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Lv H, Yang M, Cheng Y, Li K, Ji G, Huang T, Wen G. Disentangling the assembly patterns and drivers of microbial communities during thermal stratification and mixed periods in a deep-water reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174398. [PMID: 38960188 DOI: 10.1016/j.scitotenv.2024.174398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024]
Abstract
Effect of periodic thermal stratification in deep-water reservoirs on aquatic ecosystems has been a research hotspot. Nevertheless, there is limited information on the response patterns of microbial communities to environmental changes under such specialized conditions. To fill this gap, samples were collected from a typical deep-water reservoir during the thermal stratification period (SP) and mixed period (MP). Three crucial questions were answered: 1) How microbial communities develop with stratified to mixed succession, 2) how the relative importance of stochastic and deterministic processes to microbial community assembly, shifted in two periods, and 3) how environmental variables drive microbial co-occurrence networks and functional group alteration. We used Illumina Miseq high-throughput sequencing to investigate the dynamics of the microbial community over two periods, constructed molecular ecological networks (MENs), and unraveled assembly processes based on null and neutral models. The results indicated that a total of 33.9 % and 27.7 % of bacterial taxa, and 23.1 % and 19.4 % of fungal taxa were enriched in the stratified and mixed periods, respectively. Nitrate, water temperature, and total phosphorus drove the variation of microbial community structure. During the thermal stratification period, stochastic processes (dispersal limitation) and deterministic processes (variable selection) dominated the assembly of bacterial and fungal communities, followed by a shift to stochastic processes dominated by dispersal limitation in two communities. The MENs results revealed that thermal stratification-induced environmental stresses increased the complexity of microbial networks but decreased its robustness, resulting in more vulnerable ecological networks. Therefore, this work provides critical ecological insights for the longevity and sustainability of water quality management in an artificially regulated engineered system.
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Affiliation(s)
- He Lv
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Meng Yang
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ya Cheng
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kai Li
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Gang Ji
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Gang Wen
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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Zhu J, Chen G, Tang S, Cheng K, Wu K, Cai Z, Zhou J. The micro-ecological feature of colonies is a potential strategy for Phaeocystis globosa bloom formation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174134. [PMID: 38909792 DOI: 10.1016/j.scitotenv.2024.174134] [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: 01/31/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Phaeocystis globosa is among the dominant microalgae associated with harmful algal blooms. P. globosa has a polymorphic life cycle and its ecological success has been attributed to algal colony formation, however, few studies have assessed differences in microbial communities and their functional profiles between intra- and extra-colonies during P. globosa blooms. To address this, environmental and metagenomics tools were used to conduct a time-series analysis of the bacterial composition and metabolic characteristics of intra- and extra-colonies during a natural P. globosa bloom. The results show that bacterial composition, biodiversity, and network interactions differed significantly between intra- and extra-colonies. Dominant extra-colonial bacteria were Bacteroidia and Saccharimonadis, while dominant intra-colonial bacteria included Alphaproteobacteria and Gammaproteobacteria. Despite the lower richness and diversity observed in the intra-colonial bacterial community, relative to extra-colonies, the complexity and interconnectedness of the intra-colonial networks were higher. Regarding bacterial function, more functional genes were enriched in substance metabolism (polysaccharides, iron element and dimethylsulfoniopropionate) and signal communication (quorum sensing, indoleacetic acid-IAA) pathways in intra- than in extra-colonies. Conceptual model construction showed that microbial cooperative synthesis of ammonium, vitamin B12, IAA, and siderophores were strongly related to the P. globosa bloom, particularly in the intra-colonial environment. Overall, our data highlight the differences in bacterial structure and functions within and outside the colony during P. globosa blooms. These findings represent fundamental information indicating that phenotypic heterogeneity is a selective strategy that improves microbial population competitiveness and environmental adaptation, benefiting P. globosa bloom formation and persistence.
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Affiliation(s)
- Jianming Zhu
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong Province, PR China
| | - Si Tang
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Keke Cheng
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Kebi Wu
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Jin Zhou
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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Wang J, Jiao D, Yuan S, Chen H, Dai J, Wang X, Guo Y, Qiu D. Comparative analysis of microbial community under acclimation of linear alkylbenzene sulfonate (LAS) surfactants and degradation mechanisms of functional strains. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135370. [PMID: 39088956 DOI: 10.1016/j.jhazmat.2024.135370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 07/17/2024] [Accepted: 07/27/2024] [Indexed: 08/03/2024]
Abstract
Linear alkylbenzene sulfonate (LAS) is one of the most widely used anionic surfactants and a common toxic pollutant in wastewater. This study employed high throughput sequencing to explore the microbial community structure within activated sludge exposed to a high concentration of LAS. Genera such as Pseudomonas, Aeromonas, Thauera and Klebsiella exhibited a significant positive correlation with LAS concentrations. Furthermore, Comamonas and Klebsiella were significantly enriched under the stress of LAS. Moreover, bacterial strains with LAS-degrading capability were isolated and characterized to elucidate the degradation pathways. The Klebsiella pneumoniae isolate L1 could effectively transform more than 60 % of 25 mg/L of LAS within 72 h. Chemical analyses revealed that L1 utilized the LAS sulfonyl group as a sulfur source to support its growth. Genomic and transcriptomic analyses suggested that strain L1 may uptake LAS through the sulfate ABC transport system and remove sulfonate with sulfate and sulfite reductases.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dian Jiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siliang Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Han Chen
- Jingchu University of Technology, Jingmen 448000, China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xin Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Guo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dongru Qiu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Gu S, Wu S, Zeng W, Deng Y, Luo G, Li P, Yang Y, Wang Z, Hu Q, Tan L. High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes. ENVIRONMENTAL RESEARCH 2024; 257:119330. [PMID: 38830394 DOI: 10.1016/j.envres.2024.119330] [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: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.
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Affiliation(s)
- Songsong Gu
- Hunan Agricultural University, Changsha, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Weiai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Gongwen Luo
- Hunan Agricultural University, Changsha, China
| | - Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | | | | | - Qiulong Hu
- Hunan Agricultural University, Changsha, China.
| | - Lin Tan
- Hunan Agricultural University, Changsha, China.
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Sun S, Qiao Z, Sun K, Huo D. Assembly process and co-occurrence network of microbial community in response to free ammonia gradient distribution. Microbiol Spectr 2024; 12:e0105124. [PMID: 39058029 PMCID: PMC11370247 DOI: 10.1128/spectrum.01051-24] [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: 04/25/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They are vital in sustaining ecological services, especially in maintaining essential biogeochemical cycles. Recent years have seen a substantial increase in surplus nitrogenous pollutants in aquatic ecosystems due to the heightened occurrence of anthropogenic activities. Elevated levels of free ammonia (FA, NH3), stemming from the discharge of excess nitrogenous pollutants, have caused notable fluctuations in aquatic ecosystems, leading to water eutrophication and various ecological challenges. The impact of these oscillations on microbial communities in aquatic ecosystems has not been extensively studied. This study employed 16S rRNA gene amplicon sequencing to systematically investigate the dynamics, co-occurrence networks, and assembly processes of microbial communities and their subcommunities (abundant, moderate, and rare) in the Luanhe River Diversion Project in China. Our findings indicate that NH3 concentration significantly influences the dynamics of microbial communities, with a notable decrease in community Richness and Phylogenetic Distance alongside increased community dissimilarity under higher NH3 conditions. The analysis revealed that certain microbial groups, particularly Actinobacteriaota, were notably more prevalent in environments with elevated NH3 levels, suggesting their potential resilience or adaptive responses to NH3 stress. Additionally, through co-occurrence network analysis, we observed dynamic changes in network topology and increased connectedness under NH3 stress. Key nodes, identified as connectors and module hubs, played crucial roles in maintaining network structure, particularly Cyanobacteria and Actinobacteriaota. Furthermore, stochastic processes, particularly drift and dispersal limitation, predominantly shaped the microbial communities. Within the three subcommunities, the impact of drift became more pronounced as the effect of dispersal limitation diminished. Overall, elucidating the dynamics of microbial communities in aquatic ecosystems exposed to NH3 can enhance our comprehension of the ecological mechanisms of microbial communities and provide new insights into the conservation of microbial community diversity and ecological functions. IMPORTANCE The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health.
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Affiliation(s)
- Shengjie Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Zhiyi Qiao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Kexin Sun
- Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Da Huo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Li J, Wang S, Liu P, Peng J, Liu X, Sun Q, Zhou B, Lei K. Environmental DNA Metabarcoding Reveals the Influence of Environmental Heterogeneity on Microeukaryotic Plankton in the Offshore Waters of East China Sea. ENVIRONMENTAL RESEARCH 2024:119921. [PMID: 39233035 DOI: 10.1016/j.envres.2024.119921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/17/2024] [Accepted: 09/02/2024] [Indexed: 09/06/2024]
Abstract
Microeukaryotic plankton are essential to marine food webs and biogeochemical cycles, with coastal seas playing a critical role in aquatic ecosystems. Understanding the diversity of microeukaryotic plankton, deciphering their community structure and succession patterns, and identifying the key factors influencing these dynamics remain central challenges in coastal ecology. In this study, we examine patterns of biodiversity, community structure, and co-occurrence using environmental DNA (eDNA)-based methods. Our results show a linear correlation between α-diversity and distance from the shore, with nutrient-related factors, especially inorganic nitrogen, being the primary determinants of the spatial distribution of plankton communities. Alternation of coastal habitat have shifted the succession patterns of coastal eukaryotic plankton communities from stochastic to deterministic processes. Additionally, our observations indicate that the topology and structure of eukaryotic plankton symbiotic patterns and networks are significantly influenced by environmental heterogeneity such as nutrients, which increase the vulnerability and decrease the stability of offshore ecological networks. Overall, our study demonstrates that the distribution of microeukaryotic plankton communities is influenced by factors related to environmental heterogeneity.
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Affiliation(s)
- Jiangnan Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266000, China; Chinese Research Academy of Environmental Sciences, Beijing 100000, China
| | - Shuping Wang
- Chinese Research Academy of Environmental Sciences, Beijing 100000, China
| | - Pengxia Liu
- Ecological Environment Monitoring and Scientific Research Center, Taihu Basin & East China Sea Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Shanghai 200125, China
| | - Jiayu Peng
- Chinese Research Academy of Environmental Sciences, Beijing 100000, China
| | - Xinmei Liu
- Chinese Research Academy of Environmental Sciences, Beijing 100000, China
| | - Qianhang Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266000, China; Chinese Research Academy of Environmental Sciences, Beijing 100000, China
| | - Bo Zhou
- Chinese Research Academy of Environmental Sciences, Beijing 100000, China
| | - Kun Lei
- Chinese Research Academy of Environmental Sciences, Beijing 100000, China.
