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Cuartero J, Querejeta JI, Prieto I, Frey B, Alguacil MM. Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175006. [PMID: 39069184 DOI: 10.1016/j.scitotenv.2024.175006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.
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Affiliation(s)
- J Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland.
| | - J I Querejeta
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - I Prieto
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain; Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - B Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - M M Alguacil
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
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Majeed A, Liu J, Knight AJ, Pajerowska-Mukhtar KM, Mukhtar MS. Bacterial Communities Associated with the Leaves and the Roots of Salt Marsh Plants of Bayfront Beach, Mobile, Alabama, USA. Microorganisms 2024; 12:1595. [PMID: 39203436 PMCID: PMC11356468 DOI: 10.3390/microorganisms12081595] [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: 06/30/2024] [Revised: 07/23/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress.
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Affiliation(s)
- Aqsa Majeed
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
- Department of Genetics & Biochemistry, Biosystems Research Complex, Clemson University, 105 Collings St., Clemson, SC 29634, USA
| | - Jinbao Liu
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
| | - Adelle J. Knight
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
| | - Karolina M. Pajerowska-Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
- Department of Genetics & Biochemistry, Biosystems Research Complex, Clemson University, 105 Collings St., Clemson, SC 29634, USA
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Zhang P, Wang Y, Lin H, Liang J, Wang J, Bai Y, Qu J, Wang A. Bacterial evolution in Biofiltration of drinking water treatment plant: Different response of phage and plasmid to varied water sources. WATER RESEARCH 2024; 259:121887. [PMID: 38870889 DOI: 10.1016/j.watres.2024.121887] [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: 04/10/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies.
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Affiliation(s)
- Peijun Zhang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Yuhan Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Huan Lin
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China.
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, NSW 2751, Australia; School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, Tsinghua University, Beijing 100084, China
| | - Aijie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China.
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Bairoliya S, Koh J, Cho ZT, Cao B. Phototrophs as the central components of the plastisphere microbiome in coastal environments. ENVIRONMENT INTERNATIONAL 2024; 190:108901. [PMID: 39079334 DOI: 10.1016/j.envint.2024.108901] [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: 05/25/2024] [Revised: 07/19/2024] [Accepted: 07/19/2024] [Indexed: 08/28/2024]
Abstract
Upon entering the marine environment, plastics are colonized by a plethora of microorganisms to form a plastisphere, influencing the fate and transport of the plastic debris and the health of marine ecosystems. The assembly of marine plastisphere is generally believed to be dominated by stochastic processes. However, it remains elusive whether microbial interaction in the assembly of plastisphere microbial communities is conserved or not. We analyzed the plastisphere microbiomes of 137 plastic debris samples from intertidal zones at different geographical locations and habitats (seagrass, coral, mangrove, beach, and open ocean) and compared them with the surrounding sediment and seawater microbiomes. Microbial community structures of the plastisphere from different locations were more similar to each other but differed substantially from the surrounding sediment and water microbiomes, implying a common mechanism of plastisphere assembly. We used different machine learning algorithms (Multinomial Logistic Regression, Support Vector Machine, Decision Trees, Random Forest, and Artificial Neural Networks) to classify plastic debris samples with high sensitivity based on the microbiome composition. Eukaryotic and prokaryotic phototrophic organisms such as green algae, diatoms, and cyanobacteria, were found to be enriched on the plastic surfaces. Network analysis revealed the central role of the phototrophic organisms in the formation and sustenance of the plastispheres. We found that phototrophs served as core members interacting strongly with heterotrophic organisms in marine plastisphere, irrespective of the sampling location, habitats, and polymer types. This would explain the stochastic assembly of the plastisphere along with conserved properties driven by the phototrophs in the surrounding environment. Our results highlight the importance of phototrophic organisms in shaping the marine plastisphere microbial communities.
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Affiliation(s)
- Sakcham Bairoliya
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Jonas Koh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Zin Thida Cho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore.
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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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Guo P, Lin Y, Sheng Y, Gu X, Deng Y, Zhang Y, Wang W, Wang M. Comparison of the coexistence pattern of mangrove macrobenthos between natural and artificial reforestation. Ecol Evol 2024; 14:e70069. [PMID: 39091331 PMCID: PMC11289789 DOI: 10.1002/ece3.70069] [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: 06/05/2024] [Revised: 06/30/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024] Open
Abstract
The abandoned pond-to-mangrove restoration project provides greater advantages than tidal flats afforestation in restoring mangrove ecosystem services and will be the primary method for mangrove restoration in the future. The existing methods for abandoned pond-to-mangrove restoration include artificial restoration through 'dike-breaking, filling with imported soil and tree planting' and natural restoration through 'dike-breaking and natural succession'. However, little is known about which restoration strategy (natural or artificial restoration) provides more benefits to the biodiversity of mangrove macrobethos. Given a prevailing view suggested that artificial restoration should be the preferred approach for accelerating recovery of biodiversity and vegetation structure in tropical regions, we hypothesised higher macrobenthic biodiversity and more complex community structure in artificial restoration than in natural restoration. To test this hypothesis, macrobenthic biodiversity and ecological processes were monitored in a typical abandoned pond-to-mangrove area of Dongzhaigang Bay, China, where artificial and natural restoration methods were used concurrently. Differences in macrobenthic biodiversity, community structure and ecological processes were compared using diversity indices, complex network analysis and null models. Similar species composition and ecological niche overlap and width among macrobenthos were observed at artificial and natural restoration sites. The biotic heterogeneity and interaction among macrobenthos were higher at the natural restoration sites than at the artificial restoration sites. Macrobenthos community assembly at natural and artificial restoration sites was both determined by deterministic processes, with environmental filtering dominating, which explained 52% and 54% of the variations in macrobenthic community structures respectively. Although our findings did not validate the research hypothesis, higher biotic heterogeneity and species interaction among macrobenthos could support natural restoration as the primary method for abandoned pond-to-mangrove projects, because it is a nature-based solution for mangrove restoration.
