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He Q, Tan B, Li M, Su J, Lin B, Wu NP, Shen HN, Chen JJ, Zhang Q. Deciphering the influence of salinity stress on the biological aniline degradation system: Pollutants degradation performance and microbial response. ENVIRONMENTAL RESEARCH 2024; 255:119162. [PMID: 38762003 DOI: 10.1016/j.envres.2024.119162] [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: 03/10/2024] [Revised: 04/14/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
In order to evaluate the impact of salinity gradients on the aniline biodegradation system, six reactors at salinity concentrations (0%-5%) were established. The results presented the salinity except for 5% imposed negligible effects on aniline degradation performance. Nitrification had prominent resistance to salinity (0%-1.5%) while were significantly restrained when salinity increased. The total nitrogen (TN) removal efficiency of Z4 (1.5%) was 20.5% higher than Z1 (0%) during the stable operation phase. Moreover, high throughput sequencing analysis showed that halophilic bacterium, such as Halomonas, Rhodococcus, remained greater survival advantages in high salinity system. The substantial enrichment of Flavobacterium, Dokdonella, Paracoccus observed in Z4 ensured its excellent nitrogen removal performance. The close cooperation among dominant functional bacteria was strengthened when salt content was below 1.5% while exceeding 1.5% led to the collapse of metabolic capacity through integrating the toxicity of aniline and high osmotic pressure.
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Affiliation(s)
- Qi He
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Bin Tan
- CCCC Second Highway Consultants Co., Ltd., Wuhan, 430056, PR China
| | - Meng Li
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Hainan, 572024, PR China
| | - Junhao Su
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Bing Lin
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Nan-Ping Wu
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Hao-Nan Shen
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Jia-Jing Chen
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Hainan, 572024, PR China
| | - Qian Zhang
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China.
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Hu W, Zheng N, Zhang Y, Li S, Bartlam M, Wang Y. Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173186. [PMID: 38744390 DOI: 10.1016/j.scitotenv.2024.173186] [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: 03/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Ningning Zheng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Yi Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Shuhan Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China.
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Wang Y, Li W, Bao G, Bai M, Ye H. Differences in archaeal diversity and potential ecological functions between saline and hypersaline lakes on Qinghai-Tibet Plateau were driven by multiple environmental and non-environmental factors beyond the salinity. BMC Microbiol 2024; 24:153. [PMID: 38704527 PMCID: PMC11069230 DOI: 10.1186/s12866-024-03307-3] [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: 11/15/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Saline lakes are home to various archaea that play special and crucial roles in the global biogeochemical cycle. The Qinghai-Tibet Plateau hosts a large number of lakes with diverse salinity ranging from 0.1 to over 400 g/L, harboring complex and diverse archaea. To the best of our knowledge, the formation mechanisms and potential ecological roles of archaea in Qinghai-Tibetan Plateau saline lakes remain largely unknown. RESULTS Using High-throughput Illumina sequencing, we uncovered the vastly distinct archaea communities between two typical saline lakes with significant salinity differences on the Qinghai Tibet Plateau (Qinghai saline lake and Chaka hypersaline lake) and suggested archaea played different important roles in methanogenesis-related and nitrate reduction-related functions of these two lakes, respectively. Rather than the individual effect of salinity, the composite effect of salinity with diverse environmental parameters (e.g., temperature, chlorophyll a, total nitrogen, and total phosphorus) dominated the explanation of the variations in archaeal community structure in different habitats. Based on the network analysis, we further found the correlations between dominant archaeal OTUs were tight but significantly different between the two habitats, implying that archaeal interactions may also largely determine the shape of archaeal communities. CONCLUSION The present study improved our understanding of the structure and function of archaea in different saline lakes on the Qinghai-Tibet Plateau and provided a new perspective on the mechanisms underlying shaping their communities.
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Affiliation(s)
- Yaqiong Wang
- School of Ecology, Environment and Resources, Qinghai Minzu University, Bayi Road, Xining, 810007, Qinghai, China
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Xining, 810007, China
- Qinghai Provincial Biotechnology and Analytical Test Key Laboratory, Xining, 810007, China
| | - Wenxin Li
- School of Ecology, Environment and Resources, Qinghai Minzu University, Bayi Road, Xining, 810007, Qinghai, China
| | - Guoyuan Bao
- School of Ecology, Environment and Resources, Qinghai Minzu University, Bayi Road, Xining, 810007, Qinghai, China
| | - Mohan Bai
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China.
| | - Huike Ye
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China.
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4
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Zhao C, Liu X, Tan H, Yin S, Su L, Du B, Khalid M, Sinkkonen A, Hui N. Neighborhood garden's age shapes phyllosphere microbiota associated with respiratory diseases in cold seasons. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 18:100315. [PMID: 37886031 PMCID: PMC10598728 DOI: 10.1016/j.ese.2023.100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Neighborhood gardens serve as sensitive sites for human microbial encounters, with phyllosphere microbes directly impacting our respiratory health. Yet, our understanding remains limited on how factors like season, garden age, and land use shape the risk of respiratory diseases (RDs) tied to these garden microbes. Here we examined the microbial communities within the phyllosphere of 72 neighborhood gardens across Shanghai, spanning different seasons (warm and cold), garden ages (old and young), and locales (urban and rural). We found a reduced microbial diversity during the cold season, except for Gammaproteobacteria which exhibited an inverse trend. While land use influenced the microbial composition, urban and rural gardens had strikingly similar microbial profiles. Alarmingly, young gardens in the cold season hosted a substantial proportion of RDs-associated species, pointing towards increased respiratory inflammation risks. In essence, while newer gardens during colder periods show a decline in microbial diversity, they have an increased presence of RDs-associated microbes, potentially escalating respiratory disease prevalence. This underscores the pivotal role the garden age plays in enhancing both urban microbial diversity and respiratory health.
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Affiliation(s)
- Chang Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Xinxin Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Haoxin Tan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Lantian Su
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Baoming Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Muhammad Khalid
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Aki Sinkkonen
- Department of Garden Technologies, Horticulture Technologies, Natural Resources Institute Finland, Helsinki, Finland
| | - Nan Hui
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
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Cheng M, Luo S, Zhang P, Xiong G, Chen K, Jiang C, Yang F, Huang H, Yang P, Liu G, Zhang Y, Ba S, Yin P, Xiong J, Miao W, Ning K. A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau. Nat Commun 2024; 15:1438. [PMID: 38365793 PMCID: PMC10873407 DOI: 10.1038/s41467-024-45895-8] [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: 09/07/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated. The catalog contains nearly 300 million non-redundant gene clusters, of which 15% novel, and 73,864 biosynthetic gene clusters, of which 50% novel, thus expanding known functional diversity. Using these data, we investigate the Tibetan Plateau aquatic microbiome's biogeography along a distance of 2,500 km and >5 km in altitude. Microbial compositional similarity and the shared gene count with the Tibetan Plateau microbiome decline along with distance and altitude difference, suggesting a dispersal pattern. The Tibetan Plateau Microbial Catalog stands as a substantial repository for high-altitude aquatic microbiome resources, providing potential for discovering novel lineages and functions, and bridging knowledge gaps in microbiome biogeography.