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Liu Y, Wang X, Zeng D, Wang H, Ma Y, Zhao X, Guan Z, Ning Z, Qu L. Temporal variation in production performance, biochemical and oxidative stress markers, and gut microbiota in Pekin ducks during the late growth stage. Poult Sci 2024; 103:103894. [PMID: 39013293 DOI: 10.1016/j.psj.2024.103894] [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: 03/24/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 07/18/2024] Open
Abstract
In the late growth stage of commercial Pekin ducks, a significant increase in feed intake and a decline in body weight gain have been observed, leading to impaired feed conversion efficiency. To address this issue, we investigated alterations in production performance, blood biochemical indices, ileum tissue architecture, and microbial community structure in Pekin ducks. The primary objective was to provide robust data supporting the improvement of meat duck production efficiency during the late growth stage (28-42-days-old). Forty 28-day-old Pekin ducks were randomly assigned to 8 replicates, with five ducks per replicate. The rearing period lasted 14 days, with feed and water provided ad libitum. Our findings indicated a significant increase in Pekin duck body and heart weights with advancing age (P < 0.05). Moreover, serum antioxidant enzyme and high-density lipoprotein concentrations significantly increased, whereas triglyceride levels decreased (P < 0.05). Notably, the height of the ileal villi was significantly reduced (P < 0.05). The microbial community structure of the ileum exhibited significant changes as ducks aged, accompanied by a substantial increase in microbial flora diversity, particularly with the formation of more tightly connected microbial network modules. Time-dependent enrichment was observed in microbial gene functions related to energy metabolism pathways. At the genus level, Sphingomonas and Subdoligranulum have emerged as crucial players in microbial differential functional pathways and network formation. These bacteria likely serve as the key driving factors in the dynamic microbial changes that occur in Pekin ducks over time. Overall, our findings suggest a potential decline in the absorption function of the small intestine and fat deposition performance of Pekin ducks during later growth stages, which may be attributed to the maturation and proliferation of the gut microbial community.
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Affiliation(s)
- Yuchen Liu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xintong Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Dan Zeng
- Huayu Agricultural Science and Technology Co., Ltd., Handan, China
| | - Haiyan Wang
- Technical Center of Hohhot Customs, Huhhot, Inner Mongolia, China
| | - Ying Ma
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zi Guan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Li G, Zhu D, Cheng C, Chu H, Wei F, Zhang Z. Multi-omics analysis reveals the genetic and environmental factors in shaping the gut resistome of a keystone rodent species. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2679-3. [PMID: 39235557 DOI: 10.1007/s11427-024-2679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/08/2024] [Indexed: 09/06/2024]
Abstract
Understanding the emergence and spread of antibiotic resistance genes (ARGs) in wildlife is critical for the health of humans and animals from a "One Health" perspective. The gut microbiota serve as a reservoir for ARGs; however, it remains poorly understood how environmental and host genetic factors influence ARGs by affecting the gut microbiota. To elucidate this, we analyzed whole-genome resequencing data from 79 individuals of Brandt's vole in two geographic locations with different antibiotics usage, together with metabolomic data and shotgun sequencing data. A high diversity of ARGs (851 subtypes) was observed in vole's gut, with a large variation in ARG composition between individuals from Xilingol and Hulunbuir in China. The diversity and composition of ARGs were strongly correlated with variations in gut microbiota community structure. Genome-wide association studies revealed that 803 loci were significantly associated (P<5.05×10-9) with 31 bacterial species, and bipartite networks identified 906 bacterial species-ARGs associations. Structural equation modeling analysis showed that host genetic factors, air temperature, and presence of pollutants (Bisphenol A) significantly affected gut microbiota community structure, which eventually regulated the diversity of ARGs. The present study advances our understanding of the complex host-environment interactions that underlie the spread of ARGs in the natural environments.
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Affiliation(s)
- Guoliang Li
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Chaoyuan Cheng
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fuwen Wei
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Chen J, Cui Y, Xiao Q, Lin K, Wang B, Zhou J, Li X. Difference in microbial community structure along a gradient of crater altitude: insights from the Nushan volcano. Appl Environ Microbiol 2024; 90:e0075324. [PMID: 39028194 PMCID: PMC11337807 DOI: 10.1128/aem.00753-24] [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: 04/16/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.
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Affiliation(s)
- Jin Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Ye Cui
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Qingchen Xiao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Keqin Lin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Boyan Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Jing Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
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10
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Chen CZ, Yin MH, Niu LJ, Wang JX, Liu L, Sun YJ, Ju WM, Li P, Li ZH. Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching. MARINE POLLUTION BULLETIN 2024; 205:116658. [PMID: 38964192 DOI: 10.1016/j.marpolbul.2024.116658] [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: 03/21/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.
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Affiliation(s)
| | - Ming-Hao Yin
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Lin-Jing Niu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jin-Xin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China.
| | - Yong-Jun Sun
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Wen-Ming Ju
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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11
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Yan Y, Ma JJ, Liang XP, Yin Y, Wu YQ, Yu RL, Hu GR, Zhu YG, Li H. Occurrence and spatiotemporal distribution of arsenic biotransformation genes in urban dust. ENVIRONMENT INTERNATIONAL 2024; 190:108823. [PMID: 38908273 DOI: 10.1016/j.envint.2024.108823] [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: 03/19/2024] [Revised: 05/18/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Microbially-mediated arsenic biotransformation plays a pivotal role in the biogeochemical cycling of arsenic; however, the presence of arsenic biotransformation genes (ABGs) in urban dust remains unclear. To investigate the occurrence and spatiotemporal distributions of ABGs, a total of one hundred and eighteen urban dust samples were collected from different districts of Xiamen city, China in summer and winter. Although inorganic arsenic species, including arsenate [As(V)] and arsenite [As(III)], were found to be predominant, the methylated arsenicals, particularly trimethylarsine oxide [TMAs(V)O] and dimethylarsenate [DMAs(V)], were detected in urban dust. Abundant ABGs were identified in urban dust via AsChip analysis (a high-throughput qPCR chip for ABGs), of which As(III) S-adenosylmethionine methyltransferase genes (arsM), As(V) reductase genes (arsC), As(III) oxidase genes (aioA), As(III) transporter genes (arsB), and arsenic-sensing regulator genes (arsR) were the most prevalent, collectively constituting more than 90 % of ABGs in urban dust. Microbes involved in arsenic methylation were assigned to bacteria (e.g., Actinomycetes and Alphaproteobacteria), archaea (e.g., Halobacteria), and eukaryotes (e.g., Chlamydomonadaceae) in urban dust via the arsM amplicon sequencing. Temperature, a season-dependent environmental factor, profoundly affected the abundance of ABGs and the composition of microbes involved in arsenic methylation. This study provides new insights into the presence of ARGs within the urban dust.
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Affiliation(s)
- Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jin-Jin Ma
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xiu-Peng Liang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yi Yin
- 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
| | - 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
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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12
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Liu W, Zhao F, Li X, Zheng S, Li L, Zhao R, Xu K. Enhanced nutrient supply promotes mutualistic interactions between cyanobacteria and bacteria in oligotrophic ocean. Proc Biol Sci 2024; 291:20240788. [PMID: 39043236 PMCID: PMC11265871 DOI: 10.1098/rspb.2024.0788] [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: 04/03/2024] [Accepted: 05/28/2024] [Indexed: 07/25/2024] Open
Abstract
Cyanobacteria can form complex interactions with heterotrophic microorganisms, but this relationship is susceptible to nutrient concentrations. Disentangling the cyanobacteria-bacteria interactions in relation to nutrient supply is essential to understanding their roles in geochemical cycles under global change. We hypothesize that enhanced nutrient supply in oligotrophic oceans can promote interactions among cyanobacteria and bacteria. Therefore, we investigated the planktonic bacteria and their interactions with cyanobacteria in relation to elevated nutrients caused by enhanced upwelling around a shallow and a deep seamount in the tropical western Pacific Ocean. We found obviously higher complexity of network occurred with significantly more cyanobacteria in the deep chlorophyll maximum layer of the shallow seamount when compared with that of the deep seamount. Cyanobacteria can shape bacterial interaction and community evenness in response to relatively high nutrient concentrations. The effects of the nutrients on cyanobacteria-related networks were further estimated based on the Tara Oceans data. Statistical analyses further showed a facilitative effect of nitrate concentrations on cyanobacteria-bacteria mutualistic interactions in the global oligotrophic ocean. By analysing the Tara Ocean macrogenomic data, we detected functional genes related to cyanobacteria-bacteria interactions in all samples, indicating the existence of a mutualistic relationship. Our results reveal cyanobacteria-bacteria interaction in response to nutrient elevation in oligotrophic ocean and highlight the potentially negative effects of global change on the bacterial community from the view of the bio-interaction.
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Affiliation(s)
- Weiyue Liu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xuegang Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
| | - Shan Zheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
| | - Longzhao Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Rongjie Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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13
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Han C, Shi C, Liu L, Han J, Yang Q, Wang Y, Li X, Fu W, Gao H, Huang H, Zhang X, Yu K. Majorbio Cloud 2024: Update single-cell and multiomics workflows. IMETA 2024; 3:e217. [PMID: 39135689 PMCID: PMC11316920 DOI: 10.1002/imt2.217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 08/15/2024]
Abstract
Majorbio Cloud (https://cloud.majorbio.com/) is a one-stop online analytic platform aiming at promoting the development of bioinformatics services, narrowing the gap between wet and dry experiments, and accelerating the discoveries for the life sciences community. In 2024, three single-omics workflows, two multiomics workflows, and extensions were newly released to facilitate omics data mining and interpretation.
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Affiliation(s)
- Chang Han
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Caiping Shi
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Linmeng Liu
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Jichen Han
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Qianqian Yang
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Yan Wang
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Xiaodan Li
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Wenyao Fu
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Hao Gao
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Huasheng Huang
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Xianglin Zhang
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
| | - Kegang Yu
- Shanghai Majorbio Bio‐Pharm Technology Co. Ltd.ShanghaiChina
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14
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Qin S, Zhang D, Wei B, Yang Y. Dual roles of microbes in mediating soil carbon dynamics in response to warming. Nat Commun 2024; 15:6439. [PMID: 39085268 PMCID: PMC11291496 DOI: 10.1038/s41467-024-50800-4] [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: 02/05/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Understanding the alterations in soil microbial communities in response to climate warming and their controls over soil carbon (C) processes is crucial for projecting permafrost C-climate feedback. However, previous studies have mainly focused on microorganism-mediated soil C release, and little is known about whether and how climate warming affects microbial anabolism and the subsequent C input in permafrost regions. Here, based on a more than half-decade of in situ warming experiment, we show that compared with ambient control, warming significantly reduces microbial C use efficiency and enhances microbial network complexity, which promotes soil heterotrophic respiration. Meanwhile, microbial necromass markedly accumulates under warming likely due to preferential microbial decomposition of plant-derived C, further leading to the increase in mineral-associated organic C. Altogether, these results demonstrate dual roles of microbes in affecting soil C release and stabilization, implying that permafrost C-climate feedback would weaken over time with dampened response of microbial respiration and increased proportion of stable C pool.
