on the functional structure and the metabolic potential of microbial communities in freshwater lakes with different trophic status remain to be understood. We employed a metagenomics workflow to analyze the correlations between trophic status and planktonic microbiota in freshwater lakes on Yun-Gui Plateau, China. Our results revealed that microbial communities in the eutrophic and mesotrophic-oligotrophic lake ecosystems harbor distinct community structure and metabolic potential. Cyanobacteria were dominant in the eutrophic ecosystems, mainly driving the processes of aerobic respiration, fermentation, nitrogen assimilation, nitrogen mineralization, assimilatory sulfate reduction and sulfur mineralization in this ecosystem group. Actinobacteria, Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Verrucomicrobia and Planctomycetes, occurred more often in the mesotrophic-oligotrophic ecosystems than those in the eutrophic ecosystems, and these taxa potentially mediate the above metabolic processes. In these two groups of ecosystems, a difference in the abundance of functional genes involved in carbohydrate metabolism, energy metabolism, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins significantly contribute to the distinct functional structure of microbiota from surface water. Furthermore, the microbe-mediated metabolic potentials for carbon, nitrogen and sulfur transformation showed differences in the two ecosystem groups. Compared with the mesotrophic-oligotrophic ecosystems, planktonic microbial communities in the eutrophic ecosystems showed higher potential for aerobic carbon fixation, fermentation, methanogenesis, anammox, denitrification, and sulfur mineralization, but they showed lower potential for aerobic respiration, CO oxidation, nitrogen fixation, and assimilatory sulfate reduction. This study offers insights into the relationships of trophic status to planktonic microbial community structure and its metabolic potential, and identifies the main taxa responsible for the biogeochemical cycles of carbon, nitrogen and sulfur in freshwater lake environments.
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Affiliation(s)
- Mengyuan Shen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Minglei Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yan Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Juanping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Processes and Environment Change, School of Tourism and Geography, Yunnan Normal University, Kunming, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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39
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Liu F, Zhang Y, Liang H, Gao D. Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands. WATER RESEARCH 2019; 164:114936. [PMID: 31382148 DOI: 10.1016/j.watres.2019.114936] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N2O emissions decreased from 0.73 ± 0.20 kg ha-1 to -0.57 ± 0.49 kg ha-1 with the harvesting of reeds. The annual cumulative CH4 emissions also decreased from 561.88 ± 18.61 kg ha-1 to 183.13 ± 18.77 kg ha-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO2 emissions. A Pearson correlation analysis revealed that the CO2 and N2O emissions were more sensitive to temperature than the CH4 emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO2 emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.
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Affiliation(s)
- Fengqin Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yupeng Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hong Liang
- School of Environment, Harbin Institute of Technology, Harbin, China.
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China; School of Environment, Harbin Institute of Technology, Harbin, China.
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40
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Čanković M, Žučko J, Radić ID, Janeković I, Petrić I, Ciglenečki I, Collins G. Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake. Syst Appl Microbiol 2019; 42:126016. [PMID: 31635887 DOI: 10.1016/j.syapm.2019.126016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/30/2019] [Accepted: 09/07/2019] [Indexed: 01/04/2023]
Abstract
Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.
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Affiliation(s)
- Milan Čanković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Jurica Žučko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10 000 Zagreb, Croatia
| | - Iris Dupčić Radić
- Institute for Marine and Coastal Research, University of Dubrovnik, Ul. kneza Damjana Jude 12, 20 000, Dubrovnik, Croatia
| | - Ivica Janeković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Gavin Collins
- Microbial Communities Laboratory, Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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41
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Li Y, Cha QQ, Dang YR, Chen XL, Wang M, McMinn A, Espina G, Zhang YZ, Blamey JM, Qin QL. Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica. Front Microbiol 2019; 10:2408. [PMID: 31681251 PMCID: PMC6813960 DOI: 10.3389/fmicb.2019.02408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/07/2019] [Indexed: 11/17/2022] Open
Abstract
Antarctica is covered by multiple larger glaciers with diverse extreme conditions. Microorganisms in Antarctic regions are primarily responsible for diverse biogeochemical processes. The identity and functionality of microorganisms from polar glaciers are defined. However, little is known about microbial communities from the high elevation glaciers. The Union Glacier, located in the inland of West Antarctica at 79°S, is a challenging environment for life to survive due to the high irradiance and low temperatures. Here, soil and rock samples were obtained from three high mountains (Rossman Cove, Charles Peak, and Elephant Head) adjacent to the Union Glacier. Using metagenomic analyses, the functional microbial ecosystem was analyzed through the reconstruction of carbon, nitrogen and sulfur metabolic pathways. A low biomass but diverse microbial community was found. Although archaea were detected, bacteria were dominant. Taxa responsible for carbon fixation were comprised of photoautotrophs (Cyanobacteria) and chemoautotrophs (mainly Alphaproteobacterial clades: Bradyrhizobium, Sphingopyxis, and Nitrobacter). The main nitrogen fixation taxa were Halothece (Cyanobacteria), Methyloversatilis, and Leptothrix (Betaproteobacteria). Diverse sulfide-oxidizing and sulfate-reducing bacteria, fermenters, denitrifying microbes, methanogens, and methane oxidizers were also found. Putative producers provide organic carbon and nitrogen for the growth of other heterotrophic microbes. In the biogeochemical pathways, assimilation and mineralization of organic compounds were the dominant processes. Besides, a range of metabolic pathways and genes related to high irradiance, low temperature and other stress adaptations were detected, which indicate that the microbial communities had adapted to and could survive in this harsh environment. These results provide a detailed perspective of the microbial functional ecology of the Union Glacier area and improve our understanding of linkages between microbial communities and biogeochemical cycling in high Antarctic ecosystems.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Jenny M Blamey
- Fundación Científica y Cultural Biociencia, Santiago, Chile.,Faculty of Chemistry and Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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42
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Haas S, Desai DK, LaRoche J, Pawlowicz R, Wallace DWR. Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater. Environ Microbiol 2019; 21:3927-3952. [PMID: 31314947 DOI: 10.1111/1462-2920.14743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 11/30/2022]
Abstract
We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.
