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Liu S, Shi Y, Chen J, Zhang Z, Cao H, Li W, Ye M. Interspecific barrier effect driven by heavy metals makes soil bacterial functional assembly more stochastic. ENVIRONMENTAL RESEARCH 2024; 253:119153. [PMID: 38763283 DOI: 10.1016/j.envres.2024.119153] [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: 03/12/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
Residual heavy metals in soils will destroy microbial community stability and influence its aggregation. However, exploring microbial ecology under heavy-metal stress still requires a conjoint analysis of bacterial interspecies communication and the community diversity maintenance mechanism. In this study, soil samples were collected from a heavy-metal-contaminated site in China to investigate the ecological response of indigenous microbial communities through high-throughput sequencing. Results showed that bacterial taxa and functions generated unusual decoupling phenomena. There were no significant differences in the diversity of species with the increase in concentration of heavy metals (Hg, Se, and Cr), but the functional diversity was lost. Also, the average niche breadth of bacterial species increased from 1.70 to 2.28, but community stability declined and the species assembly was always a deterministic process (NST <0.5). After the bacterial functional assembly changed from a stochastic process to a deterministic process (NST <0.5), it was transformed into a stochastic process (NST >0.5) again under the stress of high-concentration heavy metals, indicating that the collective stress resistance of bacterial communities changed from positive mutation into passive functional propagation. The research results can provide new insight into understanding the adaptive evolution of communities and ecosystem restoration under the stress of soil heavy metals.
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Affiliation(s)
- Shuyue Liu
- National Engineering Laboratory of Soil Nutrients Management, Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Junhao Chen
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Zhenchang Zhang
- Academy of Environmental Planning and Design, Co.,Ltd. Nanjing University, Nanjing, 210093, China
| | - Hengxiang Cao
- Academy of Environmental Planning and Design, Co.,Ltd. Nanjing University, Nanjing, 210093, China
| | - Weiming Li
- Institute of Vegetable, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Mao Ye
- National Engineering Laboratory of Soil Nutrients Management, Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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Mao J, Zheng Z, Ma L, Wang H, Wang X, Zhu F, Xue S, Srivastava P, Sapsford DJ. Polymetallic contamination drives indigenous microbial community assembly dominated by stochastic processes at Pb-Zn smelting sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174575. [PMID: 38977087 DOI: 10.1016/j.scitotenv.2024.174575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/14/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Indigenous microbial communities in smelting areas are crucial for maintaining fragile ecosystem functions. However, the community assembly process and their responses to polymetallic pollution are poorly understood, especially the taxa in each bin from the amplicons that contributed to the assembly process. Herein, microbial diversity, co-occurrence patterns, assembly process and the intrinsic mechanisms across contamination gradients at a typical PbZn smelting site were systematically unravelled by high-throughput sequencing. The results showed a consistent compositional profile among the indigenous communities across sampling sites, wherein genera KD4-96 from Chloroflexi and Sphingomonas from Proteobacteria emerged as the most abundant taxa. Network modularity of the high- and middle-contaminated communities at Pb and Zn smelting sites was >0.44, indicating that community populations were clustered into modules to resist high heavy metal stress. Stochastic processes dominated the community assembly, with the greatest contribution from drift (DR), which was significantly correlated with Pb, Zn, Cr and Cu contents. What's particular was that the DR-controlled bins were dominated by Proteobacteria (typical r-strategists), while the HoS-controlled bins were by Chloroflexi (typical K-strategists). Furthermore, the proportion of DR in the bins dominated by Sphingomonadaceae (phylum Proteobacteria) increased gradually with the increase of heavy metal contents. These discoveries provide essential insights for community control in restoring and mitigating soil degradation at PbZn smelting sites.
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Affiliation(s)
- Jialing Mao
- Institute of Geological Survey, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Zikui Zheng
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Liyuan Ma
- Institute of Geological Survey, China University of Geosciences, Wuhan 430074, Hubei, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; School of Engineering, Cardiff University, Cardiff CF243AA, United Kingdom.
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Xingjie Wang
- Institute of Geological Survey, China University of Geosciences, Wuhan 430074, Hubei, China; School of Engineering, Cardiff University, Cardiff CF243AA, United Kingdom
| | - Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | | | - Devin J Sapsford
- School of Engineering, Cardiff University, Cardiff CF243AA, United Kingdom
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Sun J, Zhou H, Cheng H, Chen Z, Wang Y. Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106624. [PMID: 38943698 DOI: 10.1016/j.marenvres.2024.106624] [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: 04/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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4
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Shao Q, Ran Q, Li X, Dong C, Zhang Y, Han Y. Differential responses of the phyllosphere abundant and rare microbes of Eucommia ulmoides to phytohormones. Microbiol Res 2024; 286:127798. [PMID: 38964073 DOI: 10.1016/j.micres.2024.127798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Phyllosphere microbiota play a crucial role in plant productivity and adaptation, and the abundant and rare microbial taxa often possess distinct characteristics and ecological functions. However, it is unclear whether the different subcommunities of phyllosphere microbiota respond variably to the factors that influence their formation, which limits the understanding of community assembly. The effects of two phytohormones, namely, indole-3-acetic acid (IAA) and N6-(delta 2-isopentenyl)-adenine (IP), on the phyllosphere microbial subcommunities of Eucommia ulmoides were investigated using potted experiments. The results demonstrated that the phytohormones induced significant variations in the composition, diversity, and function of the abundant microbial subcommunity in the phyllosphere of E. ulmoides, however, their effects on the rare subcommunity were negligible, and their effects on the moderate subcommunity were between those of the abundant and rare taxa. The phytohormones also induced significant alterations in the phenotypic and physiological properties of E. ulmoides, which indirectly affected the phyllosphere microbial community. Leaf thickness and average leaf area were the main phenotypic variables that affected the composition of the phyllosphere microbial community. The total alkaloid content and activity of superoxide dismutase (SOD) were the main physiological variables that affected the composition of the phyllosphere microbial community. The phenotypic and physiological indices of E. ulmoides explained the variations in the phyllosphere microbial subcommunities in descending order: abundant > moderate > rare taxa. These variables explained a significant proportion of the variations in the abundant taxa, and an insignificant proportion of the variations in the rare taxa. This study improves our understanding of the assembly of the phyllosphere microbiota, which provides important theoretical knowledge for future sustainable agriculture and forestry management based on the precise regulation of phyllosphere microbiota.