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Affiliation(s)
- Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Luo
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Peng Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China
| | - Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fangdian Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China
| | - Hanhui Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guanxi Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhao Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Sang Ba
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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6
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Gu L, Yan W, Yue X, Zhong H, Wang D. Spatio-temporal distribution characteristics and influencing factors of protoporphyrin IX in the estuarine-coastal ecosystems. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106297. [PMID: 38096713 DOI: 10.1016/j.marenvres.2023.106297] [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: 06/18/2023] [Revised: 10/29/2023] [Accepted: 12/05/2023] [Indexed: 01/02/2024]
Abstract
Protoporphyrin IX (PPIX), a key precursor for the synthesis of chlorophyll and heme, is fundamental to photosynthetic eukaryotic cells and participates in light absorption, energy transduction, and numerous other cellular metabolic activities. Along with the application of genetic and biochemical techniques over the past few years, our understanding of the formation of PPIX has been largely advanced, especially regarding possible metabolic pathways. However, the ecological role and function of PPIX in natural ecosystems remains unclear. We have previously established a method for quantifying PPIX in marine ecosystems. Here, our results provide evidence that PPIX is not only subtly linked to nutrient uptake but also triggers phytoplankton productivity. PPIX and its derivatives are dynamic spatiotemporally in direct response to increased nutrient availability. Using 16 S rRNA gene amplicon sequencing, PPIX was revealed to interact strongly with many microorganisms, indicating that PPIX serves as a critical metabolite in maintaining microbial metabolism and community development. In summary, we observed that PPIX is linearly related to nutrient availability and microbial diversity. The levels of microbial PPIX reflect ecological health, and the availability of PPIX and nutrients jointly affect microbial community composition.
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Affiliation(s)
- Lide Gu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Wanli Yan
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xinli Yue
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Haowen Zhong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
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7
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Wang D, Huang Y, Jia H, Yang H. Bacterial and Microeukaryotic Community Compositions and Their Assembly Processes in Lakes on the Eastern Qinghai-Tibet Plateau. Microorganisms 2023; 12:32. [PMID: 38257859 PMCID: PMC10821157 DOI: 10.3390/microorganisms12010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Bacterial and microeukaryotic community compositions and their assembly processes have remained challenging and remained unclear in lake ecosystems on the Qinghai-Tibet Plateau (QTP). We revealed the diversity and community compositions, driving factors, ecological assembly processes, and co-occurrence networks of bacterial and microeukaryotic communities in water bodies of the eight lake ecosystems across the Eastern QTP. The results demonstrated that the predominant bacteria in most samples were Proteobacteria, with an average relative abundance of 41.78%, whereas the most abundant of microeukaryotes differed among the sample sites. The redundancy analysis revealed that latitude and pH were the most important driving factors in shaping the bacterial and microeukaryotic community compositions. Homogeneous selection (56.40%) was the dominant process in assembling the bacterial communities, whereas dispersal limitation (67.24%) was the major process in governing the microeukaryotic communities. Furthermore, dissolved organic carbon and salinity were the major factors mediating the balance of deterministic and stochastic assembly processes in the bacterial and microeukaryotic communities. Both the bacterial and microeukaryotic community co-occurrence networks exhibited topological features of modularity and non-random topological features. The results offer insights into the mechanisms underpinning bacterial and microeukaryotic diversities and communities in the lake ecosystems on the QTP.
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Affiliation(s)
- Dandan Wang
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
- Key Laboratory of Ecological Protection and High Quality Development in the Upper Yellow River, Qinghai University, Xining 810016, China
- Key Laboratory of Water Ecological Remediation and Protection at Headwater Regions of Big Rivers, Qinghai University, Xining 810016, China
| | - Yuefei Huang
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
- Key Laboratory of Ecological Protection and High Quality Development in the Upper Yellow River, Qinghai University, Xining 810016, China
- Key Laboratory of Water Ecological Remediation and Protection at Headwater Regions of Big Rivers, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Haichao Jia
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
| | - Haijiao Yang
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
- Key Laboratory of Ecological Protection and High Quality Development in the Upper Yellow River, Qinghai University, Xining 810016, China
- Key Laboratory of Water Ecological Remediation and Protection at Headwater Regions of Big Rivers, Qinghai University, Xining 810016, China
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8
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Wang L, Lian C, Wan W, Qiu Z, Luo X, Huang Q, Deng Y, Zhang T, Yu K. Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes. Appl Microbiol Biotechnol 2023; 107:6591-6605. [PMID: 37688597 DOI: 10.1007/s00253-023-12696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/24/2023] [Accepted: 07/18/2023] [Indexed: 09/11/2023]
Abstract
Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na+ or Li+ in exchange for H+. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na+/H+ antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.
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Affiliation(s)
- Li Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chunang Lian
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of ·Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of ·Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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9
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Chen C, Yin G, Hou L, Jiang Y, Sun D, Liang X, Han P, Zheng Y, Liu M. Reclamation of tidal flats to paddy soils reshuffles the soil microbiomes along a 53-year reclamation chronosequence: Evidence from assembly processes, co-occurrence patterns and multifunctionality. ENVIRONMENT INTERNATIONAL 2023; 179:108151. [PMID: 37603994 DOI: 10.1016/j.envint.2023.108151] [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: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023]
Abstract
Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation.
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Affiliation(s)
- Cheng Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yinghui Jiang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022 Jiangxi, China
| | - Dongyao Sun
- School of Geography Science and Geomatics Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China.
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Xie L, Yu S, Lu X, Liu S, Tang Y, Lu H. Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau. Microorganisms 2023; 11:2002. [PMID: 37630563 PMCID: PMC10458105 DOI: 10.3390/microorganisms11082002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem.