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Affiliation(s)
- Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- China National Botanical Garden, 100093, Beijing, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- China National Botanical Garden, 100093, Beijing, China
| | - Bin Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- China National Botanical Garden, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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15
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Feng Z, Miao Y, Sun X, Zheng Y, Luo G, Pei J, Huang L. Characterization of microbial community assembly in parasitic plant systems and the influence of microorganisms on metabolite accumulation in parasitic plants: case study of Cistanche salsa and Kalidium foliatum. Front Microbiol 2024; 15:1279536. [PMID: 39132140 PMCID: PMC11312099 DOI: 10.3389/fmicb.2024.1279536] [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: 08/18/2023] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Introduction Cistanche salsa (C.A.Mey.) G. Beck is a perennial holoparasitic herb recognized for its medicinal properties, particularly in kidney-tonifying and laxative treatments. Despite its therapeutic potential, little is known about the endophyte communities inhabiting C. salsa and its host plants, and how these microorganisms may impact the production and accumulation of metabolites in C. salsa. Methods We conducted a dual analysis focusing on metabolomics of wild C. salsa and microbiome characterization of both C. salsa and its host plant, Kalidium foliatum (Pall.) Moq. The metabolomics analysis revealed variations in metabolite composition across different parts of C. salsa. Additionally, the microbiome analysis involved studying endophytic bacteria and fungi, comparing their community structures between parasitic C. salsa and its host plant. Results Significant variations in metabolite composition were observed through metabolomic profiling, which identified 93 secondary metabolites and 398 primary metabolites across various parts of C. salsa. Emphasis was placed on differences in metabolite composition within the flowers. Microbiome analysis revealed differential community compositions of endophytic bacteria between the parasitic and host plants, whereas differences in endophytic fungi were less pronounced. Certain endophytes, such as Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota, were associated with the production of specific secondary metabolites in C. salsa, including the plant-specific compound salsaside. Discussion Our findings highlight the intricate relationship between C. salsa and its endophytic microbiota, suggesting a potential role of these microorganisms in modulating the biosynthesis of bioactive compounds. The differential preferences of endophytic bacteria and fungi across various microenvironments within the parasitic plant system underscore the complexity of these interactions. Further elucidation of these dynamics could enhance our understanding of C. salsa's medicinal properties and its ecological adaptations as a holoparasitic herb.
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Affiliation(s)
- Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiao Sun
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Jiangxi University of Chinese Medicine, Nanchang, China
| | - Guangming Luo
- Jiangxi University of Chinese Medicine, Nanchang, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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16
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Xie G, Sun C, Luo W, Gong Y, Tang X. Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake. Appl Environ Microbiol 2024; 90:e0071424. [PMID: 38940583 PMCID: PMC11267872 DOI: 10.1128/aem.00714-24] [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: 04/11/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.
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Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Chuanbo Sun
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Wenlei Luo
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- The Fuxianhu Station of Plateau Deep Lake Field Scientific Observation and Research, Yunnan, Yuxi, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
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17
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Xiao J, Wang D, Sinchan B, Mushinski R, Jin D, Deng Y. Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173413. [PMID: 38788956 DOI: 10.1016/j.scitotenv.2024.173413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.
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Affiliation(s)
- Juanjuan Xiao
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deying Wang
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Banerjee Sinchan
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Ryan Mushinski
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Fang X, Liu H, Du Y, Jiang L, Gao F, Wang Z, Chi Z, Shi B, Zhao X. Bacillus siamensis Targeted Screening from Highly Colitis-Resistant Pigs Can Alleviate Ulcerative Colitis in Mice. RESEARCH (WASHINGTON, D.C.) 2024; 7:0415. [PMID: 39015206 PMCID: PMC11249912 DOI: 10.34133/research.0415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Ulcerative colitis (UC) is often accompanied by intestinal inflammation and disruption of intestinal epithelial structures, which are closely associated with changes in the intestinal microbiota. We previously revealed that Min pigs, a native Chinese breed, are more resistant to dextran sulfate sodium (DSS)-induced colitis than commercial Yorkshire pigs. Characterizing the microbiota in Min pigs would allow identification of the core microbes that confer colitis resistance. By analyzing the microbiota linked to the disease course in Min and Yorkshire pigs, we observed that Bacillus spp. were enriched in Min pigs and positively correlated with pathogen resistance. Using targeted screening, we identified and validated Bacillus siamensis MZ16 from Min pigs as a bacterial species with biofilm formation ability, superior salt and pH tolerance, and antimicrobial characteristics. Subsequently, we administered B. siamensis MZ16 to conventional or microbiota-deficient BALB/c mice with DSS-induced colitis to assess its efficacy in alleviating colitis. B. siamensis MZ16 partially counteracted DSS-induced colitis in conventional mice, but it did not mitigate DSS-induced colitis in microbiota-deficient mice. Further analysis revealed that B. siamensis MZ16 administration improved intestinal ecology and integrity and immunological barrier function in mice. Compared to the DSS-treated mice, mice preadministered B. siamensis MZ16 exhibited improved relative abundance of potentially beneficial microbes (Lactobacillus, Bacillus, Christensenellaceae R7, Ruminococcus, Clostridium, and Eubacterium), reduced relative abundance of pathogenic microbes (Escherichia-Shigella), and maintained colonic OCLN and ZO-1 levels and IgA and SIgA levels. Furthermore, B. siamensis MZ16 reduced proinflammatory cytokine levels by reversing NF-κB and MAPK pathway activation in the DSS group. Overall, B. siamensis MZ16 from Min pigs had beneficial effects on a colitis mouse model by enhancing intestinal barrier functions and reducing inflammation in a gut microbiota-dependent manner.
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Affiliation(s)
- Xiuyu Fang
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Haiyang Liu
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Yongqing Du
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Lin Jiang
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Feng Gao
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Zhengyi Wang
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Zihan Chi
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Baoming Shi
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Xuan Zhao
- College of Animal Science and Technology,
Southwest University, Chongqing 400715, People’s Republic of China
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19
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Zhong L, Sun HJ, Pang JW, Ding J, Zhao L, Xu W, Yuan F, Zhang LY, Ren NQ, Yang SS. Ciprofloxacin affects nutrient removal in manganese ore-based constructed wetlands: Adaptive responses of macrophytes and microbes. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134579. [PMID: 38761761 DOI: 10.1016/j.jhazmat.2024.134579] [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: 11/22/2023] [Revised: 03/28/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
Ciprofloxacin (CIP) has received considerable attention in recent decades due to its high ecological risk. However, little is known about the potential response of macrophytes and microbes to varying levels of CIP exposure in constructed wetlands. Therefore, lab-scale manganese ore-based tidal flow constructed wetlands (MO-TFCWs) were operated to evaluate the responses of macrophytes and microbes to CIP over the long term. The results indicated that total nitrogen removal improved from 79.93% to 87.06% as CIP rose from 0 to 4 mg L-1. The chlorophyll content and antioxidant enzyme activities in macrophytes were enhanced under CIP exposure, but plant growth was not inhibited. Importantly, CIP exposure caused a marked evolution of the substrate microbial community, with increased microbial diversity, expanded niche breadth and enhanced cooperation among the top 50 genera, compared to the control (no CIP). Co-occurrence network also indicated that microorganisms may be more inclined to co-operate than compete. The abundance of the keystone bacterium (involved in nitrogen transformation) norank_f__A0839 increased from 0.746% to 3.405%. The null model revealed drift processes (83.33%) dominated the community assembly with no CIP and 4 mg L-1 CIP. Functional predictions indicated that microbial carbon metabolism, electron transfer and ATP metabolism activities were enhanced under prolonged CIP exposure, which may contribute to nitrogen removal. This study provides valuable insights that will help achieve stable nitrogen removal from wastewater containing antibiotic in MO-TFCWs.
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Affiliation(s)
- Le Zhong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han-Jun Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ji-Wei Pang
- China Energy Conservation and Environmental Protection Group, CECEP Digital Technology Co., Ltd., Beijing 100096, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Xu
- General Water of China Co., Ltd., Beijing 100022, China
| | - Fang Yuan
- General Water of China Co., Ltd., Beijing 100022, China
| | - Lu-Yan Zhang
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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20
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Guo Y, Gu S, Tanentzap AJ, Wang P, Li Q, Wu K, He P, Liu X, Yu J, Qiu D, Wu J, Zhang Y, Bai G, Lee SMY, Wu Z, Zhou Q. Submerged macrophyte restoration enhanced microbial carbon utilization in shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173357. [PMID: 38772483 DOI: 10.1016/j.scitotenv.2024.173357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024]
Abstract
Submerged macrophytes are integral to the functioning of shallow lakes through their interaction with microorganisms. However, we have a limited understanding of how microbial communities in shallow lakes respond when macrophytes are restored after being historically extirpated. Here, we explored the interactions between prokaryotic communities and carbon utilization in two lakes where submerged macrophytes were restored. We found restoration reduced total carbon in sediment by 8.9 %-27.9 % and total organic carbon by 16.7 %-36.9 % relative to control treatment, but had no effects on carbon content in the overlying water. Sediment microbial communities were more sensitive to restoration than planktonic microbes and showed enhanced utilization of simple carbon substrates, such as Tween 40, after restoration. The increase in carbon utilization was attributed to declines in the relative abundance of some genera, such as Saccharicenans and Desertimonas, which were found weakly associated with the utilization of different carbon substrates. These genera likely competed with microbes with high carbon utilization in restored areas, such as Lubomirskia. Our findings highlight how restoring submerged macrophytes can enhance microbial carbon utilization and provide guidance to improve the carbon sequestration capacity of restored shallow lakes.
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Affiliation(s)
- Yao Guo
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 10085, China
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Pei Wang
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qianzheng Li
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Kaixuan Wu
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Peng He
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiangfen Liu
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Junqi Yu
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dongru Qiu
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Junmei Wu
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yi Zhang
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guoliang Bai
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Simon Ming-Yuen Lee
- Department of Food Science and Nutrient, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Zhenbin Wu
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Qiaohong Zhou
- Key laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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21
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Hong W, Wu Y, Sun Z, Yang S, Cheng Q, Liu H, Lin X, Ni R, Yao Y, Wang S, Zheng Z, Sun A, Xi C, Song L. Sterile Diet Causes Gut Microbiome Collapse of Cancer Patients Post Hematopoietic Cell Transplantation, But Normal Diet Recovers Them. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403991. [PMID: 38973355 DOI: 10.1002/advs.202403991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/07/2024] [Indexed: 07/09/2024]
Abstract
Though sterile diet, post-transplantation surgery is a clinical strategy for patient care to prevent the infiltration of gut pathogens, less is known about its effects on the gut microbiome. Here, the gut microbiome dynamics of leukemia patients following a 120-day "sterile-normal" diet strategy posthematopoietic cell transplantation are examined. In contrast to the traditional idea, a sterile diet leads to the lowest gut microbiota diversity (p < 0.05) and short-chain fatty acids, promoted the proliferation of potential pathogens such as Streptococcus (up by 16.93%) and Lactobacillus (up by 40.30%), and 43.32% reduction in nodes and an 85.33% reduction in edges within the microbial interaction's network. Interestingly, a normal diet allows the gut microbiome recovery and significantly promotes the abundance of beneficial bacteria. These results indicate that a sterile diet leads to a collapse of the patient's gut microbiome and promoted the proliferation of potential pathogens. This assay is a starting point for a more sophisticated assessment of the effects of a sterile diet. The work also suggests a basic principle for the re-establishment of microbial equilibrium that supplementation of microbial taxa may be the key to the restoration of the degraded ecosystem.