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Affiliation(s)
- Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, Guizhou 550025, China
| | - Qingsong Ran
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xu Li
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, Guizhou 550025, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yanwei Zhang
- Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou 550018, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, Guizhou 550025, China.
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Xi M, Wang Y, Yang J, Bi X, Zhong S, Duan T, He Y, Tu T, Qian X. Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems. Fungal Biol 2024; 128:1815-1826. [PMID: 38876534 DOI: 10.1016/j.funbio.2024.05.001] [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: 01/09/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 06/16/2024]
Abstract
Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.
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Affiliation(s)
- Meijuan Xi
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Juanjuan Yang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohui Bi
- Shangqiu Institute of Quality Inspection and Technical Research, Shangqiu, China
| | - Shengen Zhong
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Duan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yimin He
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tieyao Tu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xin Qian
- Fujian Agriculture and Forestry University, Fuzhou, 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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Fu Y, Tang X, Sun T, Lin L, Wu L, Zhang T, Gong Y, Li Y, Wu H, Xiong J, Tang R. Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems. Front Microbiol 2024; 15:1403338. [PMID: 38873152 PMCID: PMC11169858 DOI: 10.3389/fmicb.2024.1403338] [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: 03/19/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear. Methods Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level. Results Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%). Conclusion This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.
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Affiliation(s)
- Yue Fu
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Xiumei Tang
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
| | - Tingting Sun
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Litao Lin
- Center for Ecological Civilization Research, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Lixue Wu
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Tian Zhang
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Agro-Environment and Agro-Product Safety, Guangxi University, Nanning, China
| | - Yifei Gong
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Yuting Li
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Haining Wu
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
| | - Jun Xiong
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
| | - Ronghua Tang
- Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, Guangxi, China
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Wan Y, Huang J, Tang Q, Zhang S, Qin H, Dong Y, Wang X, Qiu C, Huang M, Zhang Z, Zhang Y, Zhou R. Characterizing the Contribution of Functional Microbiota Cultures in Pit Mud to the Metabolite Profiles of Fermented Grains. Foods 2024; 13:1597. [PMID: 38890826 PMCID: PMC11171501 DOI: 10.3390/foods13111597] [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: 04/12/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 06/20/2024] Open
Abstract
Elevating the flavor profile of strong flavors Baijiu has always been a focal point in the industry, and pit mud (PM) serves as a crucial flavor contributor in the fermentation process of the fermented grains (FG). This study investigated the influence of wheat flour and bran (MC and FC) as PM culture enrichment media on the microbiota and metabolites of FG, aiming to inform strategies for improving strong-flavor Baijiu flavor. Results showed that adding PM cultures to FG significantly altered its properties: FC enhanced starch degradation to 51.46% and elevated reducing sugar content to 1.60%, while MC increased acidity to 2.11 mmol/10 g. PM cultures also elevated FG's ester content, with increases of 0.36 times for MC-FG60d and 1.48 times for FC-FG60d compared to controls, and ethyl hexanoate rising by 0.91 times and 1.39 times, respectively. Microbial analysis revealed that Lactobacillus constituted over 95% of the Abundant bacteria community, with Kroppenstedtia or Bacillus being predominant among Rare bacteria. Abundant fungi included Rasamsonia, Pichia, and Thermomyces, while Rare fungi consisted of Rhizopus and Malassezia. Metagenomic analysis revealed bacterial dominance, primarily consisting of Lactobacillus and Acetilactobacillus (98.80-99.40%), with metabolic function predictions highlighting genes related to metabolism, especially in MC-FG60d. Predictions from PICRUSt2 suggested control over starch, cellulose degradation, and the TCA cycle by fungal subgroups, while Abundant fungi and bacteria regulated ethanol and lactic acid production. This study highlights the importance of PM cultures in the fermentation process of FG, which is significant for brewing high-quality, strong-flavor Baijiu.
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Affiliation(s)
- Yingdong Wan
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Qiuxiang Tang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Suyi Zhang
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Hui Qin
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Yi Dong
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Xiaojun Wang
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Chuanfeng Qiu
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Mengyang Huang
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Zhu Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Yi Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
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Mumin R, Wang DD, Zhao W, Huang KC, Li JN, Sun YF, Cui BK. Spatial Distribution Patterns and Assembly Processes of Abundant and Rare Fungal Communities in Pinus sylvestris var. mongolica Forests. Microorganisms 2024; 12:977. [PMID: 38792806 PMCID: PMC11124154 DOI: 10.3390/microorganisms12050977] [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: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Revealing the biogeography and community assembly mechanisms of soil microorganisms is crucial in comprehending the diversity and maintenance of Pinus sylvestris var. mongolica forests. Here, we used high-throughput sequencing techniques and null model analysis to explore the distribution patterns and assembly processes of abundant, rare, and total fungal communities in P. sylvestris var. mongolica forests based on a large-scale soil survey across northern China. Compared to the abundant and total taxa, the diversity and composition of rare taxa were found to be more strongly influenced by regional changes and environmental factors. At the level of class, abundant and total taxa were dominated by Agaricomycetes and Leotiomycetes, while Agaricomycetes and Sordariomycetes were dominant in the rare taxa. In the functional guilds, symbiotrophic fungi were advantaged in the abundant and total taxa, and saprotrophic fungi were advantaged in the rare taxa. The null model revealed that the abundant, rare, and total taxa were mainly governed by stochastic processes. However, rare taxa were more influenced by deterministic processes. Precipitation and temperature were the key drivers in regulating the balance between stochastic and deterministic processes. This study provides new insights into both the biogeographical patterns and assembly processes of soil fungi in P. sylvestris var. mongolica forests.
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Affiliation(s)
| | | | | | | | | | - Yi-Fei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.M.); (D.-D.W.); (W.Z.); (K.-C.H.); (J.-N.L.)
| | - Bao-Kai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.M.); (D.-D.W.); (W.Z.); (K.-C.H.); (J.-N.L.)