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Affiliation(s)
- Linglu Xie
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Shan Yu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing 100871, China
- National Engineering Research Center for Gas Hydrate Exploration and Development, Guangzhou 511466, China
| | - Xindi Lu
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Siwei Liu
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Yukai Tang
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Hailong Lu
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing 100871, China
- National Engineering Research Center for Gas Hydrate Exploration and Development, Guangzhou 511466, China
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11
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Li X, Li X, Zhang H, Kan B, Fan F. VP3 Phage Combined with High Salt Promotes the Lysis of Biofilm-Associated Vibrio cholerae. Viruses 2023; 15:1639. [PMID: 37631982 PMCID: PMC10458087 DOI: 10.3390/v15081639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cholera, caused by pathogenic Vibrio cholerae, poses a significant public health risk through water and food transmission. Biofilm-associated V. cholerae plays a crucial role in seasonal cholera outbreaks as both a reservoir in aquatic environments and a direct source of human infection. Although VP3, a lytic phage, shows promise in eliminating planktonic V. cholerae from the aquatic environment, its effectiveness against biofilm-associated V. cholerae is limited. To address this limitation, our proposed approach aims to enhance the efficacy of VP3 in eliminating biofilm-associated V. cholerae by augmenting the availability of phage receptors on the surface of Vibrio cholerae. TolC is a receptor of VP3 and a salt efflux pump present in many bacteria. In this study, we employed NaCl as an enhancer to stimulate TolC expression and observed a significant enhancement of TolC expression in both planktonic and biofilm cells of V. cholerae. This enhancement led to improved adsorption of VP3. Importantly, our findings provide strong evidence that high salt concentrations combined with VP3 significantly improve the elimination of biofilm-associated V. cholerae. This approach offers a potential strategy to eliminate biofilm-formation bacteria by enhancing phage-host interaction.
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Affiliation(s)
- Xu Li
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xiaorui Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huayao Zhang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Fenxia Fan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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12
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Ma JW, Wu YQ, Xu CL, Luo ZX, Yu RL, Hu GR, Yan Y. Inhibitory effect of polyethylene microplastics on roxarsone degradation in soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131483. [PMID: 37116328 DOI: 10.1016/j.jhazmat.2023.131483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/19/2023]
Abstract
Roxarsone (3-nitro-4-hydroxyphenylarsonic acid, Rox(V)), an extensively used organoarsenical feed additive, enters soils through the application of Rox(V)-containing manure and further degrades to highly toxic arsenicals. Microplastics, as emerging contaminants, are also frequently detected in soils. However, the effects of microplastics on soil Rox(V) degradation are unknown. A microcosm experiment was conducted to investigate soil Rox(V) degradation responses to polyethylene (PE) microplastics and the underlying mechanisms. PE microplastics inhibited soil Rox(V) degradation, with the main products being 3-amino-4-hydroxyphenylarsonic acid [3-AHPAA(V)], N-acetyl-4-hydroxy-m-arsanilic acid [N-AHPAA(V)], arsenate [As(V)], and arsenite [As(III)]. This inhibition was likely driven by the decline in soil pH by PE microplastic addition, which may directly enhance Rox(V) sorption in soils. The decreased soil pH further suppressed the nfnB gene related to nitroreduction of Rox(V) to 3-AHPAA(V) and nhoA gene associated with acetylation of 3-AHPAA(V) to N-AHPAA(V), accompanied by a decrease in the relative abundance of possible Rox(V)-degrading bacteria (e.g., Pseudomonadales), although the diversity, composition, network complexity, and assembly of soil bacterial communities were largely influenced by Rox(V) rather than PE microplastics. Our study emphasizes microplastic-induced inhibition of Rox(V) degradation in soils and the need to consider the role of microplastics in better risk assessment and remediation of Rox(V)-contaminated soils.
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Affiliation(s)
- Jie-Wen Ma
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Ya-Qing Wu
- Instrumental Analysis Center of Huaqiao University, Huaqiao University, Xiamen 361021, China
| | - Chen-Lu Xu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Zhuan-Xi Luo
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Rui-Lian Yu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Gong-Ren Hu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China.
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Wang J, Wang C, Hu M, Bian L, Qu L, Sun H, Wu X, Ren G. Bacterial co-occurrence patterns are more complex but less stable than archaea in enhanced oil recovery applied oil reservoirs. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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14
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Lin X, Zhang C, Xie W. Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea. Front Microbiol 2023; 14:1185436. [PMID: 37426005 PMCID: PMC10324572 DOI: 10.3389/fmicb.2023.1185436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.
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Affiliation(s)
- Xizheng Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
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Yang G, Jiang L, Li W, Li E, Lv G. Structural Characteristics and Assembly Mechanisms of Soil Microbial Communities under Water-Salt Gradients in Arid Regions. Microorganisms 2023; 11:microorganisms11041060. [PMID: 37110483 PMCID: PMC10142023 DOI: 10.3390/microorganisms11041060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Exploring the structural characteristics of arid soil microbial communities and their assembly mechanisms is important for understanding the ecological characteristics of arid zone soils and promoting ecological restoration. In this study, we used Illumina high-throughput sequencing technology to study soils in the arid zone of the Lake Ebinur basin, determined the differences among soil microbial community structures in the study area under different water-salt gradients, and investigated the effects of environmental factors on microbial community structure and assembly mechanisms. The results show the following: the microbial community alpha diversity exhibited a significantly higher low water-salt gradient (L) than high water-salt gradient (H) and medium water-salt gradient (M). The pH was most strongly correlated with soil microbial community structure, where the alpha diversity indices of the bacterial community and fungal community were significantly negatively correlated with pH, and the Bray-Curtis distance of bacterial community was significantly positively correlated with pH (p < 0.05). The complexity of bacterial community co-occurrence networks showed a significantly higher L than H and M, and the complexity of fungal community co-occurrence network showed a significantly lower L than H and M. The cooperative relationship of H and M in the co-occurrence networks was stronger than that of the L, and the key species of the microbial co-occurrence network were different under different water-salt gradients. Stochastic processes dominated the assembly mechanism of the microbial community structure of soil, and the explanation rates of deterministic and stochastic processes were different under different water-salt gradients, with the highest explanation rate of stochastic processes on the L accounting for more than 90%. In summary, the soil microbial community structure and assembly mechanisms significantly differed across water-salt gradients, and these findings can help provide a reference for further research on soil microbiology in arid zones.
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Affiliation(s)
- Guang Yang
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Lamei Jiang
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Wenjing Li
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Eryang Li
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Guanghui Lv
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
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16
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Zhang Z, Sun J, Li T, Shao P, Ma J, Dong K. Plants changed the response of bacterial community to the nitrogen and phosphorus addition ratio. FRONTIERS IN PLANT SCIENCE 2023; 14:1168111. [PMID: 37051075 PMCID: PMC10083283 DOI: 10.3389/fpls.2023.1168111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Human activities have increased the nitrogen (N) and phosphorus (P) supply ratio of the natural ecosystem, which affects the growth of plants and the circulation of soil nutrients. However, the effect of the N and P supply ratio and the effect of plant on the soil microbial community are still unclear. METHODS In this study, 16s rRNA sequencing was used to characterize the response of bacterial communities in Phragmites communis (P.communis) rhizosphere and non-rhizosphere soil to N and P addition ratio. RESULTS The results showed that the a-diversity of the P.communis rhizosphere soil bacterial community increased with increasing N and P addition ratio, which was caused by the increased salt and microbially available C content by the N and P ratio. N and P addition ratio decreased the pH of non-rhizosphere soil, which consequently decreased the a-diversity of the bacterial community. With increasing N and P addition ratio, the relative abundance of Proteobacteria and Bacteroidetes increased, while that of Actinobacteria and Acidobacteria decreased, which reflected the trophic strategy of the bacterial community. The bacterial community composition of the non-rhizosphere soil was significantly affected by salt, pH and total carbon (TC) content. Salt limited the relative abundance of Actinobacteria, and increased the relative abundance of Bacteroidetes. The symbiotic network of the rhizosphere soil bacterial community had lower robustness. This is attributed to the greater selective effect of plants on the bacterial community influenced by nutrient addition. DISCUSSION Plants played a regulatory role in the process of N and P addition affecting the bacterial community, and nutrient uptake by the root system reduced the negative impact of N and P addition on the bacterial community. The variations in the rhizosphere soil bacterial community were mainly caused by the response of the plant to the N and P addition ratio.