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Affiliation(s)
- Wenqing Hong
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Yun Wu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Zimin Sun
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
- Blood and Cell Therapy Institute, Division of Life Sciences and Medicine, Anhui Provincial Key Laboratory of Blood Research and Applications, University of Science and Technology of China, Hefei, 230027, China
| | - Shu Yang
- Institute of Public Health Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Qing Cheng
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Huilan Liu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Xiaoxing Lin
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Renjie Ni
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Yuping Yao
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Zihao Zheng
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Anyi Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
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22
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Liang XP, Wang HJ, Zheng JR, Wang XR, Lin DM, Wu YQ, Yu RL, Hu GR, Yan Y. Comprehensive analysis of metal(loid)s and associated metal(loid) resistance genes in atmospheric particulate matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173038. [PMID: 38719055 DOI: 10.1016/j.scitotenv.2024.173038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/15/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Despite global concerns about metal(loid)s in atmospheric particulate matter (PM), the presence of metal(loid) resistance genes (MRGs) in PM remains unknown. Therefore, we conducted a comprehensive investigation of the metal(loid)s and associated MRGs in PMs in two seasons (summer and winter) in Xiamen, China. According to the geoaccumulation index (Igeo), most metal(loid)s, except for V and Mn, exhibited enrichment in PM, suggesting potential anthropogenic sources. By employing Positive Matrix Factorization (PMF) model, utilizing a dataset encompassing both total and bioaccessible metal(loid)s, along with backward trajectory simulations, traffic emissions were determined to be the primary potential contributor of metal(loid)s in summer, whereas coal combustion was observed to have a dominant contribution in winter. The major contributor to the carcinogenic risk of metal(loid)s in both summer and winter was predominantly attributed to coal combustion, which serves as the main source of bioaccessible Cr. Bacterial communities within PMs showed lower diversity and network complexity in summer than in winter, with Pseudomonadales being the dominant order. Abundant MRGs, including the As(III) S-adenosylmethionine methyltransferase gene (arsM), Cu(I)-translocating P-type ATPase gene (copA), Zn(II)/Cd(II)/Pb(II)-translocating P-type ATPase gene (zntA), and Zn(II)-translocating P-type ATPase gene (ziaA), were detected within the PMs. Seasonal variations were observed for the metal(loid) concentration, bacterial community structure, and MRG abundance. The bacterial community composition and MRG abundance within PMs were primarily influenced by temperature, rather than metal(loid)s. This research offers novel perspectives on the occurrence of metal(loid)s and MRGs in PMs, thereby contributing to the control of air pollution.
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Affiliation(s)
- Xiu-Peng Liang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - He-Jing Wang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jie-Ru Zheng
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xiao-Ru Wang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Dao-Ming Lin
- 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
| | - 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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23
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Wu T, Ding J, Wang S, Pang JW, Sun HJ, Zhong L, Ren NQ, Yang SS. Insight into effect of polyethylene microplastic on nitrogen removal in moving bed biofilm reactor: Focusing on microbial community and species interactions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173033. [PMID: 38723954 DOI: 10.1016/j.scitotenv.2024.173033] [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: 01/16/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
Microplastics (MPs) pollution has emerged as a global concern, and wastewater treatment plants (WWTPs) are one of the potential sources of MPs in the environment. However, the effect of polyethylene MPs (PE) on nitrogen (N) removal in moving bed biofilm reactor (MBBR) remains unclear. We hypothesized that PE would affect N removal in MBBR by influencing its microbial community. In this study, we investigated the impacts of different PE concentrations (100, 500, and 1000 μg/L) on N removal, enzyme activities, and microbial community in MBBR. Folin-phenol and anthrone colorimetric methods, oxidative stress and enzyme activity tests, and high-throughput sequencing combined with bioinformation analysis were used to decipher the potential mechanisms. The results demonstrated that 1000 μg/L PE had the greatest effect on NH4+-N and TN removal, with a decrease of 33.5 % and 35.2 %, and nitrifying and denitrifying enzyme activities were restrained by 29.5-39.6 % and 24.6-47.4 %. Polysaccharide and protein contents were enhanced by PE, except for 1000 μg/L PE, which decreased protein content by 65.4 mg/g VSS. The positive links of species interactions under 1000 μg/L PE exposure was 52.07 %, higher than under 500 μg/L (51.05 %) and 100 μg/L PE (50.35 %). Relative abundance of some metabolism pathways like carbohydrate metabolism and energy metabolism were restrained by 0.07-0.11 % and 0.27-0.4 %. Moreover, the total abundance of nitrification and denitrification genes both decreased under PE exposure. Overall, PE reduced N removal by affecting microbial community structure and species interactions, inhibiting some key metabolic pathways, and suppressing key enzyme activity and functional gene abundance. This paper provides new insights into assessing the risk of MPs to WWTPs, contributing to ensuring the health of aquatic ecosystems.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ji-Wei Pang
- China Energy Conservation and Environmental Protection Group, CECEP Digital Technology Co., Ltd., Beijing 100096, China
| | - Han-Jun Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Le Zhong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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24
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Geng Y, Yang L, Lian CA, Pavlostathis SG, Qiu Z, Xiong Z, Liu Y, Li B, Hu J, Fan W, Luo X, Yu K. Resourceful application and mechanism of oyster shell-microalgae synergistic system:Sustainable treatment of harsh low carbon nitrogen ratio actual wastewater. ENVIRONMENTAL RESEARCH 2024; 252:118775. [PMID: 38548250 DOI: 10.1016/j.envres.2024.118775] [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: 01/23/2024] [Revised: 03/03/2024] [Accepted: 03/21/2024] [Indexed: 06/07/2024]
Abstract
Microalgal technology holds great promise for both low C/N wastewater treatment and resource recovery simultaneously. Nevertheless, the advancement of microalgal technology is hindered by its reduced nitrogen removal efficiency in low C/N ratio wastewater. In this work, microalgae and waste oyster shells were combined to achieve a total inorganic nitrogen removal efficiency of 93.85% at a rate of 2.05 mg L-1 h-1 in low C/N wastewater. Notably, over four cycles of oyster shell reuse, the reactor achieved an average 85% ammonia nitrogen removal extent, with a wastewater treatment cost of only $0.092/ton. Moreover, microbial community analysis during the reuse of oyster shells revealed the critical importance of timely replacement in inhibiting the growth of non-functional bacteria (Poterioochromonas_malhamensi). The work demonstrated that the oyster shell - microalgae system provides a time- and cost-saving, environmental approach for the resourceful treatment of harsh low C/N wastewater.
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Affiliation(s)
- Yanni Geng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen, 518055, China
| | - Liming Yang
- Key Laboratory of Jiangxi Province for Persistent Pollutants Prevention Control and Resource Reuse, Nanchang Hangkong University, Nanchang, 330063, China
| | - Chun-Ang Lian
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen, 518055, China
| | - Spyros G Pavlostathis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0512, USA
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen, 518055, China
| | - Zhensheng Xiong
- Key Laboratory of Jiangxi Province for Persistent Pollutants Prevention Control and Resource Reuse, Nanchang Hangkong University, Nanchang, 330063, China
| | - Yuanqi Liu
- Key Laboratory of Jiangxi Province for Persistent Pollutants Prevention Control and Resource Reuse, Nanchang Hangkong University, Nanchang, 330063, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Jincheng Hu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen, 518055, China
| | - Wenbo Fan
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen, 518055, China
| | - Xubiao Luo
- Key Laboratory of Jiangxi Province for Persistent Pollutants Prevention Control and Resource Reuse, Nanchang Hangkong University, Nanchang, 330063, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen, 518055, China.
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25
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Wang W, Guo Y, Yang L, Adams JM. Methanogen-methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane. Mol Ecol 2024; 33:e17416. [PMID: 38801181 DOI: 10.1111/mec.17416] [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: 01/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high-throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross-feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance-decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.
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Affiliation(s)
- Wenqi Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Lin Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
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26
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Li W, Cheng L, He X, He G, Liu Y, Sang Z, Wang Y, Shao M, Xiong T, Xu H, Zhao J. Gut fungi of black-necked cranes (Grus nigricollis) respond to dietary changes during wintering. BMC Microbiol 2024; 24:232. [PMID: 38951807 PMCID: PMC11218170 DOI: 10.1186/s12866-024-03396-0] [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: 01/03/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about the dynamics of diet and gut fungi during the wintering period in black-necked cranes (Grus nigricollis). RESULTS In this work, we performed amplicon sequencing of the trnL-P6 loop and ITS1 regions to characterize the dietary composition and gut fungal composition of black-necked cranes during wintering. Results indicated that during the wintering period, the plant-based diet of black-necked cranes mainly consisted of families Poaceae, Solanaceae, and Polygonaceae. Among them, the abundance of Solanaceae, Polygonaceae, Fabaceae, and Caryophyllaceae was significantly higher in the late wintering period, which also led to a more even consumption of various food types by black-necked cranes during this period. The diversity of gut fungal communities and the abundance of core fungi were more conserved during the wintering period, primarily dominated by Ascomycota and Basidiomycota. LEfSe analysis (P < 0.05, LDA > 2) found that Pyxidiophora, Pseudopeziza, Sporormiella, Geotrichum, and Papiliotrema were significantly enriched in early winter, Ramularia and Dendryphion were significantly enriched in mid-winter, Barnettozyma was significantly abundant in late winter, and Pleuroascus was significantly abundant in late winter. Finally, mantel test revealed a significant correlation between winter diet and gut fungal. CONCLUSIONS This study revealed the dynamic changes in the food composition and gut fungal community of black-necked cranes during wintering in Dashanbao. In the late wintering period, their response to environmental and migratory pressures was to broaden their diet, increase the intake of non-preferred foods, and promote a more balanced consumption ratio of various foods. Balanced food composition played an important role in stabilizing the structure of the gut fungal community. While gut fungal effectively enhanced the host's food utilization rate, they may also faced potential risks of introducing pathogenic fungi. Additionally, we recongnized the limitations of fecal testing in studying the composition of animal gut fungal, as it cannot effectively distinguished between fungal taxa from food or soil inadvertently ingested and intestines. Future research on functions such as cultivation and metagenomics may further elucidate the role of fungi in the gut ecosystem.