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10
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Liu H, Wang H, Nie Z, Tao Z, Peng H, Shi H, Zhao P, Liu H. Combined application of arbuscular mycorrhizal fungi and selenium fertilizer increased wheat biomass under cadmium stress and shapes rhizosphere soil microbial communities. BMC PLANT BIOLOGY 2024; 24:359. [PMID: 38698306 PMCID: PMC11067182 DOI: 10.1186/s12870-024-05032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND Selenium (Se) fertilizer and arbuscular mycorrhizal fungi (AMF) are known to modulate cadmium (Cd) toxicity in plants. However, the effects of their co-application on wheat growth and soil microbial communities in Cd-contaminated soil are unclear. RESULTS A pot experiment inoculation with two types of AMF and the application of Se fertilizer under Cd stress in wheat showed that inoculation AMF alone or combined with Se fertilizer significantly increased wheat biomass. Se and AMF alone or in combination significantly reduced available Cd concentration in wheat and soil, especially in the Se combined with Ri treatment. High throughput sequencing of soil samples indicated that Se and AMF application had stronger influence on bacterial community compared to fungal community and the bacterial network seemed to have more complex interconnections than the fungal network, and finally shaped the formation of specific microflora to affect Cd availability. CONCLUSION These results indicate that the application of Se and AMF, particularly in combination, could successfully decrease soil Cd availability and relieve the harm of Cd in wheat by modifying rhizosphere soil microbial communities.
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Affiliation(s)
- Haiyang Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China
| | - Haoquan Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China
| | - Zhaojun Nie
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China
| | - Zhikang Tao
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China
| | - Hongyu Peng
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Peng Zhao
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China
| | - Hongen Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450046, China.
- Key Laboratory of Soil Pollution Control and Remediation in Henan Province, Zhengzhou, 450046, China.
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11
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Li J, Jin MK, Huang L, Liu ZF, Wang T, Chang RY, Op de Beeck M, Lambers H, Hui D, Xiao KQ, Chen QL, Sardans J, Peñuelas J, Yang XR, Zhu YG. Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland. ENVIRONMENT INTERNATIONAL 2024; 187:108688. [PMID: 38685158 DOI: 10.1016/j.envint.2024.108688] [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: 02/26/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.
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Affiliation(s)
- Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Lijie Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Zhan-Feng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tao Wang
- Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Rui-Ying Chang
- Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Michiel Op de Beeck
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia; Department of Plant Nutrition, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plan-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, TN, USA
| | - Ke-Qing Xiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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12
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Qin H, Zhang S, Wang C, Pan Q, Dong Y, Cai X, Wang X, Huang M, Huang J, Zhou R. Revealing the influence of exogenously inoculated Bacillus spp. on the microbiota and metabolic potential of medium-temperature Daqu: A meta-omics analysis. Food Res Int 2024; 182:114152. [PMID: 38519180 DOI: 10.1016/j.foodres.2024.114152] [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: 11/29/2023] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
To determine the unique contribution of the bioturbation to the properties of the medium-temperature Daqu, we investigated the differences in microbiota and metabolic composition using the meta-omics approach. Bioturbation increased the amounts of microbial specie and influenced the contribution of the core microbiota to the metabolome. Specifically, inoculated synthetic microbiota (MQB) enhanced the abundance of Bacillus amyloliquefaciens, while Bacillus licheniformis (MQH) increased the abundance of the two Aspergillus species and four species level of lactic acid bacteria. These changes of the microbial profiles significantly increased the potentials of carbohydrate metabolism, amino acid metabolism, and biosynthesis of ester compounds. Consequently, both patterns significantly increased the content of volatile compounds and free amino acids, which were 27.61% and 21.57% (MQB), as well as 15.14% and 17.83% (MQH), respectively. In addition, the contents of lactic acid in MQB and MQH decreased by 65.42% and 42.99%, respectively, closely related to the up- or down-regulation of the expression of their corresponding functional enzyme genes. These results suggested that bioturbation drove the assembly of the core microbiota, rather than becoming critical functional species. Overall, our study provides new insights into the functional role of exogenous isolates in the Daqu microecosystem.
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Affiliation(s)
- Hui Qin
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Suyi Zhang
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Chao Wang
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Qianglin Pan
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Yi Dong
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Xiaobo Cai
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Xiaojun Wang
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Mengyang Huang
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; Luzhou Laojiao Co., Ltd., Luzhou 646699, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Rongqing Zhou
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China; College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
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13
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Li Y, Ma G, Xi Y, Wang S, Zeng X, Jia Y. Divergent adaptation strategies of abundant and rare bacteria to salinity stress and metal stress in polluted Jinzhou Bay. ENVIRONMENTAL RESEARCH 2024; 245:118030. [PMID: 38151148 DOI: 10.1016/j.envres.2023.118030] [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: 10/29/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Understanding how abundant (AT) and rare (RT) taxa adapt to diverse environmental stresses is vital for assessing ecological processes, yet remains understudied. We collected sediment samples from Liaoning Province, China, representing rivers (upstream of wastewater outlet), estuaries (wastewater outlets), and Jinzhou Bay (downstream of wastewater outlets), to comprehensively evaluate AT and RT adaptation strategies to both natural stressors (salinity stress) and anthropogenic stressors (metal stress). Generally, RT displayed higher α- and β-diversities and taxonomic groups compared to AT. Metal and salinity stresses induced distinct α-diversity responses in AT and RT, while β-diversity remained consistent. Both subcommunities were dominated by Woeseia genus. Metal stress emerged as the primary driver of diversity and compositional discrepancies in AT and RT. Notably, AT responded more sensitively to salinity stress than RT. Stress increased topological parameters in the biotic network of AT subcommunities while decreasing values in RT subcommunities, concurrently loosening interactions of AT with other taxa and strengthening interactions of RT with others in biotic networks. RT generally exhibited greater diversity of metal resistance genes compared to AT. Greater numbers of genes related to salinity tolerance was observed for the RT than for AT. Compared to AT, RT demonstrated higher diversity of metal resistance genes and a greater abundance of genes associated with salinity tolerance. Additionally, deterministic processes governed AT community assembly, reinforced by salinity stress. However, the opposite trend was observed in the RT, where the importance of stochastic process gradually increased with metal stresses. The study is centered on exploring the adaptation strategies of both AT and RT to environmental stress. It underscores the importance of future research incorporating diverse ecosystems and a range of environmental stressors to draw broader and more reliable conclusions. This comprehensive approach is essential for gaining a thorough understanding of the adaptive mechanisms employed by these microorganisms.