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Affiliation(s)
- Zehao Zhang
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, China
- College of Forestry, Shandong Agricultural University, Taian, China
| | - Jingkuan Sun
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, China
| | - Tian Li
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, China
| | - Pengshuai Shao
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, China
| | - Jinzhao Ma
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, China
| | - Kaikai Dong
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, China
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Liu J, Ye L, Jing C. Active microbial arsenic methylation in saline-alkaline paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161077. [PMID: 36572312 DOI: 10.1016/j.scitotenv.2022.161077] [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: 09/23/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Seawater rice has been cultivated to ensure food security. The salt-tolerant rice strains are resistant to saline and alkali but may be vulnerable to elevated arsenic (As) near coastal regions. Herein, the saline-alkaline paddy soil was incubated with natural irrigation river for three months to explore the mobility and transformation of As. The incubation results showed that 65 ± 1.2 % solid-bound As(V) was reduced to As(III) within two weeks with the release of As(III) to porewater. The dissolved As(III) was methylated after two weeks, resulting in dimethyl arsenate (DMA) as the dominant As species (87 %-100 %). The elevated As methylation was attributed to the most abundant arsenite methyltransferase gene (arsM) (4.1-10.4 × 107/g dry soil), over three orders of magnitude higher than As redox-related genes. The analysis of arsM operational taxonomic units (OTUs) suggested the highest sequence similarity to Proteobacteria (25.7-39.5 %), Actinobacteria (24.9-30.5 %), Gemmatimonadetes (7.5-11.9 %), Basidiomycota (5.1-12.5 %), and Chloroflexi (4.1-8.7 %). Specifically, Chloroflexi and Actinobacteria are salt-tolerant bacteria, probably responsible for As methylation. The As in grain was within a safe regulatory level, and the dominance of methylated As in porewater did not enhance its accumulation in rice grains.
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Affiliation(s)
- Jing Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Li Ye
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Yang X, Dai Z, Yuan R, Guo Z, Xi H, He Z, Wei M. Effects of Salinity on Assembly Characteristics and Function of Microbial Communities in the Phyllosphere and Rhizosphere of Salt-Tolerant Avicennia marina Mangrove Species. Microbiol Spectr 2023; 11:e0300022. [PMID: 36744884 PMCID: PMC10101020 DOI: 10.1128/spectrum.03000-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/06/2023] [Indexed: 02/07/2023] Open
Abstract
It is of great significance to explore the structure and salinity response of microbial communities in salt-tolerant plants to understand the mechanisms of plant-microbe interactions. Herein, we investigated the phyllosphere and rhizosphere microbial communities of Avicennia marina, a pioneer salt-tolerant plant, at three sites with different salinities in the coastal intertidal zone. The results showed that salinity had different effects on phyllosphere and rhizosphere microbial communities and had a greater impact on bacterial communities and bacterial network interactions. The rhizosphere bacterial community alpha diversity significantly increased with increasing salinity. Moreover, the relative abundance of Proteobacteria decreased significantly, while that of Bacteroidota and Actinobacteriota, with stronger salt tolerance and nutrient utilization capacity, increased significantly. Functional prediction indicated that the microbial communities could produce catalase, peroxidase, 3-phytase, and tryptophan synthase, which may exert potential antistress and growth-promoting functions. Among them, catalase, 3-phytase, alkaline phosphatase, and acid phosphatase increased significantly in the phyllosphere and rhizosphere bacterial communities and the phyllosphere fungal community with increasing salinity. Importantly, the dominant taxa Kushneria and Bacillus, which are salt tolerant and growth promoting, were isolated from the phyllosphere and rhizosphere, respectively, and verified to have the ability to alleviate salt stress and promote the growth of rice. IMPORTANCE Avicennia marina is a pioneer salt-tolerant plant in coastal intertidal mangroves, an efficient blue carbon ecosystem. It is of great importance to explore how salinity affects the phyllosphere and rhizosphere microbial communities of A. marina. This study showed that the microbial communities in the phyllosphere and rhizosphere of A. marina had different constitutive properties, adaptive network interactions, and potential stress-promoting functions. Furthermore, the dominant bacteria Kushneria and Bacillus were obtained from the phyllosphere and rhizosphere, respectively, and their coculture with rice could effectively alleviate salt stress and promote rice growth. Additionally, the effects of salinity changes on microbial community structure, associations, and functional potential in the phyllosphere and rhizosphere of A. marina were observed. This study has enriched our understanding of the microbial community structure, function, and ecological stability of mangrove species in coastal intertidal zones and has practical significance for improving crop yield by using salt-tolerant plant microbiomes.