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Affiliation(s)
- Wenhao Li
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya'an, Sichuan, 625014, China
| | - Lijun Cheng
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Xin He
- Sichuan Academy of Grassland Sciences, Chengdu, 610000, China
| | - Guiwen He
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Yutong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, 610000, China
| | - Zhenglin Sang
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya'an, Sichuan, 625014, China.
| | - Junsong Zhao
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China.
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China.
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Zou M, Zhang Q, Li F, Chen L, Qiu Y, Yin Q, Zhou S. Impacts of multiple environmental factors on soil bacterial community assembly in heavy metal polluted paddy fields. Sci Rep 2024; 14:14696. [PMID: 38926471 PMCID: PMC11208537 DOI: 10.1038/s41598-024-65678-x] [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: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Soil microorganisms play pivotal roles in driving essential biogeochemical processes in terrestrial ecosystems, and they are sensitive to heavy metal pollution. However, our understanding of multiple environmental factors interaction in heavy metal polluted paddy fields to shape microbial community assembly remain limited. In the current study, we used 16S rRNA amplicon sequencing to characterize the microbial community composition in paddy soils collected from a typical industry town in Taihu region, eastern China. The results revealed that Cd and Pb were the major pollutant, and Proteobacteria, Acidobacteria and Chloroflexi were the dominate indigenous bacterial phyla. Linear regression and random forest analysis demonstrated that soil pH was the most important predictor of bacterial diversity. Mantel analysis showed that bacterial community structure was mainly driven by pH, CEC, silt, sand, AK, total Cd and DTPA-Cd. The constructed bacterial co-occurrence network, utilizing a random matrix theory-based approach, exhibited non-random with scale-free and modularity features. The major modules within the networks also showed significant correlations with soil pH. Overall, our study indicated that soil physiochemical properties made predominant contribution to bacterial community diversity, structure and their association in Cd/Pb polluted paddy fields. These findings expand our knowledge of the key environmental drivers and co-occurrence patterns of bacterial community in polluted paddy fields.
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Affiliation(s)
- Mengmeng Zou
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Qi Zhang
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Fengchun Li
- Testing Center of Shandong Bureau of China Metallurgy and Geology, Jinan, 250014, People's Republic of China
| | - Long Chen
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Yifei Qiu
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Qiqi Yin
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Shenglu Zhou
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China.
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China.
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Li Z, Xu K, Meng M, Xu Y, Ji D, Wang W, Xie C. Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172692. [PMID: 38663622 DOI: 10.1016/j.scitotenv.2024.172692] [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: 11/19/2023] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/09/2024]
Abstract
The response of marine biodiversity to mariculture has long been a research focus in marine ecology. However, the effects of seaweed cultivation on biological community assembly are poorly understood, especially in diverse communities with distinct ecological characteristics. In this study, we used environmental DNA metabarcoding to investigate the spatial distribution patterns of bacterial, protistan, and metazoan diversity, aiming to reveal the mechanisms of community assembly in the Pyropia haitanensis cultivation zone along the Fujian coast, China. We found that, compared with the biological communities in control zones, those in P. haitanensis cultivation zones exhibited stronger geographic distance-decay patterns and displayed more complex and stable network structures. Deterministic processes (environmental selection) played a more important role in the assembly of bacterial, protistan, and metazoan communities in P. haitanensis cultivation zones, especially metazoan communities. Variance partitioning analysis showed that environmental variables made greater contributions to the diversity of the three types of communities within the P. haitanensis cultivation zones than in the control zones. Partial least squares path modeling analysis identified nitrate‑nitrogen (NO3-N), pH, particulate organic carbon (POC), and dissolved organic carbon (DOC) as the key environmental variables affecting biodiversity. Overall, the environmental heterogeneity caused by the large-scale cultivation of P. haitanensis could be the crucial factor influencing the composition and structure of various biological communities. Our results highlight the importance of the responses of multi-group organisms to the cultivation of seaweed, and provide insights into the coexistence patterns of biodiversity at the spatial scale.
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Affiliation(s)
- Zongtang Li
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Muhan Meng
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China.
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China.
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Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [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: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Yan H, Wu S, Li P, Jin X, Shi D, Tu D, Zeng WA, Tan L. Tobacco crop rotation enhances the stability and complexity of microbial networks. Front Microbiol 2024; 15:1416256. [PMID: 38962123 PMCID: PMC11220274 DOI: 10.3389/fmicb.2024.1416256] [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: 04/12/2024] [Accepted: 05/28/2024] [Indexed: 07/05/2024] Open
Abstract
Introduction The effects of continuous cropping and rotation cropping, two important tobacco cultivation practices, on soil microbial communities at different stages remain unclear. Different planting patterns have been shown to influence soil physical and chemical properties, which in turn can affect the composition and diversity of soil microbial communities. Methods In order to investigate the impact of different planting methods on soil microbial community structure, we selected two representative planting methods: continuous cropping (tobacco) and rotational cropping (tobacco-maize). These methods were chosen as the focal points of our research to explore the potential effects on soil microbial communities. High-throughput sequencing technology was employed to investigate the structure of soil microbial communities, as well as their relationships with soil environmental factors, by utilizing the 16S rRNA, ITS, and 18S genes. Furthermore, the interaction among microorganisms was explored through the application of the Random Matrix Theory (RMT) molecular ecological network approach. Results There was no significant difference in α diversity, but significant difference in β diversity based on Jaccard distance test. Compared to continuous cropping, crop rotation significantly increased the abundance of beneficial prokaryotes Verrucomicrobia and Rhodanobacter. These findings indicate that crop rotation promotes the enrichment of Verrucomicrobia and Rhodanobacter in the soil microbial community. AP and NH4-N had a greater effect on the community structure of prokaryotes and fungi in tobacco soil, while only AP had a greater effect on the community structure of protist. Molecular ecological network analysis showed that the network robustness and Cohesion of rotation were significantly higher than that of continuous cropping, indicating that the complexity and stability of molecular ecological networks were higher in the rotational, and the microbial communities cooperated more effectively, and the community structure was more stable. Discussion From this point of view, rotational cropping is more conducive to changing the composition of soil microbial community, enhancing the stability of microbial network structure, and enhancing the potential ecological functions in soil.
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Affiliation(s)
- Huilin Yan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Ping Li
- Academy of Agriculture and Forestry Science of Qinghai University, Xining, Qinghai, China
| | - Xin Jin
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Dejun Shi
- Qinghai Province Grassland Improvement Experimental Station, Gonghe, Qinghai, China
| | - Danjia Tu
- Qinghai Province Grassland Improvement Experimental Station, Gonghe, Qinghai, China
| | - Wei-ai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Lin Tan
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
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Li S, Yan X, Abdullah Al M, Ren K, Rensing C, Hu A, Tsyganov AN, Mazei Y, Smirnov A, Mazei N, Yang J. Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems. mSystems 2024; 9:e0046924. [PMID: 38767347 PMCID: PMC11237591 DOI: 10.1128/msystems.00469-24] [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: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024] Open
Abstract
Microbiomes are integral to ecological health and human well-being; however, their ecological and evolutionary drivers have not been systematically investigated, especially in urban park ecosystems. As microbes have different levels of tolerance to environmental changes and habitat preferences, they can be categorized into habitat generalists and specialists. Here, we explored the ecological and evolutionary characteristics of both prokaryotic and microeukaryotic habitat generalists and specialists from six urban parks across five habitat types, including moss, soil, tree hole, water, and sediment. Our results revealed that different ecological and evolutionary processes maintained and regulated microbial diversity in urban park ecosystems. Under ecological perspective, community assembly of microbial communities was mainly driven by stochastic processes; however, deterministic processes were higher for habitat specialists than generalists. Microbial interactions were highly dynamic among habitats, and habitat specialists played key roles as module hubs in intradomain networks. In aquatic interdomain networks, microeukaryotic habitat specialists and prokaryotic habitat specialists played crucial roles as module hubs and connectors, respectively. Furthermore, analyzing evolutionary characteristics, our results revealed that habitat specialists had a much higher diversification potential than generalists, while generalists showed shorter phylogenetic branch lengths as well as larger genomes than specialists. This study broadens our understanding of the ecological and evolutionary features of microbial habitat generalists and specialists in urban park ecosystems across multi-habitat. IMPORTANCE Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.
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Affiliation(s)
- Shuzhen Li
- 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, China
| | - Xue Yan
- 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, China
- University of Chinese Academy of Sciences, Beijing, 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, China
| | - 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, China
| | - Christopher Rensing
- 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, China
- Institute of Environmental Microbiology, College of Resources and the Environment, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | | | - Yuri Mazei
- Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biolog, St. Petersburg University, St Petersburg, Russia
| | | | - 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, China
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Wu T, Ding J, Zhao YJ, Ding L, Zang Y, Sun HJ, Zhong L, Pang JW, Li Y, Ren NQ, Yang SS. Microplastics shaped performance, microbial ecology and community assembly in simultaneous nitrification, denitrification and phosphorus removal process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172651. [PMID: 38653406 DOI: 10.1016/j.scitotenv.2024.172651] [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: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
The widespread use of microplastics (MPs) has led to an increase in their discharge to wastewater treatment plants. However, the knowledge of impact of MPs on macro-performance and micro-ecology in simultaneous nitrification, denitrification, and phosphorus removal (SNDPR) systems is limited, hampering the understanding of potential risks posed by MPs. This study firstly comprehensively investigated the performance, species interactions, and community assembly under polystyrene (PS) and polyvinyl chloride (PVC) exposure in SNDPR systems. The results showed under PS (1, 10 mg/L) and PVC (1, 10 mg/L) exposure, total nitrogen removal was reduced by 3.38-10.15 %. PS and PVC restrained the specific rates of nitrite and nitrate reduction (SNIRR, SNRR), as well as the activities of nitrite and nitrate reductase enzymes (NIR, NR). The specific ammonia oxidation rate (SAOR) and activity of ammonia oxidase enzyme (AMO) were reduced only at 10 mg/L PVC. PS and PVC enhanced the size of co-occurrence networks, niche breadth, and number of key species while decreasing microbial cooperation by 5.85-13.48 %. Heterogeneous selection dominated microbial community assembly, and PS and PVC strengthened the contribution of stochastic processes. PICRUSt prediction further revealed some important pathways were blocked by PS and PVC. Together, the reduced TN removal under PS and PVC exposure can be attributed to the inhibition of SAOR, SNRR, and SNIRR, the restrained activities of NIR, NR, and AMO, the changes in species interactions and community assembly mechanisms, and the suppression of some essential metabolic pathways. This paper offers a new perspective on comprehending the effects of MPs on SNDPR systems.