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Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Guoqing Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yimei Xi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
| | - Shaofeng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xiangfeng Zeng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China.
| | - Yongfeng Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
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14
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Zabihollahi S, Rahmani A, Aghadadashi V, Khazaei M, Samadi MT, Leili M, Afshar S, Safari Sinegani AA, Karami P, Zafari D. Investigation of the effects of different substrates on the promotion of the soil microbial consortium, encompassing bacteria and fungi, in the bioremediation of decabromodiphenyl ether (BDE-209). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16359-16374. [PMID: 38316742 DOI: 10.1007/s11356-024-32152-0] [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: 08/28/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Decabromodiphenyl ether (BDE-209) is recognized as an emerging and hazardous pollutant in numerous ecosystems. Despite this, only a few studies have concurrently investigated the biodegradation of BDE-209 by a microbial consortium comprising both bacteria and fungi. Consequently, the interactions between bacterial and fungal populations and their mutual effects on BDE-209 degradation remain unclear. Our main objective was to concurrently assess the changes and activity of bacterial and fungal communities during the biodegradation of BDE-209 in a real soil matrix. In the present study, various organic substrates were employed to promote soil biomass for the biodegradation of BDE-209. Soil respiration and molecular analysis were utilized to monitor biological activity and biomass community structure, respectively. The findings revealed that the use of wheat straw in the soil matrix resulted in the highest soil respiration and microbial activity among the treatments. This approach obviously provided suitable habitats for the soil microflora, which led to a significant increase in the biodegradability of BDE-209 (49%). Biomass survival efforts and the metabolic pathway of lignin degradation through co-metabolism contributed to the biodegradation of BDE-209. Microbial community analysis identified Proteobacteria (Alphaproteobacteria-Betaproteobacteria), Firmicutes, Bacteroides (bacterial phyla), as well as Ascomycota and Basidiomycota (fungal phyla) as the key microorganisms in the biological community involved in the biodegradation of BDE-209. This study demonstrated that applying wheat straw can improve both the biological activity and the biodegradation of BDE-209 in the soil of polluted sites.
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Affiliation(s)
- Solmaz Zabihollahi
- Department of Environmental Health Engineering, School of Public Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
- Student Research Committee, Department of Environmental Health Engineering,, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Alireza Rahmani
- Department of Environmental Health Engineering, School of Public Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Vahid Aghadadashi
- Iranian National Institute for Oceanography and Atmospheric Sciences (INIOAS), Tehran, Iran
| | - Mohammad Khazaei
- Department of Environmental Health Engineering, School of Public Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Taghi Samadi
- Department of Environmental Health Engineering, School of Public Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mostafa Leili
- Department of Environmental Health Engineering, School of Public Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, cancer research center, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Pezhman Karami
- Department of Microbiology, Hamadan University of Medical Sciences, Hamadan, Iran
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Dostmorad Zafari
- Department of Plant Protection, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
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15
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Yang K, Liu W, Lin HM, Chen T, Yang T, Zhang B, Wen X. Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China. ENVIRONMENTAL RESEARCH 2024; 243:117749. [PMID: 38061589 DOI: 10.1016/j.envres.2023.117749] [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: 09/09/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023]
Abstract
The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.
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Affiliation(s)
- Kuo Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Wei Liu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui-Min Lin
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tan Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China
| | - Ting Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China
| | - Bing Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China.
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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16
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Li J, Fan M, Wei Z, Zhang K, Ma X, Shangguan Z. Broad environmental adaptation of abundant microbial taxa in Robinia pseudoacacia forests during long-term vegetation restoration. ENVIRONMENTAL RESEARCH 2024; 242:117720. [PMID: 37996008 DOI: 10.1016/j.envres.2023.117720] [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: 08/25/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Vegetation restoration has significant impacts on ecosystems, and a comprehensive understanding of microbial environmental adaptability could facilitate coping with ecological challenges such as environmental change and biodiversity loss. Here, abundant and rare soil bacterial and fungal communities were characterized along a 15-45-year chronosequence of forest vegetation restoration in the Loess Plateau region. Phylogenetic-bin-based null model analysis (iCAMP), niche breadth index, and co-occurrence network analysis were used to assess microbial community assembly and environmental adaptation of a Robinia pseudoacacia plantation under long-term vegetation restoration. The drift process governed community assembly of abundant and rare soil fungi and bacteria. With increasing soil total phosphorus content, the relative importance of drift increased, while dispersal limitation and heterogeneous selection exhibited opposite trends for abundant and rare fungi. Rare soil fungal composition dissimilarities were dominated by species replacement processes. Abundant microbial taxa had higher ecological niche width and contribution to ecosystem multifunctionality than rare taxa. Node property values (e.g., degree and betweenness) of abundant microbial taxa were substantially higher than those of rare microbial taxa, indicating abundant species occupied a central position in the network. This study provides insights into the diversity and stability of microbial communities during vegetation restoration in Loess Plateau. The findings highlight that abundant soil fungi and bacteria have broad environmental adaptation and major implications for soil multifunctionality under long-term vegetation restoration.
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Affiliation(s)
- Jiajia Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Miaochun Fan
- Department of Grassland Science, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Zhenhao Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Kang Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xing Ma
- Department of Grassland Science, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Zhouping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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17
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Feng Z, Li N, Deng Y, Yu Y, Gao Q, Wang J, Chen S, Xing R. Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China. Ecol Evol 2024; 14:e11001. [PMID: 38352203 PMCID: PMC10862184 DOI: 10.1002/ece3.11001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Soil microorganisms play vital roles in regulating multiple ecosystem functions. Recent studies have revealed that the rare microbial taxa (with extremely low relative abundances, which are still largely ignored) are also crucial in maintaining the health and biodiversity of the soil and may respond differently to environmental pressure. However, little is known about the soil community structures of abundant and rare taxa and their assembly processes in different soil layers on the Qinghai-Tibet Plateau (QTP). The present study investigated the community structure and assembly processes of soil abundant and rare microbial taxa on the northeastern edge of the QTP. Soil microbial abundance was defined by abundant taxa, whereas rare taxa contributed to soil microbial diversity. The results of null model show that the stochastic process ruled the assembly processes of all sub-communities. Dispersal limitation contributed more to the assembly of abundant microbial taxa in the different soil layers. In contrast, drift played a more critical role in the assembly processes of the rare microbial taxa. In addition, in contrast to previous studies, the abundant taxa played more important roles in co-occurrence networks, most likely because of the heterogeneity of the soil, the sparsity of amplicon sequencing, the sampling strategy, and the limited samples in the present study. The results of this study improve our understanding of soil microbiome assemblies on the QTP and highlight the role of abundant taxa in sustaining the stability of microbial co-occurrence networks in different soil layers.