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Affiliation(s)
- Xiangxia Yang
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhian Dai
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Rongwei Yuan
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhenhua Guo
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hanxiao Xi
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 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, China
| | - Mi Wei
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
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Wang M, Wang C, Yu Z, Wang H, Wu C, Masoudi A, Liu J. Fungal diversities and community assembly processes show different biogeographical patterns in forest and grassland soil ecosystems. Front Microbiol 2023; 14:1036905. [PMID: 36819045 PMCID: PMC9928764 DOI: 10.3389/fmicb.2023.1036905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Soil fungal community has been largely explored by comparing their natural diversity. However, there is a relatively small body of literature concerned with fungal community assembly processes and their co-occurrence network correlations carried out across large spatial-temporal scales with complex environmental gradients in natural ecosystems and different habitats in China. Thus, soil fungal community assembly processes were assessed to predict changes in soil function in 98 different forest and grassland sites from the Sichuan, Hubei, and Hebei Provinces of China using high-throughput sequencing of nuclear ribosomal internal transcribed spacer 2 (ITS-2). The 10 most abundant fungal phyla results showed that Ascomycota was the most abundant phylum in forests from Sichuan province (64.42%) and grassland habitats from Hebei province (53.46%). Moreover, core fungal taxa (487 OTUs) represented 0.35% of total fungal OTUs. We observed higher fungal Shannon diversity and richness (the Chao1 index) from diverse mixed forests of the Sichuan and Hubei Provinces than the mono-cultured forest and grassland habitats in Hebei Province. Although fungal alpha and beta diversities exhibited different biogeographical patterns, the fungal assembly pattern was mostly driven by dispersal limitation than selection in different habitats. Fungal co-occurrence analyses showed that the network was more intense at Saihanba National Forest Park (SNFP, Hebei). In contrast, the co-occurrence network was more complex at boundaries between forests and grasslands at SNFP. Additionally, the highest number of positive (co-presence or co-operative) correlations of fungal genera were inferred from grassland habitat, which led fungal communities to form commensalism relationships compared to forest areas with having higher negative correlations (mutual exclusion or competitive). The generalized additive model (GAM) analysis showed that the association of fungal Shannon diversity and richness indices with geographical coordinates did not follow a general pattern; instead, the fluctuation of these indices was restricted to local geographical coordinates at each sampling location. These results indicated the existence of a site effect on the diversity of fungal communities across our sampling sites. Our observation suggested that higher fungal diversity and richness of fungal taxa in a particular habitat are not necessarily associated with more complex networks.
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Li X, Liu Q, Yu X, Zhang C, Liu M, Zhou X, Gu C, Wang M, Shao H, Li J, Jiang Y. Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20615-20630. [PMID: 36255574 DOI: 10.1007/s11356-022-23572-x] [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: 01/19/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.
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Affiliation(s)
- Xianrong Li
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chenru Zhang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chengxiang Gu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 2661000, China
| | - Hongbing Shao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jiansen Li
- Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, 810008, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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21
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Zhang S, Yan L, Cao J, Wang K, Luo Y, Hu H, Wang L, Yu R, Pan B, Yu K, Zhao J, Bao Z. Salinity significantly affects methane oxidation and methanotrophic community in Inner Mongolia lake sediments. Front Microbiol 2023; 13:1067017. [PMID: 36687579 PMCID: PMC9853545 DOI: 10.3389/fmicb.2022.1067017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Methanotrophs oxidize methane (CH4) and greatly help in mitigating greenhouse effect. Increased temperatures due to global climate change can facilitate lake salinization, particularly in the regions with cold semiarid climate. However, the effects of salinity on the CH4 oxidation activity and diversity and composition of methanotrophic community in the sediment of natural lakes at a regional scale are still unclear. Therefore, we collected lake sediment samples from 13 sites in Mongolian Plateau; CH4 oxidation activities of methanotrophs were investigated, and the diversity and abundance of methanotrophs were analyzed using real-time quantitative polymerase chain reaction and high throughput sequencing approach. The results revealed that the diversity of methanotrophic community decreased with increasing salinity, and community structure of methanotrophs was clearly different between the hypersaline sediment samples (HRS; salinity > 0.69%) and hyposaline sediment samples (HOS; salinity < 0.69%). Types II and I methanotrophs were predominant in HRS and HOS, respectively. Salinity was significantly positively correlated with the relative abundance of Methylosinus and negatively correlated with that of Methylococcus. In addition, CH4 oxidation rate and pmoA gene abundance decreased with increasing salinity, and salinity directly and indirectly affected CH4 oxidation rate via regulating the community diversity. Moreover, high salinity decreased cooperative association among methanotrophs and number of key methanotrophic species (Methylosinus and Methylococcus, e.g). These results suggested that salinity is a major driver of CH4 oxidation in lake sediments and acts by regulating the diversity of methanotrophic community and accociation among the methanotrophic species.
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Affiliation(s)
- Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lei Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiahui Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kexin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ying Luo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Haiyang Hu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lixin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Ruihong Yu
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Baozhu Pan
- Institute of Water Resources and Hydro-electric Engineering, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China,*Correspondence: Zhihua Bao, ✉
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22
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Mo Y, Peng F, Jeppesen E, Gamfeldt L, Xiao P, Al MA, Yang J. Microbial network complexity drives non-linear shift in biodiversity-nutrient cycling in a saline urban reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158011. [PMID: 35970466 DOI: 10.1016/j.scitotenv.2022.158011] [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: 06/22/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Aquatic biodiversity is important in mediating ecosystem functioning, contributing to ecosystem sustainability and human wellbeing. However, how microbial network complexity affects the biodiversity-nutrient cycling relationship in saline freshwater ecosystems remains underexplored. Using high-resolution time-series data, we examined the relationships between microeukaryotic-bacterial community network complexity, biodiversity and multi-nutrient cycling in an urban reservoir undergoing a freshwater salinization-desalinization cycle. We found that low microbial diversity enhanced ecosystem multi-nutrient cycling under high salinity stress. In addition, multi-nutrient cycling declined with increased network complexity. Further, we found a non-linear relationship between salinity-induced shifts in the complexity of the microbial network and biodiversity-nutrient cycling (BNC) relationship of keystone taxa, i.e. the strength of the BNC relationship first became weak and then strong with increased network complexity. Together, these results highlighted the significant insight that there is not always positive relationship between biodiversity/network complexity and multi-nutrient cycling, even between network complexity and BNC relationship in real-world ecosystems, suggesting that preserving microbial association is important in aquatic health managing and evaluating the freshwater salinization problem.
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Affiliation(s)
- Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Peng
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Erik Jeppesen
- Department of Ecoscience, Aarhus University, Silkeborg 8600, Denmark; Sino-Danish Centre for Education and Research, Beijing 100049, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara 06800, Turkey; Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin 33731, Turkey
| | - Lars Gamfeldt
- Department of Marine Sciences, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Peng Xiao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Mamun Abdullah Al
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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23
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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24
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Li H, Luo N, Ji C, Li J, Zhang L, Xiao L, She X, Liu Z, Li Y, Liu C, Guo Q, Lai H. Liquid Organic Fertilizer Amendment Alters Rhizosphere Microbial Community Structure and Co-occurrence Patterns and Improves Sunflower Yield Under Salinity-Alkalinity Stress. MICROBIAL ECOLOGY 2022; 84:423-438. [PMID: 34535834 DOI: 10.1007/s00248-021-01870-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Response of rhizosphere microbial community structure and co-occurrence patterns to liquid organic fertilizer in sunflower cropland was investigated. Moderate and severe saline-alkaline soils were treated with liquid organic fertilizer containing mainly small molecular organic compounds (450 g L-1) at a rate of 4500 L ha-1 year-1 over 2 years. Compared with the untreated soils, organic fertilizer treatment increased soil nutrient concentrations by 13.8-137.1% while reducing soil pH and salinity by 5.6% and 54.7%, respectively. Organic fertilizer treatment also improved sunflower yield, plant number, and plant height by 28.6-67.3%. Following organic fertilizer treatment, fungal α-diversity was increased, and the effects of salinity-alkalinity stress on rhizosphere microbial communities were alleviated. The relative abundances of some halotolerant microbes and phytopathogenic fungi were reduced in organic fertilizer-treated soils, in contrast to increases in the relative abundances of plant growth-promoting microbes and organic matter decomposers, such as Nocardioides, Rhizophagus, and Stachybotrys. Network analysis revealed that severe salinity-alkalinity stress stimulated cooperation among bacteria, while organic fertilizer treatment tended to stimulate the ecosystem functions of fungi with higher proportions of fungi-bacteria and fungi-fungi links. More keystone taxa (e.g., Amycolatopsis, Variovorax, and Gemmatimonas) were positively correlated with soil nutrient concentrations and crop yield-related traits in organic fertilizer-treated soils. Overall, liquid organic fertilizer amendment could attenuate the adverse effects of salinity-alkalinity stress on sunflower yield by improving soil quality and optimizing rhizosphere microbial community structure and co-occurrence patterns.