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Affiliation(s)
- Tong Wu
- Department of Analytical Chemistry, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ying-Jun Zhao
- Zhe Jiang University of Technology Engineering Design Group CO., Ltd, China
| | - Lan Ding
- Department of Analytical Chemistry, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
| | - Yani Zang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han-Jun Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Le Zhong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ji-Wei Pang
- China Energy Conservation and Environmental Protection Group, CECEP Digital Technology Co., Ltd., Beijing 100096, China
| | - Yan Li
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Wang YC, Lv YH, Wang C, Deng Y, Lin YT, Jiang GY, Hu XR, Crittenden JC. Stochastic processes shape microbial community assembly in biofilters: Hidden role of rare taxa. BIORESOURCE TECHNOLOGY 2024; 402:130838. [PMID: 38740312 DOI: 10.1016/j.biortech.2024.130838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/03/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Stochastic and deterministic processes are the major themes governing microbial community assembly; however, their roles in bioreactors are poorly understood. Herein, the mechanisms underlying microbial assembly and the effect of rare taxa were studied in biofilters. Phylogenetic tree analysis revealed differences in microbial communities at various stages. Null model analysis showed that stochastic processes shaped the community assembly, and deterministic processes emerged only in the inoculated activated sludge after domestication. This finding indicates the dominant role of stochastic factors (biofilm formation, accumulation, and aging). The Sloan neutral model corroborated the advantages of stochastic processes and mainly attributed these advantages to rare taxa. Cooccurrence networks revealed the importance of rare taxa, which accounted for more than 85% of the keystones. Overall, these results provide good foundations for understanding community assembly, especially the role of rare taxa, and offer theoretical support for future community design and reactor regulation.
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Affiliation(s)
- Yong-Chao Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin 300072, China
| | - Ya-Hui Lv
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin 300072, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin 300072, China.
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yu-Ting Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin 300072, China
| | - Guan-Yu Jiang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin 300072, China
| | - Xu-Rui Hu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin 300072, China
| | - John C Crittenden
- Brook Byers Institute of Sustainable Systems, School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
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Shen Z, Yu B, Gong Y, Shao K, Gao G, Tang X. Unraveling the impact of climatic warming and wetting on eukaryotic microbial diversity and assembly mechanisms: A 10-year case study in Lake Bosten, NW China. WATER RESEARCH 2024; 256:121559. [PMID: 38579508 DOI: 10.1016/j.watres.2024.121559] [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: 11/11/2023] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Over the last six decades, northwest China has undergone a significant climatic shift from "warm-dry" to "warm-wet", profoundly impacting the structures and functions of lake ecosystem across the region. However, the influences of this climatic transition on the diversity patterns, co-occurrence network, and assembly processes of eukaryotic microbial communities in lake ecosystem, along with the underlying mechanisms, remain largely unexplored. To bridge this knowledge gap, our study focused on Lake Bosten, the largest inland freshwater body in China, conducting a comprehensive analysis. Firstly, we examined the dynamics of key water quality parameters in the lake based on long-term monitoring data (1992-2022). Subsequently, we collected 93 water samples spanning two distinctive periods: low water level (WL) and high total dissolved solids (TDS) (PerWLTDS; 2010-2011; attributed to "warm-dry" climate), and high WL and low TDS (PerTDSWL; 2021-2022; associated with "warm-wet" climate). Eukaryotic microorganisms were further investigated using 18S rRNA gene sequencing and various statistical methods. Our findings revealed that climatic warming and wetting significantly increased eukaryotic microbial α-diversity (all Wilcox. test: P<0.05), while simultaneously reducing β-diversity (all Wilcox. test: P<0.001) and network complexity. Through the two sampling periods, assembly mechanisms of eukaryotic microorganisms were predominantly influenced by dispersal limitation (DL) and drift (DR) within stochastic processes, alongside homogeneous selection (HoS) within deterministic processes. WL played a mediating role in eukaryotic microbial DL and HoS processes in the PerTDSWL, whereas water quality and α-diversity influenced the DL process in the PerWLTDS. Collectively, these results underscore the direct and indirect impacts of "warm-wet" conditions on the eukaryotic microorganisms within Lake Bosten. This study provides valuable insights into the evolutionary dynamics of lake ecosystems under such climatic conditions and aids in predicting the ecological ramifications of global climatic changes.
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Affiliation(s)
- Zhen Shen
- 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, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bobing Yu
- 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, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yi Gong
- 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, PR 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, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - 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, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - 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, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Liu Q, Zhou S, Zhang B, Zhao K, Wang F, Li K, Zhang Y. The development of the biological soil crust regulates the fungal distribution and the stability of fungal networks. Front Microbiol 2024; 15:1347704. [PMID: 38873143 PMCID: PMC11169694 DOI: 10.3389/fmicb.2024.1347704] [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: 12/01/2023] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
The heterogeneous composition of fungi plays an indispensable role in the foundation of the multifunctionalities of ecosystems within drylands. The precise mechanisms that govern fluctuations in soil fungal assemblages in dryland ecosystems remain incompletely elucidated. In this study, biological soil crusts (biocrusts) at different successional stages in the Gurbantunggut Desert were used as substrates to examine the characteristics and driving factors that influence fungal abundance and community dynamics during biocrust development using qPCR and high-throughput sequencing of the ITS2 region. The findings showed that the physicochemical properties changed significantly with the development of biocrusts. In particular, total nitrogen increased 4.8 times, along with notable increases in ammonium, total phosphorus (2.1 times) and soil organic carbon (6.5 times). Initially, there was a rise in fungal abundance, which was subsequently followed by a decline as the biocrust developed, with the highest abundance detected in lichen crust (2.66 × 107 copies/g soil) and the lowest in bare sand (7.98 × 106 copies/g soil). Ascomycetes and Basidiomycetes emerged as dominant phyla, collectively forming 85% of the fungal community. As the biocrust developed, noticeable alterations occurred in fungal community compositions, resulting from changes in the relative proportions of Dothideomycetes, Lecanoromycetes and unclassified ascomycetes. Nitrogen, phosphorus, organic carbon content, and pH of biocrusts were identified as direct or indirect regulators of fungal abundance and community structure. The complexity of fungal networks increased as biocrusts developed as revealed by network analysis, but reduced in the stability of fungal communities within algal and lichen crusts. Keystone species within the fungal community also underwent changes as biocrust developed. These results suggested that shifts in interspecies relationships among fungi could further contribute to the variation in fungal communities during the development of biocrusts.
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Affiliation(s)
- Qian Liu
- College of Life Sciences, Shanxi Normal University, Taiyuan, China
| | - Shuping Zhou
- College of Life Sciences, Shanxi Normal University, Taiyuan, China
| | - Bingchang Zhang
- Geographical Science College, Shanxi Normal University, Taiyuan, China
| | - Kang Zhao
- College of Life Sciences, Shanxi Normal University, Taiyuan, China
| | - Fei Wang
- College of Life Sciences, Shanxi Normal University, Taiyuan, China
| | - Kaikai Li
- Geographical Science College, Shanxi Normal University, Taiyuan, China
| | - Yali Zhang
- Geographical Science College, Shanxi Normal University, Taiyuan, China
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Gao Z, Zheng Y, Li Z, Ruan A. Effects of 17β-Estradiol Pollution on Microbial Communities and Methane Emissions in Aerobic Water Bodies. TOXICS 2024; 12:373. [PMID: 38787152 PMCID: PMC11126138 DOI: 10.3390/toxics12050373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
17β-Estradiol (E2) is a widely present trace pollutant in aquatic environments. However, its impact on microbial communities in aerobic lake waters, which are crucial for methane (CH4) production, remains unclear. This study conducted an E2 contamination experiment by constructing laboratory-simulated aerobic microecosystems. Using 16S rRNA high-throughput sequencing, the effects of E2 on bacterial and archaeal communities were systematically examined. Combined with gas chromatography, the patterns and mechanisms of E2's impact on CH4 emissions in aerobic aquatic systems were uncovered for the first time. Generally, E2 contamination increased the randomness of bacterial and archaeal community assemblies and weakened microbial interactions. Furthermore, changes occurred in the composition and ecological functions of bacterial and archaeal communities under E2 pollution. Specifically, two days after exposure to E2, the relative abundance of Proteobacteria in the low-concentration (L) and high-concentration (H) groups decreased by 6.99% and 4.01%, respectively, compared to the control group (C). Conversely, the relative abundance of Planctomycetota was 1.81% and 1.60% higher in the L and H groups, respectively. E2 contamination led to an increase in the relative abundance of the methanogenesis functional group and a decrease in that of the methanotrophy functional group. These changes led to an increase in CH4 emissions. This study comprehensively investigated the ecotoxicological effects of E2 pollution on microbial communities in aerobic water bodies and filled the knowledge gap regarding aerobic methane production under E2 contamination.
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Affiliation(s)
- Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zhendong Li
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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Zhang Z, Xu D, Huang T, Zhang Q, Li Y, Zhou J, Zou R, Li X, Chen J. High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171529. [PMID: 38453065 DOI: 10.1016/j.scitotenv.2024.171529] [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: 11/01/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.
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Affiliation(s)
- Zihua Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Daolong Xu
- Inner Mongolia Academy of Science and Technology, Hohhot 010010, Inner Mongolia, China
| | - Tao Huang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Qing Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Yingyue Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Jing Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Ruifan Zou
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoyu Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China.
| | - Jin Chen
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China.
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Han D, Yang Y, Guo Z, Chen K, Dai S, Zhu Y, Wang Y, Yu Z, Wang K, Liu P, Rong C, Yu Y. Metagenomics profiling of the microbial community and functional differences in solid-state fermentation vinegar starter (seed Pei) from different Chinese regions. Front Microbiol 2024; 15:1389737. [PMID: 38756727 PMCID: PMC11096547 DOI: 10.3389/fmicb.2024.1389737] [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: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction The starter used in solid-state fermentation (SSF) vinegar, known as seed Pei is a microbial inoculant from the previous batch that is utilized during the acetic acid fermentation stage. The seed Pei, which has a notable impact on vinegar fermentation and flavor, is under-researched with comparative studies on microorganisms. Methods Herein metagenomics was employed to reveal the microbes and their potential metabolic functions of four seed Pei from three regions in China. Results The predominant microbial taxa in all four starters were bacteria, followed by viruses, eukaryotes, and archaea, with Lactobacillus sp. or Acetobacter sp. as main functional taxa. The seed Pei used in Shanxi aged vinegar (SAV) and Sichuan bran vinegar (SBV) exhibited a higher similarity in microbial composition and distribution of functional genes, while those used in two Zhenjiang aromatic vinegar (ZAV) differed significantly. Redundancy analysis (RDA) of physicochemical factors and microbial communities indicated that moisture content, pH, and reducing sugar content are significant factors influencing microbial distribution. Moreover, seven metagenome-assembled genomes (MAGs) that could potentially represent novel species were identified. Conclusions There are distinctions in the microbiome and functional genes among different seed Pei. The vinegar starters were rich in genes related to carbohydrate metabolism. This research provides a new perspective on formulating vinegar fermentation starters and developing commercial fermentation agents for vinegar production.