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Affiliation(s)
- Zhilin Feng
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Na Li
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Yanfang Deng
- Service Center of Qilian Mountain National Park in Qinghai ProvinceXiningQinghaiChina
| | - Yao Yu
- Service Center of Qilian Mountain National Park in Qinghai ProvinceXiningQinghaiChina
| | - Qingbo Gao
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
| | - Jiuli Wang
- Qinghai Nationalities UniversityXiningQinghaiChina
| | - Shi‐long Chen
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
| | - Rui Xing
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
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18
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Xiong X, Wan W, Ding B, Cai M, Lu M, Liu W. Type VI secretion system drives bacterial diversity and functions in multispecies biofilms. Microbiol Res 2024; 279:127570. [PMID: 38096690 DOI: 10.1016/j.micres.2023.127570] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.
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Affiliation(s)
- Xiang Xiong
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Bangjing Ding
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Miaomiao Cai
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Mingzhu Lu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China.
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Li Y, Sun X, Zhang M, Khan A, Sun W. Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132807. [PMID: 37879275 DOI: 10.1016/j.jhazmat.2023.132807] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.
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Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Ajmal Khan
- Department of Environmental Sciences, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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20
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Qian X, Tang X, Tian W, Xiao X, Wang Y, Lv Q, Li H, Feng S. Climate factors and host chemical profiles jointly drives the bacterial community assembly in Mussaenda pubescens stems. ENVIRONMENTAL RESEARCH 2023; 235:116687. [PMID: 37467942 DOI: 10.1016/j.envres.2023.116687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Endophytic bacteria residing within host plants can significantly impact on the host's growth, health, and overall relationship with its surrounding environment. However, the process that shape the community assembly of stem bacterial endophytes (SBEs) remains poorly understood. This study explored the community structure, co-occurrence patterns, and ecological processes of the SBEs inhabiting the shrub host, Mussaenda pubescens, across seven locations in southeastern China. We found that the absolute abundances, alpha diversity, and community composition of SBE communities exhibited notable differences among various host populations. Stem chemical characteristics were the most important factors influencing SBE community distribution, followed by geographic distance and climatic factors. The beta diversity decomposition analyses indicated that SBE community dissimilarities between sites were nearly equally driven by similarity, replacement diversity, and richness difference. The co-occurrence network analysis revealed that the keystone taxa were mostly observed in rare species, which may be essential for preserving the ecosystem's functions. Conditionally abundant taxa (CAT) showcased the highest closeness centrality, while exhibiting the lowest degree centrality and betweenness centrality as opposed to rare taxa. In addition, stochastic processes also played an important role in structuring SBE communities, with ecological drift being the dominant factor for both abundant and rare taxa. This study would deepen our understanding of the ecological dynamics and microbial interactions within plant endophytic microbiomes.
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Affiliation(s)
- Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinghao Tang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Academy of Forestry Sciences, Fuzhou, 350012, China
| | - Weiwei Tian
- Sichuan Academy of Chinese Medical Sciences, Chengdu, 610041, China
| | - Xiangxi Xiao
- Fujian Academy of Forestry Sciences, Fuzhou, 350012, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, 014030, China
| | - Qixin Lv
- Nanjing Agricultural University, Nanjing, 210095, China
| | - Hanzhou Li
- Wuhan Benagen Technology Company, Wuhan, 430000, China
| | - Song Feng
- College of Civil Engineering, Fuzhou University, Fuzhou, 350108, China.
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Garrido-Sanz D, Čaušević S, Vacheron J, Heiman CM, Sentchilo V, van der Meer JR, Keel C. Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere. MICROBIOME 2023; 11:214. [PMID: 37770950 PMCID: PMC10540321 DOI: 10.1186/s40168-023-01660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed. RESULTS We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network. CONCLUSIONS The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.
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Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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22
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Sun J, Zhang A, Zhang Z, Liu Y, Zhou H, Cheng H, Chen Z, Li H, Zhang R, Wang Y. Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106082. [PMID: 37429213 DOI: 10.1016/j.marenvres.2023.106082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Aoqi Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Zhongxian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Yang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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23
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Ohore OE, Ifon BE, Wang Y, Kazmi SSUH, Zhang J, Sanganyado E, Jiao X, Liu W, Wang Z. Vertical changes in water depth and environmental variables drove the antibiotics and antibiotic resistomes distribution, and microbial food web structures in the estuary and marine ecosystems. ENVIRONMENT INTERNATIONAL 2023; 178:108118. [PMID: 37517178 DOI: 10.1016/j.envint.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/29/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
The influence of vertical changes in water depth on emerging pollutants distribution and microbial food web remains elusive. We investigated the influence of vertical transition in water depth on the environmental variables, antibiotics and antibiotic resistomes, and microbial community structures in estuary and marine ecosystems (0-50 m). Stepwise multiple linear regression model showed that among investigated environmental variables, change in water salinity was the most influential factor dictating the fluoroquinolone and macrolides concentrations, while dissolved oxygen and turbidity were the key influencers of sulfonamides and beta-lactam concentrations, respectively. Bacterial and eukaryotic diversity and niche breadth significantly increased with the increasing water depth. Ecosystem food web structure at the bottom depths was more stable than at the middle and surface depths. At the surface depth, the top 5 keystone genera were Cryothecomonas, Syndiniales, Achromobacter, Pseudopirsonia, and Karlodinium. Whereas Eugregarinorida, Neptuniibacter, Mychonastes, Novel_Apicomplexa_Class_1, Aplanochytrium and Dietzia, Halodaphnea, Luminiphilus, Aplanochytrium, Maullinia dominated the top 5 genera at the middle and the bottom depth, respectively. Absolute abundance of antibiotic resistance genes (ARGs) was drastically increased at the surface depth compared with the middle and bottom depths. Abundance of the top 10 ARGs and mobile genetic elements (MGEs) detected including tnpA-05, aadA2-03, mexF, aadA1, intI-1(clinic), qacEdelta1-02, aadA-02, qacEdelta1-01, cmlA1-01, and aadA-01 were amplified at the surface depth. This study demonstrated that ARGs abundance was disproportionate to bacterial diversity, and anthropogenic disturbances, confinement, MGEs, and ecosystem stability play primary roles in the fate of ARGs. The findings of this study also implicate that vertical changes in the water depth on environmental conditions can influence antibiotic concentrations and microbial community dramatically.