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Affiliation(s)
- Sebastian Haas
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Dhwani K Desai
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Rich Pawlowicz
- Department of Earth and Ocean Sciences, University of British Columbia, 6339 Stores Road, Vancouver, British Columbia, Canada
| | - Douglas W R Wallace
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
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43
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Pjevac P, Dyksma S, Goldhammer T, Mujakić I, Koblížek M, Mußmann M, Amann R, Orlić S. In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica. Environ Microbiol 2019; 21:3896-3908. [PMID: 31299137 DOI: 10.1111/1462-2920.14739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/08/2023]
Abstract
Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.
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Affiliation(s)
- Petra Pjevac
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Stefan Dyksma
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tobias Goldhammer
- MARUM Center for Marine Environmental Sciences, Bremen, Germany.,Department of Chemical Analytics and Biogeochemistry, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Izabela Mujakić
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - Michal Koblížek
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - Marc Mußmann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandi Orlić
- Ruđer Bošković Institute, Zagreb, Croatia.,Center of Excellence for Science and Technology Integrating Mediterranean Region, Microbial Ecology, Zagreb, Croatia
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44
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Ren Z, Qu X, Peng W, Yu Y, Zhang M. Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China. PeerJ 2019; 7:e7318. [PMID: 31338262 PMCID: PMC6628883 DOI: 10.7717/peerj.7318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/18/2019] [Indexed: 02/04/2023] Open
Abstract
In river-lake systems, sediment and water column are two distinct habitats harboring different bacterial communities which play a crucial role in biogeochemical processes. In this study, we employed Phylogenetic Investigation of Communities by Reconstruction of Unobserved States to assess the potential functions and functional redundancy of the bacterial communities in sediment and water in a eutrophic river-lake ecosystem, Poyang Lake in China. Bacterial communities in sediment and water had distinct potential functions of carbon, nitrogen, and sulfur metabolisms as well as phosphorus cycle, while the differences between rivers and the lake were inconspicuous. Bacterial communities in sediment had a higher relative abundance of genes associated with carbohydrate metabolism, carbon fixation pathways in prokaryotes, methane metabolism, anammox, nitrogen fixation, and dissimilatory sulfate reduction than that of water column. Bacterial communities in water column were higher in lipid metabolism, assimilatory nitrate reduction, dissimilatory nitrate reduction, phosphonate degradation, and assimilatory sulfate reduction than that of sediment bacterial communities. Furthermore, the variations in functional composition were closely associated to the variations in taxonomic composition in both habitats. In general, the bacterial communities in water column had a lower functional redundancy than in sediment. Moreover, comparing to the overall functions, bacterial communities had a lower functional redundancy of nitrogen metabolism and phosphorus cycle in water column and lower functional redundancy of nitrogen metabolism in sediment. Distance-based redundancy analysis and mantel test revealed close correlations between nutrient factors and functional compositions. The results suggested that bacterial communities in this eutrophic river-lake system of Poyang Lake were vulnerable to nutrient perturbations, especially the bacterial communities in water column. The results enriched our understanding of the bacterial communities and major biogeochemical processes in the eutrophic river-lake ecosystems.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Flathead Lake Biological Station, University of Montana, Polson, MT, USA
| | - Xiaodong Qu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Wenqi Peng
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Yang Yu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Min Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
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45
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Deja-Sikora E, Gołębiewski M, Kalwasińska A, Krawiec A, Kosobucki P, Walczak M. Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters. MICROBIAL ECOLOGY 2019; 78:85-101. [PMID: 30341500 PMCID: PMC6560000 DOI: 10.1007/s00248-018-1270-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/03/2018] [Indexed: 05/25/2023]
Abstract
Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm3), salinity (1.3-3.2%), and depth of extraction (60-660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148-300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous.