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Affiliation(s)
- Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yunsong Yang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhantong Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ken Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shuwen Dai
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Chunchi Rong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
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Tian W, Li Q, Luo Z, Wu C, Sun B, Zhao D, Chi S, Cui Z, Xu A, Song Z. Microbial community structure in a constructed wetland based on a recirculating aquaculture system: Exploring spatio-temporal variations and assembly mechanisms. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106413. [PMID: 38507984 DOI: 10.1016/j.marenvres.2024.106413] [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: 11/20/2023] [Revised: 01/10/2024] [Accepted: 02/17/2024] [Indexed: 03/22/2024]
Abstract
The diversity, composition and performance of microbial communities within constructed wetlands (CW) were markedly influenced by spatio-temporal variations. A pilot-scale integrated vertical-flow constructed wetland (IVCW) as the biological purification unit within a recirculating aquaculture system (RAS) was established and monitored in this study. The investigation aimed to elucidate the responses of community structure, co-occurrence networks, and assembly mechanisms of the microbial community to spatial and temporal changes. Spatially, all a-diversity indices and microbial networks complexity were significantly higher in the upstream pool of the IVCW than in the downstream pool. Temporally, the richness increased over time, while the evenness showed a decreasing trend. The number of nodes and edges of microbial networks increased over time. Notably, the stable pollutant removal efficiencies were observed during IVCW operations, despite a-diversity and bacterial community networks exhibited significant variations across time. Functional redundancy emerged as a likely mechanism contributing to the stability of microbial ecosystem functions. Null model and neutral model analyses revealed the dominance of deterministic processes shaping microbial communities over time, with deterministic influences being more pronounced at lower a-diversity levels. DO and inorganic nitrogen emerged as the principal environmental factor influencing microbial community dynamics. This study provides a theoretical foundation for the regulation of microbial communities and environmental factors within the context of IVCW.
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Affiliation(s)
- Wenjie Tian
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Qiufen Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Zijun Luo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Chao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Bo Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Danting Zhao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Saisai Chi
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Zhengguo Cui
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Ailing Xu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, China
| | - Zhiwen Song
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, China
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Jin Y, Ren S, Wu Y, Zhang X, Chen Z, Xie B. Microbial community structures and bacteria-Cylindrospermopsis raciborskii interactions in Yilong Lake. FEMS Microbiol Ecol 2024; 100:fiae048. [PMID: 38578661 PMCID: PMC11057442 DOI: 10.1093/femsec/fiae048] [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: 10/20/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Cylindrospermopsis raciborskii-dominated harmful algae blooms have been reported globally in recent years. However, our understanding of the ecology of C. raciborskii in natural conditions is still poor. In this study, we collected the water samples from a C. raciborskii-blooming lake, Yilong Lake, in Yunnan province, China, and used both culture-dependent and culture-independent approaches to investigate their microbial communities and the interactions between C. raciborskii and the other bacteria. The composition and diversity of microbial communities were revealed with 16S rRNA gene high-throughput sequencing data analysis. Microbial co-occurrences analysis suggests C. raciborskii may have complex associations with other bacteria. Based on co-inoculation tests, we obtained 14 strains of bacterial strains from the water samples that exhibited either algicidal or promoting effects on a strain of C. raciborskii. Two bacterial isolates exhibited a consistent performance between co-occurrence analysis and experimental results. Effects of these bacteria-algae interspecies interactions on the bloom event are discussed. All these results may provide new insights into the C. raciborskii-dominated blooms and how its interspecies relationships with other bacteria may influence the bloom events in eutrophic waters throughout the world.
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Affiliation(s)
- Yuanpei Jin
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Sanguo Ren
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Yichi Wu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Xu Zhang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Zhengjun Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Xie
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
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Yao J, Zhang Q, Gou M, Tang YQ. High synthetic cost-amino acids reduce member interactions of acetate-degrading methanogenic microbial community. Front Microbiol 2024; 15:1368215. [PMID: 38605716 PMCID: PMC11007023 DOI: 10.3389/fmicb.2024.1368215] [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: 01/10/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction The cooperation among members of microbial communities based on the exchange of public goods such as 20 protein amino acids (AAs) has attracted widespread attention. However, little is known about how AAs availability affects interactions among members of complex microbial communities and the structure and function of a community. Methods To investigate this question, trace amounts of AAs combinations with different synthetic costs (low-cost, medium-cost, high-cost, and all 20 AAs) were supplemented separately to acetate-degrading thermophilic methanogenic reactors, and the differences in microbial community structure and co-occurring networks of main members were compared to a control reactor without AA supplementation. Results The structure of the microbial community and the interaction of community members were influenced by AAs supplementation and the AAs with different synthetic costs had different impacts. The number of nodes, links, positive links, and the average degree of nodes in the co-occurrence network of the microbial communities with AAs supplementation was significantly lower than that of the control without AAs supplementation, especially for all 20 AAs supplementation followed by the medium- and high-cost AAs supplementation. The average proportion of positive interactions of microbial members in the systems supplemented with low-cost, medium-cost, high-cost, all AAs, and the control group were 0.42, 0.38, 0.15, 0.4, and 0.45, respectively. In addition, the ecological functions of community members possibly changed with the supplementation of different cost AAs. Discussion These findings highlight the effects of AAs availability on the interactions among members of complex microbial communities, as well as on community function.
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Affiliation(s)
- Jian Yao
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China
| | - Quan Zhang
- SINOPEC (Dalian) Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian, Liaoning, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China
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Li R, Jiao H, Sun B, Song M, Yan G, Bai Z, Wang J, Zhuang X, Hu Q. Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics. Microorganisms 2024; 12:683. [PMID: 38674627 PMCID: PMC11052110 DOI: 10.3390/microorganisms12040683] [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: 03/03/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.
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Affiliation(s)
- Rui Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou 256606, China;
| | - Haihua Jiao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- Department of Biological Sciences and Technology, Changzhi University, Changzhi 046011, China
| | - Bo Sun
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manjiao Song
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojun Yan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiancheng Wang
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou 256606, China;
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Hu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Innovation Institute, Xiongan New Area, Baoding 071000, China
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Liu J, Wang J, Zhang M, Wang X, Guo P, Li Q, Ren J, Wei Y, Wu T, Chai B. Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170386. [PMID: 38280613 DOI: 10.1016/j.scitotenv.2024.170386] [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: 11/26/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiayi Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Xue Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Ping Guo
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Qianru Li
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiali Ren
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Yuqi Wei
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, GA 30460-8042, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China.
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Zhang B, Xiao J, Liu H, Zhai D, Wang Y, Liu S, Xiong F, Xia M. Vertical habitat preferences shape the fish gut microbiota in a shallow lake. Front Microbiol 2024; 15:1341303. [PMID: 38572242 PMCID: PMC10987288 DOI: 10.3389/fmicb.2024.1341303] [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: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Understanding the interactions between fish gut microbiota and the aquatic environment is a key issue for understanding aquatic microorganisms. Environmental microorganisms enter fish intestines through feeding, and the amount of invasion varies due to different feeding habits. Traditional fish feeding habitat preferences are determined by fish morphology or behavior. However, little is known about how the feeding behavior of fish relative to the vertical structure in a shallow lake influences gut microbiota. In our study, we used nitrogen isotopes to measure the trophic levels of fish. Then high-throughput sequencing was used to describe the composition of environmental microbiota and fish gut microbiota, and FEAST (fast expectation-maximization for microbial source tracking) method was used to trace the source of fish gut microbiota. We investigated the microbial diversity of fish guts and their habitats in Lake Sanjiao and verified that the sediments indeed played an important role in the assembly of fish gut microbiota. Then, the FEAST analysis indicated that microbiota in water and sediments acted as the primary sources in half of the fish gut microbiota respectively. Furthermore, we classified the vertical habitat preferences using microbial data and significant differences in both composition and function of fish gut microbiota were observed between groups with distinct habitat preferences. The performance of supervised and unsupervised machine learning in classifying fish gut microbiota by habitat preferences actually exceeded classification by fish species taxonomy and fish trophic level. Finally, we described the stability of fish co-occurrence networks with different habitat preferences. Interestingly, the co-occurrence network seemed more stable in pelagic fish than in benthic fish. Our results show that the preferences of fish in the vertical structure of habitat was the main factor affecting their gut microbiota. We advocated the use of microbial interactions between fish gut and their surrounding environment to reflect fish preferences in vertical habitat structure. This approach not only offers a novel perspective for understanding the interactions between fish gut microbiota and environmental factors, but also provides new methods and ideas for studying fish habitat selection in aquatic ecosystems.
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Affiliation(s)
- Bowei Zhang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Jiaman Xiao
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Hongyan Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Dongdong Zhai
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Shujun Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Ming Xia
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
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Zhu T, Pan Q, Xiao K, Zuo C, Liu Q, Zhou D, Tu K. Stilbenes-enriched peanut sprouts alleviated physical fatigue via regulating interactions of nutrients-microbiota-metabolites revealed by multi-omics analysis. Food Funct 2024; 15:2960-2973. [PMID: 38407402 DOI: 10.1039/d3fo04076c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In this study, the antifatigue effect and mechanism of peanut sprouts were explored. BALB/c mice divided into three groups (control, dark and UV-C) were respectively supplemented with a normal diet, peanut sprouts (dark germination) added diet and stilbenes-enriched peanut sprouts (UV-C radiated germination) added diet. Results showed that swimming time and levels of blood glucose and antioxidant enzymes significantly increased, while contents of triglyceride and malondialdehyde notably decreased by peanut sprout supplementation. Besides, combined analysis of gut microbiota gene sequencing and targeted metabolomics of fecal metabolites revealed that peanut sprout supplementation up-regulated abundances and metabolic transformations of Catenibacillus, Odoribacter, Prevotellaceae-UCG-001 and Butyricicoccus while it down-regulated the abundance of Parabacteroides. Consequently, contents of sebacic acid, azelaic acid, suberic acid, heptanoic acid, pimelic acid, aminoadipic acid and mono-phenolics notably increased, which were markedly correlated with the antifatigue effect. Compared with the dark group, the swimming time, glutathione peroxidase activity, methylmalonylcarnitine content and abundances of Butyricicoccus, Catenibacillus and Lachnospiraceae NK4A136 were higher in the UV-C group, while opposite results were obtained for the levels of triglyceride, malondialdehyde, alpha-linolenic acid, gamma-linolenic acid, 10Z-heptadecenoic acid and palmitelaidic acid. Overall, peanut sprout supplementation could alleviate fatigue by modulating gut microbiota composition to promote fatty acid oxidation and lysine and stilbene catabolism to increase energy supply and regulate redox balance. UV-C-radiated peanut sprout supplementation could alleviate fatigue more effectively by up-regulating abundances of Butyricicoccus, Catenibacillus and Lachnospiraceae NK4A136 to promote long-chain fatty acid oxidation and catabolism of flavonoids and stilbenes efficiently.