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Affiliation(s)
- Okugbe Ebiotubo Ohore
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Binessi Edouard Ifon
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Laboratory of Physical Chemistry, University of Abomey-Calavi, Republic of Benin, Cotonou 01 BP 4521, Benin
| | - Yuwen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Syed Shabi Ul Hassan Kazmi
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Jingli Zhang
- Department of Clinical Medicine, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Edmond Sanganyado
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE2 4PB, UK
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
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Li M, Yao J, Sunahara G, Duran R, Liu B, Cao Y, Li H, Pang W, Liu H, Jiang S, Zhu J, Zhang Q. Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131153. [PMID: 36893604 DOI: 10.1016/j.jhazmat.2023.131153] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/20/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.
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Affiliation(s)
- Miaomiao Li
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Jun Yao
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Geoffrey Sunahara
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China; Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Drive, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Bang Liu
- Universite de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Ying Cao
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Hao Li
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Wancheng Pang
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Houquan Liu
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shun Jiang
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Junjie Zhu
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
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25
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Li Y, Gao W, Wang C, Gao M. Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162413. [PMID: 36842601 DOI: 10.1016/j.scitotenv.2023.162413] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
The increasing application of plastic film has caused the "white pollution" of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.
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Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Wenlong Gao
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, PR China; Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Caixia Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Miao Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China.
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26
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Zhu M, Qi X, Yuan Y, Zhou H, Rong X, Dang Z, Yin H. Deciphering the distinct successional patterns and potential roles of abundant and rare microbial taxa of urban riverine plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131080. [PMID: 36842200 DOI: 10.1016/j.jhazmat.2023.131080] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Microbial colonization on microplastics has provoked global concern; however, many studies have not considered the successional patterns and potential roles of abundant and rare taxa of the plastisphere during colonization. Hence, we investigate the taxonomic composition, assembly, interaction and function of abundant and rare taxa in the riverine plastisphere by conducting microcosm experiments. Results showed that rare taxa occupied significantly high community diversity and niche breadth than the abundant taxa, which implies that rare taxa are essential components in maintaining the community stability of the plastisphere. However, the abundant taxa played a major role in driving the succession of plastisphere communities during colonization. Both stochastic and deterministic processes signally affected the plastisphere community assemblies; while, the deterministic patterns (heterogeneous selection) were especially pronounced for rare biospheres. Plastisphere microbial networks were shaped by the enhancement of network modularity and reinforcement of positive interactions. Rare taxa played critical roles in shaping stable plastisphere by occupying the key status in microbial networks. The strong interaction of rare and non-rare taxa suggested that multi-species collaboration might be conducive to the formation and stability of the plastisphere. Both abundant and rare taxa were enriched with plentiful functional genes related to carbon, nitrogen, phosphorus and sulfur cycling; however, their potential metabolic functions were significantly discrepant, implying that the abundant and rare microbes may play different roles in ecosystems. Overall, this study strengthens our comprehending of the mechanisms regarding the formation and maintenance of the plastisphere.
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Affiliation(s)
- Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Heyang Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xufa Rong
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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Huang W, Li S, Li S, Laanbroek HJ, Zhang Q. Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian. Front Microbiol 2023; 14:1151768. [PMID: 37180236 PMCID: PMC10169824 DOI: 10.3389/fmicb.2023.1151768] [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: 01/26/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.
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Affiliation(s)
- Weihong Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Shuantong Li
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Saisai Li
- Zhejiang Wanli University, Ningbo, China
| | - Hendrikus J. Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Qiufang Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
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Shentu J, Chen Q, Cui Y, Wang Y, Lu L, Long Y, Zhu M. Disturbance and restoration of soil microbial communities after in-situ thermal desorption in a chlorinated hydrocarbon contaminated site. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130870. [PMID: 36709742 DOI: 10.1016/j.jhazmat.2023.130870] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Thermal desorption technology has been widely used for the remediation of organic contaminated soil, but the heating process may alter the soil properties and its safety reutilization. After thermal remediation, the target pollutants including chloroform, 1,2-dichloroethane, 1,1,2-trichloroethane, 1,2,3-trichloropropane and vinyl chloride in the chlorinated hydrocarbon contaminated site were reduced significantly. The soil microbial α-diversity was also reduced by more than half. Notably, the relative abundance of Chloroflexi decreased by 9.0%, while Firmicutes had a 9.0% increase after thermal remediation. By water regulation and exogenous microorganism addition, the soil microbial community could not be restored to its initial state before thermal remediation in a relatively short time (30 days). The relative abundance of Proteobacteria increased from 25.4% to 41.7% and 51.0% by water regulation and exogenous microorganism addition, respectively. The modularity of the microbial co-occurrence network was strengthened after microbial restoration, but the interaction among microorganisms was weakened. Thermal remediation might be conducive to the C- and N-cycle related processes, but severely weakened the sulfide oxidation processes. Notably, microbial restoration would benefit the recovery of the S-cycle functional groups. These results provided a new perspective for the safety reutilization of soil after thermal remediation.
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Affiliation(s)
- Jiali Shentu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou 310012, China
| | - Qianqian Chen
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yuxue Cui
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yangyang Wang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Li Lu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou 310012, China
| | - Min Zhu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou 310012, China.
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29
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Liu H, Yao J, Liu B, Li M, Liu J, Jiang S, Yu W, Zhao Y, Duran R. Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161133. [PMID: 36566868 DOI: 10.1016/j.scitotenv.2022.161133] [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: 11/02/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.