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Affiliation(s)
- Haiyang Li
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Nanyan Luo
- Tongchuan Institute of Agricultural Sciences, Tongchuan, 727000, China
| | - Chenglong Ji
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Jin Li
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Lan Zhang
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Li Xiao
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Xiaolin She
- Tongchuan Institute of Agricultural Sciences, Tongchuan, 727000, China
| | - Zhe Liu
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Yulong Li
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Cunshou Liu
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
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25
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Li K, Guan W, He P, Li K. Comparison of bacterial communities on the surface of concrete breakwater structures and ambient bacterioplankton. Lett Appl Microbiol 2022; 75:1193-1202. [PMID: 35831926 DOI: 10.1111/lam.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/03/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Breakwater structures made of concrete are used widely around the world, and the bacteria living on these surfaces can cause the concrete to deteriorate. In this study, we collected bacterial biofilms from concrete breakwater structures located along the coast of an island, a mainland coast, and a freshwater riverbank as well as planktonic water samples from each site, and we analyzed their bacterial community structures using Illumina sequencing. At the phylum level, Proteobacteria and Actinobacteria dominated planktonic samples, whereas Cyanobacteria, Proteobacteria, and Bacteroidetes dominated the biofilm samples. High Cyanobacteria abundance was found in all biofilm samples. Bacterial communities significantly varied between planktonic and biofilm samples and between biofilm samples from seawater and freshwater. Only a small number of bacterial operational taxonomic units were shared by planktonic and biofilm samples from each sampling site. The permanganate index in ambient water had a more significant impact on biofilm bacterial communities than on planktonic samples. Additionally, ammonia nitrogen and total nitrogen contents were positively correlated and salinity was negatively correlated with bacterial beta diversity in biofilm samples.
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Affiliation(s)
- Kui Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Weibing Guan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kejun Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
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26
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Abstract
Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.
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Hu X, Shu Q, Guo W, Shang Z, Qi L. Secondary Succession Altered the Diversity and Co-Occurrence Networks of the Soil Bacterial Communities in Tropical Lowland Rainforests. PLANTS (BASEL, SWITZERLAND) 2022; 11:1344. [PMID: 35631769 PMCID: PMC9148129 DOI: 10.3390/plants11101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The characteristics of plant and soil bacterial communities in forest ecosystems have been reported, but our understanding of the relationship between plant communities and soil bacteria in different stages of secondary tropical rainforest succession is still poor. In June 2018, three different natural successional stages of tropical lowland rainforests, early (33 years), early-mid (60 years), and mid successional stage (73 years), in Hainan Island, China, were selected for this study. By conducting field investigation and 16S rRNA gene high-throughput sequencing, the composition and diversity of tree communities, the niche overlap of tree species with legumes among tree species, and the diversity and composition of soil bacterial communities and co-occurrence networks within communities across the successional stages were investigated. The results showed that plant richness and species diversity increased significantly during the secondary succession of tropical lowland rainforests. The order of positive correlations between nitrogen-fixing legumes and other species in plant communities was early-mid > mid > early successional stage. Soil nutrient content and soil bacterial richness were highest in the early-mid stages of succession, followed by mid and early stages of succession. Organic matter (OM), total nitrogen (TN), alkali nitrogen (AN), and available phosphorus (AP) had a stronger positive impact on soil bacterial communities. Co-occurrence network analysis showed that with the advancement of rainforests succession, the negative correlation between soil bacterial species decreased, and the community stability increased. Overall, as a result of tropical lowland rainforest secondary natural succession, the richness and diversity of plant communities increased, which altered the living conditions of nitrogen-fixing legumes and the soil properties, and the network complexity of soil bacterial communities increased with the rising of rainforest soil nutrient content.
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Affiliation(s)
- Xuan Hu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing 100102, China; (X.H.); (W.G.)
- National Positioning and Monitoring Station for Ecosystem of Bamboo and Rattan, Sanya 572000, China;
| | - Qi Shu
- National Positioning and Monitoring Station for Ecosystem of Bamboo and Rattan, Sanya 572000, China;
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100089, China
| | - Wen Guo
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing 100102, China; (X.H.); (W.G.)
| | - Zean Shang
- Shaanxi Academy of Forestry, Xi’an 710082, China;
| | - Lianghua Qi
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing 100102, China; (X.H.); (W.G.)
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28
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Liu C, Wu F, Jiang X, Hu Y, Shao K, Tang X, Qin B, Gao G. Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China. Front Microbiol 2022; 13:841686. [PMID: 35495662 PMCID: PMC9039746 DOI: 10.3389/fmicb.2022.841686] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
The arid and semiarid areas experienced remarkable lake shrinkage during recent decades due to intensive human activities and climate change, which would result in unprecedented changes of microeukaryotic communities. However, little is known about how climate change affects the structure and ecological mechanisms of microeukaryotic communities in this area. Here, we used an 18S rRNA gene-based high-throughput sequencing approach to explore the structure, interspecies interaction, and assembly processes of the microeukaryotic community in lake ecosystems of the Inner Mongolia Plateau. As a direct result of climate change, salinity has become the key determinant of the lacustrine microeukaryotic community in this region. The microeukaryotic community in this ecosystem can be divided into three groups: salt (Lake Daihai), brackish (Lake Dalinuoer) and freshwater lakes. Co-occurrence network analysis revealed that salinity shapes the interspecies interactions of the microeukaryotic community. This causes interspecies interactions to change from antagonistic to cooperative with an increase in salinity. Phylogenetic-based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated the microeukaryotic community assembly in lake ecosystems of the Inner Mongolia Plateau, and salinity stress drove the assembly processes of the microeukaryotic community from stochastic to deterministic. Overall, these findings expand the current understanding of interspecies interactions and assembly processes of microeukaryotic communities during climate change in lake ecosystems of the Inner Mongolia Plateau.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Boqiang Qin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (CAS), Nanjing, China
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29
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Chen Y, Liu Y, Liu K, Ji M, Li Y. Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau. Front Microbiol 2022; 12:784273. [PMID: 35154026 PMCID: PMC8829297 DOI: 10.3389/fmicb.2021.784273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/27/2021] [Indexed: 12/05/2022] Open
Abstract
Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.