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Affiliation(s)
- Edyta Deja-Sikora
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Toruń, Poland.
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
| | - Marcin Gołębiewski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Arkadiusz Krawiec
- Department of Geology and Hydrogeology, Faculty of Earth Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Przemysław Kosobucki
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326, Bydgoszcz, Poland
| | - Maciej Walczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
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46
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Gulliver D, Lipus D, Ross D, Bibby K. Insights into microbial community structure and function from a shallow, simulated CO 2 -leakage aquifer demonstrate microbial selection and adaptation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:338-351. [PMID: 29984552 DOI: 10.1111/1758-2229.12675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/30/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2 ), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO2 -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1.15 g l-1 . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO2 exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO2 utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO2 leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.
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Affiliation(s)
- Djuna Gulliver
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, USA
| | - Daniel Lipus
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Daniel Ross
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, USA
- AECOM, Pittsburgh, PA, USA
| | - Kyle Bibby
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, South Bend, IN, USA
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47
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Qin H, Wang S, Feng K, He Z, Virta MPJ, Hou W, Dong H, Deng Y. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. MICROBIOME 2019; 7:71. [PMID: 31054577 PMCID: PMC6500586 DOI: 10.1186/s40168-019-0688-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 05/07/2023]
Abstract
Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.
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Affiliation(s)
- Huayu Qin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhili He
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Marko P J Virta
- Department of Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, United States
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China.
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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48
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Deng Y, Wang Y, Xia Y, Zhang AN, Zhao Y, Zhang T. Genomic resolution of bacterial populations in saccharin and cyclamate degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 658:357-366. [PMID: 30579193 DOI: 10.1016/j.scitotenv.2018.12.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.
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Affiliation(s)
- Yu Deng
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China; Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Yu Xia
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - An Ni Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Yuehao Zhao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Tong Zhang
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China; Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China.
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Lai YS, Ontiveros‐Valencia A, Coskun T, Zhou C, Rittmann BE. Electron‐acceptor loadings affect chloroform dechlorination in a hydrogen‐based membrane biofilm reactor. Biotechnol Bioeng 2019; 116:1439-1448. [DOI: 10.1002/bit.26945] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 11/09/2022]
Affiliation(s)
- YenJung Sean Lai
- School of Sustainable Engineering and the Built EnvironmentArizona State University, Biodesign InstituteTempe Arizona
| | - Aura Ontiveros‐Valencia
- School of Sustainable Engineering and the Built EnvironmentArizona State University, Biodesign InstituteTempe Arizona
- Present address: Escuela de Ingenieria y CienciasTecnologico de Monterrey, Campus PueblaPuebla Pue Mexico
| | - Tamer Coskun
- School of Sustainable Engineering and the Built EnvironmentArizona State University, Biodesign InstituteTempe Arizona
| | - Chen Zhou
- School of Sustainable Engineering and the Built EnvironmentArizona State University, Biodesign InstituteTempe Arizona
| | - Bruce E. Rittmann
- School of Sustainable Engineering and the Built EnvironmentArizona State University, Biodesign InstituteTempe Arizona
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Menéndez-Serra M, Triadó-Margarit X, Castañeda C, Herrero J, Casamayor EO. Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:343-353. [PMID: 30199680 DOI: 10.1016/j.scitotenv.2018.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Soil microbial communities (both Bacteria and Archaea) were studied after 16S rRNA genes massive sequencing in two hypersaline and gypsum-rich contrasted sites located in NE Spain. Soil microbial communities were also locally analysed according to environmental variables, including geological, physico-chemical, biogeochemically, and climatic data. Typical soil characteristics, climate data, and plant composition clearly split the two sites and major differences among the microbial communities for the areas were initially expected. Overall, high values of microbial species richness (up to 2300 taxa) and ecological diversity was detected in both sites. High genetic novelty levels were found mostly to environmental sequences, highlighting the high potential for microbiological studies. In contrast to the initial expectations, a substantial overlapping between Monegros and Gallocanta microbes was observed, indicating a high similarity despite of the geographical, botanical and environmental distances between sites, in agreement with both high dispersal and local selection inherent to the microbial world. The potential biogeochemical cycling showed small differences between sites, with presence of photosynthetic green and purple sulfur bacteria, cyanobacteria and aerobic and anaerobic chemolitotrophs. Potential for aerobic methane oxidation and anaerobic methanogenesis was observed in both sites, with predominance of potential nitrification mostly by ammonia-oxidizing archaea, nitrite oxidation and denitrification, and minor contribution for nitrate reduction and nitrate ammonification. The predicted functions based on the taxonomic composition showed high overlapping between the two studied regions, despite their difference in gypsum richness.
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Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Carmen Castañeda
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Juan Herrero
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain.
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