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Affiliation(s)
- Houquan Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China.
| | - Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| | - Miaomiao Li
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jianli Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shun Jiang
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Wenjing Yu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Yuhui Zhao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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30
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Qin Z, Zhao Z, Xia L, Wang S, Yu G, Miao A. Responses of abundant and rare prokaryotic taxa in a controlled organic contaminated site subjected to vertical pollution-induced disturbances. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158625. [PMID: 36089032 DOI: 10.1016/j.scitotenv.2022.158625] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/20/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Soil microbiota as the key role mediates the natural attenuation process of organic contaminated sites, and therefore illuminating the mechanisms underlying the responses of abundant and rare species is essential for understanding ecological processes, maintaining ecosystem stability, and regulating natural attenuation well. Here, we explored the distributional characteristics, ecological diversities, and co-occurrence patterns of abundant and rare prokaryotic subcommunities using 16S rRNA high-throughput sequencing in vertical soil profiles of a controlled organic contaminated site. Results showed that abundant prokaryotic taxa were widespread across all soil samples, whereas rare counterparts were unbalancedly distributed. Rare subcommunity had more taxonomic groups and higher α- and β-diversities than abundant subcommunity. Both of these two subcommunities surviving in the organic polluted site possessed the potential of degrading organic contaminants. Abundant subcommunity was little affected by abiotic factors and mainly shaped by soil depth, while rare one was sensitive to environmental disturbances and presented a non-depth-dependent structure. Co-occurrence analysis revealed that rare taxa were more situated at the center of the network and more inclined to cooperate with non-abundant species than abundant taxa, which might play crucial roles in enhancing the resilience and resistance of prokaryotic community and maintaining its structure and stability. Overall, our results suggest that abundant and rare prokaryotic subcommunities present different responses to physicochemical factors and pollution characteristics along vertical soil profiles of organic contaminated sites undergoing natural attenuation.
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Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China
| | - Shiyu Wang
- Beijing Municipal Ecological and Environmental Monitoring Center, Beijing 100048, China
| | - Guangwen Yu
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Aihua Miao
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
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31
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Wang R, Xu S, Zhu Y, Zhang T, Ge S. Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process. Front Microbiol 2022; 13:1074316. [PMID: 36605517 PMCID: PMC9808034 DOI: 10.3389/fmicb.2022.1074316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Denitrifying anaerobic methane-oxidizing bacteria (DAMO bacteria) plays an important role in reducing methane emissions from river ecosystems. However, the assembly process of their communities underlying different hydrologic seasons remains unclarified. In this study, the dynamics of DAMO bacterial communities in river networks of the Taihu Basin were investigated by amplicon sequencing across wet, normal, and dry seasons followed by multiple statistical analyses. Phylogenetic analysis showed that Group B was the major subgroup of DAMO bacteria and significant dynamics for their communities were observed across different seasons (constrained principal coordinate analysis, p = 0.001). Furthermore, the neutral community model and normalized stochasticity ratio model were applied to reveal the underlying assembly process. Stochastic process and deterministic process dominated the assembly process in wet season and normal season, respectively and similar contributions of deterministic and stochastic processes were observed in dry season. Meanwhile, abundant (relative abundance >0.1%) and rare (relative abundance <0.01%) DAMO bacterial communities were found to be shaped via distinct assembly processes. Deterministic and stochastic processes played a considerable role in shaping abundant DAMO bacterial communities, while deterministic process mainly shaped rare DAMO bacterial communities. Results of this study revealed the dynamics of DAMO bacterial communities in river networks and provided a theoretical basis for further understanding of the assembly process.
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Affiliation(s)
- Ruyue Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Sai Xu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China,*Correspondence: Sai Xu,
| | - Yuxiang Zhu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Tao Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China,Shijian Ge,
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32
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Liu GH, Liu DQ, Wang P, Chen QQ, Che JM, Wang JP, Li WJ, Zhou SG. Temperature drives the assembly of Bacillus community in mangrove ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157496. [PMID: 35870580 DOI: 10.1016/j.scitotenv.2022.157496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO3-N and NH4-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Ding-Qi Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qian-Qian Chen
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jian-Mei Che
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province 350002, PR China.
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Temporal Dynamics of Rare and Abundant Soil Bacterial Taxa from Different Fertilization Regimes Under Various Environmental Disturbances. mSystems 2022; 7:e0055922. [PMID: 36121168 PMCID: PMC9600180 DOI: 10.1128/msystems.00559-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Global climate change has emerged as a critical environmental problem. Different types of climate extremes drive soil microbial communities to alternative states, leading to a series of consequences for soil microbial ecosystems and related functions. An effective method is urgently needed for buffering microbial communities to tackle environmental disturbances. Here, we conducted a series of mesocosm experiments in which the organic (NOF) and chemical fertilizer (NCF) long-term-amended soil microbiotas were subjected to environmental disturbances that included drought, flooding, freeze-thaw cycles, and heat. We subsequently tracked the temporal dynamics of rare and abundant bacterial taxa in NOF and NCF treatment soils to assess the efficiencies of organic amendments in recovery of soil microbiome. Our results revealed that freeze-thaw cycles and drought treatments showed weaker effects on bacterial communities than flooding and heat. The turnover between rare and abundant taxa occurred in postdisturbance succession of flooding and heat treatments, indicating that new equilibria were tightly related to the rare taxa in both NCF and NOF treatment soils. The Bayesian fits of modeling for the microbiome recovery process revealed that the stability of abundant taxa in NOF was higher than that in NCF soil. In particular, the NOF treatment soil reduced the divergence from the initial bacterial community after weak perturbations occurred. Together, we demonstrated that long-term organic input is an effective strategy to enhance the thresholds for transition to alternative states via enhancing the stability of abundant bacterial species. These findings provide a basis for the sustainable development of agricultural ecosystems in response to changing climates. IMPORTANCE Different climate extremes are expected to be a major threat to crop production, and the soil microbiome has been known to play a crucial role in agricultural ecosystems. In recent years, we have known that organic amendments are an effective method for optimizing the composition and functioning of the soil microbial community and maintaining the health of the soil ecosystem. However, the effects of organic fertilization on buffering bacterial communities against environmental disturbances and the underlying mechanisms are still unclear. We conducted a series of mesocosm experiments and showed that organic fertilizers had additional capacities in promoting the soil microbiome to withstand climate change effects. Our study provides both mechanistic insights as well as a direct guide for the sustainable development of agricultural ecosystems in response to climate change.