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Affiliation(s)
- Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yang Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
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The impact of different rotation regime on the soil bacterial and fungal communities in an intensively managed agricultural region. Arch Microbiol 2022; 204:142. [PMID: 35043270 DOI: 10.1007/s00203-021-02615-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
The continuous wheat-maize planting has led to the increase in epidemic frequency of wheat diseases under climate change. Analyzation of the soil microbial composition in different rotation crops is essential to select alternative rotation regime. This study investigated the bacterial and fungal community abundance and composition, and potential microbe-microbe interactions in three rotations, including wheat-maize → spring maize (WMFS), wheat-soybean (WS) and continuous wheat-maize (WM) planting. The results revealed that there were 110, 156, and 195 bacterial, and 17, 8, and 15 fungal operational taxonomic units respectively enriched by WMFS, WS, and WM. WM increased the relative abundance of Actinobacteria and α-Proteobacteria in wheat, and the relative abundance and copy number of genus Fusarium in maize. WMFS and WS could decrease the abundance of Fusarium in summer-crop across the growth stages and in wheat at elongation. WS also increased the copy number of ammonia-oxidizing bacteria in wheat at flowering and harvest. Network analysis revealed that WM resulted in simple and isolated wheat network with small modules dominating and none Nitrospirae and β-Proteobacteria in the main modules. WS formed interconnected and intricate wheat network with the maximum number of large modules and module connectors. Under WS, positive correlation between antagonistic Streptomyces (Actinobacteria) and genus Fusarium was found in wheat. Soil physicochemical properties explained the majority of the variation in bacterial and fungal β-diversity in wheat (P < 0.01). Rotation regime switching from WM to WMFS and WS may effectively damp the risk of wheat disease and maintain the wheat yield in intensive cereal production.
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Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, Gao C, Li X, Zhang W, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, Suttle CA, McMinn A, Tian J, Wang M. Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. iScience 2021; 24:103439. [PMID: 34988389 PMCID: PMC8710556 DOI: 10.1016/j.isci.2021.103439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/10/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022] Open
Abstract
The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.
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Affiliation(s)
- Chengxiang Gu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Jiansen Li
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Chen Gao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xianrong Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yeong Yik Sung
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jiwei Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- The affiliated hospital of Qingdao University, Qingdao 266000, China
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Gupta CL, Avidov R, Kattusamy K, Saadi I, Varma VS, Blum SE, Zhu YG, Zhou XY, Su JQ, Laor Y, Cytryn E. Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles. Comput Struct Biotechnol J 2021; 19:6201-6211. [PMID: 34900133 PMCID: PMC8637134 DOI: 10.1016/j.csbj.2021.11.020] [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: 09/05/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 11/08/2022] Open
Abstract
Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.
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Affiliation(s)
- Chhedi Lal Gupta
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
| | - Ran Avidov
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Karuppasamy Kattusamy
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
| | - Ibrahim Saadi
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Vempalli Sudharsan Varma
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Shlomo E Blum
- Department of Bacteriology, Kimron Veterinary Institute, 50250 Beit Dagan, Israel
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Yuan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yael Laor
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
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Bhattarai B, Bhattacharjee AS, Coutinho FH, Goel RK. Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake. Front Microbiol 2021; 12:701414. [PMID: 34650523 PMCID: PMC8506154 DOI: 10.3389/fmicb.2021.701414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.
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Affiliation(s)
- Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
| | - Ananda S Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ramesh K Goel
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
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High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling. Appl Environ Microbiol 2021; 87:e0136621. [PMID: 34406835 DOI: 10.1128/aem.01366-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m-1). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.
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Mo Y, Peng F, Gao X, Xiao P, Logares R, Jeppesen E, Ren K, Xue Y, Yang J. Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir. MICROBIOME 2021; 9:128. [PMID: 34082826 PMCID: PMC8176698 DOI: 10.1186/s40168-021-01079-w] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity. RESULTS Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics. CONCLUSIONS Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.
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Affiliation(s)
- Yuanyuan Mo
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Feng Peng
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Xiaofei Gao
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xiao
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Ramiro Logares
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003 Barcelona, Spain
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, 8600 Silkeborg, Denmark
- Sino-Danish Centre for Education and Research, Beijing, 100049 China
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, 06800 Ankara, Turkey
- Institute of Marine Sciences, Middle East Technical University, 33731 Erdemli-Mersin, Turkey
| | - Kexin Ren
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Yuanyuan Xue
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Jun Yang
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
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Chen W, Wen D. Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion. ENVIRONMENTAL MICROBIOME 2021; 16:10. [PMID: 33941277 PMCID: PMC8091715 DOI: 10.1186/s40793-021-00377-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/02/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora (S. alterniflora) invasion in China. However, little is known about mangrove sediment microbial community assembly processes and interactions under S. alterniflora invasion. Here, we investigated the assembly processes and co-occurrence networks of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China. RESULTS Assembly of overall archaeal and bacterial communities was driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analyses showed that the network structure of bacteria was more complex than that of the archaea. The keystone taxa often had low relative abundances (conditionally rare taxa), suggesting low abundance taxa may significantly contribute to network stability. Moreover, S. alterniflora invasion increased bacterial and archaeal drift process (part of stochastic processes), and improved archaeal network complexity and stability, but decreased the network complexity and stability of bacteria. This could be attributed to S. alterniflora invasion influenced microbial communities diversity and dispersal ability, as well as soil environmental conditions. CONCLUSIONS This study fills a gap in the community assembly and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem under S. alterniflora invasion. Thereby provides new insights of the plant invasion on mangrove microbial biogeographic distribution and co-occurrence network patterns.