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Affiliation(s)
- Tong Zhu
- College of Food Science and Technology/Yunnan Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, P. R. China
- College of Food Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, P. R. China.
| | - Qi Pan
- College of Food Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, P. R. China.
| | - Kunpeng Xiao
- College of Food Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, P. R. China.
| | - Changzhou Zuo
- College of Food Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, P. R. China.
| | - Qiang Liu
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, P. R. China
| | - Dandan Zhou
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Kang Tu
- College of Food Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, P. R. China.
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Liu J, He T, Yang Z, Peng S, Zhu Y, Li H, Lu D, Li Q, Feng Y, Chen K, Wei Y. Insight into the mechanism of nano-TiO 2-doped biochar in mitigating cadmium mobility in soil-pak choi system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:169996. [PMID: 38224887 DOI: 10.1016/j.scitotenv.2024.169996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 01/17/2024]
Abstract
Soil cadmium (Cd) pollution poses severe threats to food security and human health. Previous studies have reported that both nanoparticles (NPs) and biochar have potential for soil Cd remediation. In this study, a composite material (BN) was synthesized using low-dose TiO2 NPs and silkworm excrement-based biochar, and the mechanism of its effect on the Cd-contaminated soil-pak choi system was investigated. The application of 0.5 % BN to the soil effectively reduced 24.8 % of diethylenetriaminepentaacetic acid (DTPA) Cd in the soil and promoted the conversion of Cd from leaching and HOAc-extractive to reducible forms. BN could improve the adsorption capacity of soil for Cd by promoting the formation of humic acid (HA) and increasing the cation exchange capacity (CEC), as well as activating the oxygen-containing functional groups such as CO and CO. BN also increased soil urease and catalase activities and improved the synergistic network among soil bacterial communities to promote soil microbial carbon (C) and nitrogen (N) cycling, thus enhancing Cd passivation. Moreover, BN increased soil biological activity-associated metabolites like T-2 Triol and altered lipid metabolism-related fatty acids, especially hexadecanoic acid and dodecanoic acid, crucial for bacterial Cd tolerance. In addition, BN inhibited Cd uptake and root-to-shoot translocation in pak choi, which ultimately decreased Cd accumulation in shoots by 51.0 %. BN significantly increased the phosphorus (P) uptake in shoots by 59.4 % by improving the soil microbial P cycling. This may serve as a beneficial strategy for pak choi to counteract Cd toxicity. These findings provide new insights into nanomaterial-doped biochar for remediation of heavy metal contamination in soil-plant systems.
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Affiliation(s)
- Jing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tieguang He
- Agricultural Resources and Environmental Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning 530007, China
| | - Zhixing Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China; CAS Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shirui Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Yanhuan Zhu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Li
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Dan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Qiaoxian Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Yaxuan Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Kuiyuan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Yanyan Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530005, China.
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Liu Y, Wang H, Tan X, Fu S, Liu D, Shen W. Increased precipitation alters the effects of nitrogen deposition on soil bacterial and fungal communities in a temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170017. [PMID: 38219995 DOI: 10.1016/j.scitotenv.2024.170017] [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: 11/18/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Anthropogenic nitrogen (N) deposition and increased precipitation are known to alter soil microbial communities. However, the combined effects of elevated N deposition and increased precipitation on soil microbial community dynamics and co-occurrence networks in temperate forests remain elusive. In this study, we conducted a field manipulation experiment by applying N solution and water to the forest canopy to simulate natural N deposition and increased precipitation in a temperate forest. We collected samples in the litter layer, organic soil layer, and mineral soil layer in 2018-2019 after 6-7 years of N and water treatments, and explored how elevated N deposition and increased precipitation regulate soil microbial diversity, community composition, and co-occurrence networks in different soil layers and at different sampling times. We found that the effects of N deposition and increased precipitation on soil microbial communities varied with soil layers and sampling times. Compared to the ambient environment, single canopy N addition (CN) or single canopy water addition (CW) did not affect bacterial Shannon diversity in the mineral soil layer in 2018, but the combined canopy N and water additions (CNW) decreased it in this layer at this time. CN increased fungal OTU richness in the organic and mineral soil layers in 2018; however, CW and CNW did not have an effect on it in the same layer at the same time. CW and CNW, but not CN, significantly affected bacterial and fungal community compositions in the litter layer in 2018 and in the organic soil layer in 2019. In contrast, CN, but not CW or CNW, significantly affected fungal community composition in the litter layer in 2019. CNW exhibited higher complexities of bacterial and fungal co-occurrence networks than CN and the ambient environment, indicating increased precipitation can strengthen the effect of N deposition on the complexity of bacterial and fungal co-occurrence networks. Our findings suggest that increased precipitation alters the effects of atmospheric N deposition on soil bacterial and fungal communities in this temperate forest, depending on soil layer and sampling time. Moreover, both bacterial and fungal community compositions are sensitive to increased precipitation, but the bacterial community composition is more sensitive to N deposition than the fungal community composition in the organic and mineral soil layers in this forest.
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Affiliation(s)
- Yang Liu
- Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Tibetan Plateau, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Hang Wang
- National Plateau Wetlands Research Center/Wetlands College, Southwest Forestry University, Kunming, China.
| | - Xiangping Tan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shenglei Fu
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Environment and Planning, Henan University, Kaifeng, China
| | - Dan Liu
- Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Tibetan Plateau, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Weijun Shen
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China.
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Sun Y, Teng Y, Li R, Wang X, Zhao L. Microbiome resistance mediates stimulation of reduced graphene oxide to simultaneous abatement of 2,2',4,4',5-pentabromodiphenyl ether and 3,4-dichloroaniline in paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133121. [PMID: 38056279 DOI: 10.1016/j.jhazmat.2023.133121] [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: 08/29/2023] [Revised: 10/12/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Paddy soils near electrical and electronic waste recycling sites generally suffer from co-pollution of polybrominated diphenyl ethers and 3,4-dichloroaniline (3,4-DCA). This study tested the feasibility of reduced graphene oxide (rGO) to stimulate the simultaneous abatement of 2,2',4,4',5-pentabromodiphenyl ether (BDE99) and 3,4-DCA in percogenic paddy soil (PPS) and hydromorphic paddy soil (HPS). rGO improved the debromination extent of BDE99 and the transformation rate of 3,4-DCA in PPS, but did not affect their abatement in HPS. The inhibition of specific fermenters, acetogens, and methanogens after rGO addition contributed to BDE99 debromination by obligate organohalide-respiring bacteria (OHRB) in PPS, but relevant soil microbiomes (e.g., fermenters, acetogens, methanogens, and obligate OHRB) responded little to rGO in HPS. For 3,4-DCA, the enhanced activities of nitrogen-metabolic chloroaniline degraders by rGO increased its transformation rate in PPS, but was compensated by the decreased biotransformation from 3,4-DCA to 3,4-dichloroacetanilide after the addition of rGO to HPS. The discrepant stimulation of rGO between PPS and HPS was mediated by soil microbiome resistance. rGO has the application potential to stimulate the simultaneous abatement of polybrominated diphenyl ethers and chloroanilines in paddy soils with relatively low microbiome resistance.
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Affiliation(s)
- Yi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ran Li
- State Key Laboratory of Nutrient Use and Management, Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Tang Z, Vogel TM, Wang Q, Wei C, Ali M, Song X. Microbial defluorination of TFA, PFOA, and HFPO-DA by a native microbial consortium under anoxic conditions. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133217. [PMID: 38101019 DOI: 10.1016/j.jhazmat.2023.133217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
In this study, the biodegradability of trifluoroacetate (TFA), perfluorooctanoic acid (PFOA), and perfluoro-2-methyl-3-oxahexanoic acid (HFPO-DA) by a native microbial community was evaluated over a 10-month incubation period. The observed microbial defluorination ratios and removal efficiency were 3.46 ( ± 2.73) % and 8.03 ( ± 3.03) %, 8.44 ( ± 1.88) % and 13.52 ( ± 4.96) %, 3.02 ( ± 0.62) % and 5.45 ( ± 2.99) % for TFA, PFOA and HFPO-DA, respectively. The biodegradation intermediate products, TFA and pentafluoropropionic acid (PFA), of PFOA and HFPO-DA were detected in their biodegradation treatment groups. Furthermore, the concentrations of the PFOA metabolites, perfluorohexanoic acid (PFHxA) and perfluoroheptanoic acid (PFHpA), in the aqueous solutions after incubation were quantified to be 0.21 and 4.14 µg/L. TFA, PFOA and HFPO-DA significantly reduced the microbial diversity and changed the structure of the community. The co-occurrence network analysis showed that low abundance species, such as Flexilinea flocculi, Bacteriovorax stolpii, and g_Sphingomonas, are positively correlated with the generation of fluoride ion, implying their potential collaborative functions contributing to the observed biodefluorination. The findings in this study can provide insights for the biodegradation of perfluoroalkyl carboxylic acids and their emerging alternatives by indigenous microorganisms in the environment.
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Affiliation(s)
- Zhiwen Tang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Timothy M Vogel
- Ecologie Microbienne, Université Claude Bernard Lyon 1, Villeurbanne F-69622, France
| | - Qing Wang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changlong Wei
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mukhtiar Ali
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Song
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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50
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Peng X, Zhang X, Zhang S, Li Z, Zhang H, Zhang L, Wu Z, Liu B. Revealing the response characteristics of periphyton biomass and community structure to sulfamethoxazole exposure in aquaculture water: The perspective of microbial network relationships. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123301. [PMID: 38190873 DOI: 10.1016/j.envpol.2024.123301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/08/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
The widespread application of sulfonamide antibiotics in aquaculture has raised concerns about their adverse environmental impacts. Periphyton plays a crucial role in the aquatic ecosystem. In this study, we examined sulfamethoxazole (SMX) effects on the community structure and interactions of periphyton in simulated aquaculture water. Our findings indicated that the total biomass of periphyton decreased, while the biomass of periphytic algae and the secretion of extracellular polymeric substances (EPS) increased at 0.7 × 10-3 mg/L. Under higher SMX concentrations (5 mg/L and 10 mg/L), periphyton growth was severely inhibited, the microbial community structure of periphyton were sharply altered, characterized by the cyanobacteria growth suppression and decrease in the diversity index of community. Furthermore, elevated SMX concentrations (5 mg/L and 10 mg/L) increased the ratio of negative relationships from 45.4% to 49.4%, which suggested that high SMX concentrations promoted potential competition among microbes and disrupted the microbial food webs in periphyton. The absolute abundance of sul1 and sul2 genes in T2 and T3 groups were 2-3 orders of magnitude higher than those in control group after 30 days of SMX exposure, which elevated the risk of resistance gene enrichment and dissemination in the natural environment. The study contributes to our understanding of the detrimental effects of antibiotic pollution, which can induce changes in the structure and interaction relationship of microbial communities in aquaculture water.
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Affiliation(s)
- Xue Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xinyi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuxian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuxi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Haokun Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Biyun Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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