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Yang Y, Cheng K, Li K, Jin Y, He X. Deciphering the diversity patterns and community assembly of rare and abundant bacterial communities in a wetland system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156334. [PMID: 35660444 DOI: 10.1016/j.scitotenv.2022.156334] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Water microorganisms that have distinct contributions to community dynamics, including many rare taxa and few abundant taxa, are crucial to the wetland ecosystem functions. In this study, we comprehensively investigated the diversity patterns and assembly processes of rare and abundant taxa to strengthen our understanding of ecosystem function and diversity in a wetland system. The results showed that TN and NH3-N were the most significant factors affecting the community structure in this wetland. Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed that functions associated with nitrogen removal were the most prevalent metabolic pathways in samples of regenerated wetland (RW). Co-occurrence network analysis revealed that nonrare taxa exhibited more interactions with rare taxa than with conspecifics and some microbial hubs belonged to rare taxa, which might play an instrumental role in maintaining the stability of the community structure. We found that the assembly of rare taxa with a lower niche breadth was mainly governed by homogeneous selection, implying that their higher sensitivity of these to environmental disturbances and changes in TN played significant roles in community assembly of rare taxa. In contrast, the assembly of abundant taxa with higher niche breadth was dominated by stochastic processes (undominated process and dispersal limitation) indicating that abundant taxa had greater responsibility for maintaining community structure when exposed to environmental fluctuations. These results broaden our understanding of the microbial structure, interactions and ecological assembly mechanisms underlying microbial dynamics in aquatic ecosystems, which are crucial for the management of microorganisms in the wetlands.
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Affiliation(s)
- Yan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kexin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kaihang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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35
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Zhu M, Yin H, Yuan Y, Liu H, Qi X, Ren Y, Dang Z. Discrepancy strategies of sediment abundant and rare microbial communities in response to floating microplastic disturbances: Study using a microcosmic experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155346. [PMID: 35489492 DOI: 10.1016/j.scitotenv.2022.155346] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Floating microplastics (FMPs) in surface water have been extensively studied, but their influence on sedimentary microbial ecosystems is poorly understood. Here, we investigated response patterns of abundant and rare sedimentary microbes to FMP disturbances by performing microcosmic experiments using fluvial sediment with polyethylene (PE), polylactic acid (PLA), polystyrene (PS) and polyvinyl chloride (PVC) MPs. The results indicated that FMPs altered sediment microbial community diversity and composition. Some organic-degrading, nitrifying and denitrifying bacteria significantly decreased in response to FMP disturbances, which may affect the sediment carbon and nitrogen cycles. Rare taxa persisted under FMP disturbances, whereas abundant taxa were more susceptible to FMP disturbances, suggesting a higher sensitivity of abundant taxa to FMP disturbances. Although stochastic processes governed the assembly of the overall microbial communities, the assembly mechanisms of abundant and rare populations have significantly different responses to FMP interference. The relative contribution of deterministic processes was reinforced by enhanced homogenous selection in abundant populations, while it markedly decreased in rare populations under FMP disturbances. Furthermore, FMPs substantially decreased the network complexity, loosened the coexistence relationships, and increased the negative correlations. Rare species play an important role in reshaping complex microbial interactions and coexistence networks in response to FMP disturbances. This research broadens our perspectives for comprehensively evaluating the ecological effects of FMPs in the aquatic environment to formulate further policy controls.
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Affiliation(s)
- Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
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36
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Zhu Y, Ge X, Wang L, You Y, Cheng Y, Ma J, Chen F. Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress. Front Microbiol 2022; 13:972300. [PMID: 35983321 PMCID: PMC9378816 DOI: 10.3389/fmicb.2022.972300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.
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Affiliation(s)
- Yanfeng Zhu
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Xiaoping Ge
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Liping Wang
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
- Liping Wang,
| | - Yunnan You
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Yanjun Cheng
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Jing Ma
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
- School of Public Administration, Hohai University, Nanjing, China
| | - Fu Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
- School of Public Administration, Hohai University, Nanjing, China
- *Correspondence: Fu Chen,
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Zhu P, Yang S, Wu Y, Ru Y, Yu X, Wang L, Guo W. Shifts in Soil Microbial Community Composition, Function, and Co-occurrence Network of Phragmites australis in the Yellow River Delta. Front Microbiol 2022; 13:858125. [PMID: 35928147 PMCID: PMC9344067 DOI: 10.3389/fmicb.2022.858125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
Soil microorganisms play vital roles in regulating biogeochemical processes. The composition and function of soil microbial community have been well studied, but little is known about the responses of bacterial and fungal communities to different habitats of the same plant, especially the inter-kingdom co-occurrence pattern including bacteria and fungi. Herein, we used high-throughput sequencing to investigate the bacterial and fungal communities of five Phragmites australis habitats in the Yellow River Delta and constructed their inter-kingdom interaction network by network analysis. The results showed that richness did not differ significantly among habitats for either the bacterial or fungal communities. The distribution of soil bacterial community was significantly affected by soil physicochemical properties, whereas that of the fungal community was not. The main functions of the bacterial and fungal communities were to participate in the degradation of organic matter and element cycling, both of which were significantly affected by soil physicochemical properties. Network analysis revealed that bacteria and fungi participated in the formation of networks through positive interactions; the role of intra-kingdom interactions were more important than inter-kingdom interactions. In addition, rare species acted as keystones played a critical role in maintaining the network structure, while NO3−−N likely played an important role in maintaining the network topological properties. Our findings provided insights into the inter-kingdom microbial co-occurrence network and response of the soil microbial community composition and function to different P. australis habitats in coastal wetlands, which will deepen our insights into microbial community assembly in coastal wetlands.
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Affiliation(s)
- Pengcheng Zhu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Shuren Yang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuxin Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuning Ru
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Xiaona Yu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Lushan Wang,
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
- *Correspondence: Weihua Guo, whguo@
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