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Affiliation(s)
- Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871 China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871 China
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Guan Y, Jiang N, Wu Y, Yang Z, Bello A, Yang W. Disentangling the role of salinity-sodicity in shaping soil microbiome along a natural saline-sodic gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142738. [PMID: 33097264 DOI: 10.1016/j.scitotenv.2020.142738] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 05/16/2023]
Abstract
Increasing salinity and sodicity have been recognized as threats to soil fertility and crop yield worldwide. In recent years, salt-affected soils have received great attentions due to the shortage of arable land. This study therefore aims to characterize soil bacterial community, assembly process and co-occurrence network along natural saline-sodic gradients across Songnen Plain, Northeast China. As revealed by Miseq sequencing, 8482 bacterial OTUs were annotated at 97% identity across 120 soil samples. Our results indicated that soil salinity-sodicity not only significantly decreased bacterial richness and but also impacted bacterial community composition. The dominant bacterial phyla included Proteobacteria (28.89%), Actinobacteria (19.96%) and Gemmatimonadetes (16.71%). By applying threshold indicator species analysis (TITAN), OTUs from Gemmatimonadetes were found to be the taxa with the most prevalent and strongest preference for high salinity-sodicity. Null model analysis revealed that the majority (76.4%) of βNTI values were below -2 or above 2, indicating deterministic process was dominant across all samples. Notably, deterministic process contributed to a greater extent in higher saline-sodic soils. The bacterial co-occurrence network was more complex in slightly saline-sodic soils than in moderately and extremely saline-sodic soils, reflected by more nodes, more hubs and stronger connections, which was mainly driven by soil pH. These results provide strong evidence that salinity-sodicity was a key determinant in shaping soil bacterial community, assembly process and co-occurrence network pattern.
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Affiliation(s)
- Yupeng Guan
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Nana Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Yanxiang Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Zhongzan Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China.
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Tang X, Xie G, Shao K, Tian W, Gao G, Qin B. Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels. Microorganisms 2021; 9:208. [PMID: 33498349 PMCID: PMC7909399 DOI: 10.3390/microorganisms9020208] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/26/2022] Open
Abstract
Due to the recent decades of climate change and intensive human activities, endorheic lakes are threatened by both salinization and eutrophication. However, knowledge of the aquatic bacterial community's response to simultaneous increasing salinity and trophic status is still poor. To address this knowledge gap, we collected 40 surface water samples from five lakes and six rivers on the semi-arid Inner Mongolia Plateau, and investigated their bacterial communities using 16S rRNA gene-targeted amplicon sequencing. We found that bacterial species diversity significantly decreased from the mesotrophic freshwater river habitat to the eutrophic high-brackish lake habitat; salinity was more important than trophic status in explaining this decreased diversity. Salinity was the most important environmental factor in shaping community composition, while increased nitrogen loading was more important in structuring predicted functional composition. Within the lake habitats, the impact of environmental filtering on bacterial community assembly increased with the increasing salinity. The results suggested that the elevated salinity and nutrients have combined effects on the aquatic bacterial community, resulting in dramatic declines in species diversity, and promoted the importance of deterministic processes in community assembly. Our findings provide new insights into bacterial communities' responses to the intensified climate-driven and anthropogenic environmental changes in aquatic ecosystems.
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Affiliation(s)
- Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; (G.X.); (K.S.); (W.T.); (G.G.); (B.Q.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guijuan Xie
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; (G.X.); (K.S.); (W.T.); (G.G.); (B.Q.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; (G.X.); (K.S.); (W.T.); (G.G.); (B.Q.)
| | - Wei Tian
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; (G.X.); (K.S.); (W.T.); (G.G.); (B.Q.)
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; (G.X.); (K.S.); (W.T.); (G.G.); (B.Q.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boqiang Qin
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; (G.X.); (K.S.); (W.T.); (G.G.); (B.Q.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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Yang J, Jiang H, Sun X, Huang J, Han M, Wang B. Distinct co-occurrence patterns of prokaryotic community between the waters and sediments in lakes with different salinity. FEMS Microbiol Ecol 2020; 97:5989694. [PMID: 33206972 DOI: 10.1093/femsec/fiaa234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Temporal variations and co-occurrence patterns of the prokaryotic community in saline lakes remain elusive. In this study, we investigated the temporal variations of the prokaryotic community in six lakes with different salinity by using Illumina sequencing. The results showed that prokaryotic community compositions exhibited temporal variations in all studied lakes, which may be partially caused by temporal fluctuations of environmental variables (e.g. salinity, temperature, total nitrogen). Salinity fluctuations exhibited stronger influences on temporal variations of prokaryotic community composition in the lakes with low salinity than in those with high salinity. Stochastic factors (i.e. neutral processes) also contributed to temporal variations of prokaryotic community composition, and their contributions decreased with increasing salinity in the studied saline lakes. Network analysis showed that prokaryotic co-occurrence networks of the studied lakes exhibited non-random topology. Salinity affected the phylogenetic composition of nodes in the studied networks. The topological features (e.g. average connectivity and modularity) of the studied networks significantly differed between lake waters and sediments. Collectively, these results expand our knowledge of the mechanisms underlying prokaryotic community assembly and co-occurrence relationships in saline lakes with different salinity.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China.,Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
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40
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Zhang G, Bai J, Tebbe CC, Zhao Q, Jia J, Wang W, Wang X, Yu L. Salinity controls soil microbial community structure and function in coastal estuarine wetlands. Environ Microbiol 2020; 23:1020-1037. [PMID: 33073448 DOI: 10.1111/1462-2920.15281] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022]
Abstract
Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, Braunschweig, 38116, Germany
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China.,Ecology Institute of Shandong Academy of Sciences, Jinan, 250103, China
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Lu Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Mise K, Iwasaki W. Environmental Atlas of Prokaryotes Enables Powerful and Intuitive Habitat-Based Analysis of Community Structures. iScience 2020; 23:101624. [PMID: 33117966 PMCID: PMC7581931 DOI: 10.1016/j.isci.2020.101624] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/03/2020] [Accepted: 09/24/2020] [Indexed: 01/01/2023] Open
Abstract
The recent prevalence of high-throughput sequencing has been producing numerous prokaryotic community structure datasets. Although the trait-based approach is useful to interpret those datasets from ecological perspectives, available trait information is biased toward culturable prokaryotes, especially those of clinical and public health relevance, and thus may not represent the breadth of microbiota found across many of Earth's environments. To facilitate habitat-based analysis free of such bias, here we report a ready-to-use prokaryotic habitat database, ProkAtlas. ProkAtlas comprehensively links 16S rRNA gene sequences to prokaryotic habitats, using public shotgun metagenome datasets. We also developed a computational pipeline for habitat-based analysis of given prokaryotic community structures. After confirmation of the method effectiveness using 16S rRNA gene sequence datasets from individual genomes and the Earth Microbiome Project, we showed its validness and effectiveness in drawing ecological insights by applying it to six empirical prokaryotic community datasets from soil, aquatic, and human gut samples. We developed a database, ProkAtlas, denoting the habitat preferences of prokaryotes ProkAtlas represents a prokaryotic community using habitat preferences of its members The powerfulness of ProkAtlas is showcased by six datasets from various environments We provide web interface of ProkAtlas at https://msk33.github.io/prokatlas.html
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Affiliation(s)
- Kazumori Mise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author
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