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Affiliation(s)
- Pingping Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Yufeng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Yifei Sheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Xuan Gu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Yijuan Deng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Yamian Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
| | - Mao Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & EcologyXiamen UniversityXiamenChina
- Zhangjiang Estuary Mangrove Wetland Ecosystem Station, National Observation and Research Station for the Taiwan Strait Marine EcosystemXiamen UniversityZhangzhouChina
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Kudjordjie EN, Santos SS, Topalović O, Vestergård M. Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism. ENVIRONMENTAL MICROBIOME 2024; 19:53. [PMID: 39068487 DOI: 10.1186/s40793-024-00597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND The interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants. RESULTS As expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms. CONCLUSION Our results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
| | - Susana S Santos
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
| | - Olivera Topalović
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark.
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Wang W, Portal-Gonzalez N, Wang X, Li J, Li H, Portieles R, Borras-Hidalgo O, He W, Santos-Bermudez R. Insights into the microbial assembly and metabolites associated with ginger (Zingiber officinale L. Roscoe) microbial niches and agricultural environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174395. [PMID: 38992353 DOI: 10.1016/j.scitotenv.2024.174395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Ginger, a vegetable export from China, is well-known for its spicy flavour and use in traditional Chinese medicine. By examining the interactions of ginger plants' microbiome and metabolome, we can gain insights to advance agriculture, the environment, and other fields. Our study used metataxonomic analysis to investigate ginger plants' prokaryotic and fungal microbiomes in open fields and greenhouses. We also conducted untargeted metabolomic analysis to identify specific metabolites closely associated with ginger microbiome assembly under both agricultural conditions. Various bacteria and fungi were classified as generalists or specialists based on their ability to thrive in different environments and microbial niches. Our results indicate that ginger plants grown in greenhouses have a greater prokaryotic diversity, while those grown in open fields exhibit a greater fungal diversity. We have identified specific co-occurring prokaryotic and fungal genera associated with ginger plant agroecosystems that can enhance the health and growth of ginger plants while maintaining a healthy environment. In the open field these genera include Sphingomonas, Methylobacterium-Methylorubrum, Bacillus, Acidovorax, Rhizobium, Microbacterium, unclassified_f_Comamonadaceae, Herbaspirillum, Klebsiella, Enterobacter, Chryseobacterium, Nocardioides, Subgroup_10, Enterococcus, Pseudomonas, Devosia, g_unclassified_f_Chaetomiaceae, Pseudaleuria, Mortierella, Cheilymenia, and Pseudogymnoascus. In the greenhouse, the enriched genera were Rhizobium, Stenotrophomonas, Aureimonas, Bacillus, Nocardioides, Pseudomonas, Enterobacter, Delftia, Trichoderma, Mortierella, Cheilymenia, Schizothecium, and Actinomucor. Our research has identified several previously unknown microbial genera for ginger plant agroecosystems. Furthermore, our study has important implications for understanding the correlation between ginger's microbiome and metabolome profiles in diverse environments and may pave the way for future research. Specific microbial genera in crop production environments are associated with essential metabolites, including Safingol, Docosatrienoic acid, P-acetaminophen, and Hypoglycin B.
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Affiliation(s)
- Wenbo Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Nayanci Portal-Gonzalez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China
| | - Xia Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Roxana Portieles
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao 276826, Shandong, People's Republic of China.
| | - Orlando Borras-Hidalgo
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao 276826, Shandong, People's Republic of China.
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Ramon Santos-Bermudez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
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Ningthoujam R, Pinyakong O. Exploring di (2-ethylhexyl) phthalate degradation by a synthetic marine bacterial consortium: Genomic insights, pathway and interaction prediction, and application in sediment microcosms. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134557. [PMID: 38735188 DOI: 10.1016/j.jhazmat.2024.134557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/01/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]
Abstract
Di (2-ethylhexyl) phthalate (DEHP), a toxic phthalate ester (PAE) plasticizer, is often detected in marine sediment and biota. Our understanding of DEHP-degrading marine bacteria and the associated genetic mechanisms is limited. This study established a synthetic bacterial consortium (A02) consisting of three marine bacteria (OR05, OR16, and OR21). Consortium A02 outperformed the individual strains in DEHP degradation. Investigations into the degradation of DEHP intermediates revealed that OR05 and OR16 likely contributed to enhanced DEHP degradation by Consortium A02 via the utilization of DEHP intermediates, such as protocatechuic acid and mono (ethylhexyl) phthalate, with OR21 as the key DEHP degrader. A pathway of DEHP degradation by Consortium A02 was predicted based on genome analysis and experimental degradation. Bioaugmentation with Consortium A02 led to 80% DEHP degradation in 26 days in saline sediment (100 mg/kg), surpassing the 53% degradation by indigenous microbes, indicating the potential of A02 for treating DEHP-contaminated sediments. Meanwhile, bioaugmentation notably changed the bacterial community, with the exclusive presence of certain bacterial genera in the A02 bioaugmented microcosms, and was predicted to result in a more dynamic and active sediment bacterial community. This study contributes to the limited literature on DEHP degradation by marine bacteria and their associated genes.
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Affiliation(s)
- Ritu Ningthoujam
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand.
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Qin Z, Wang S, Wu Y, Sun J, Zhao F. Seasonal dynamics of intestinal microbiota in juvenile Chinese mitten crab ( Eriocheir sinensis) in the Yangtze Estuary. Front Cell Infect Microbiol 2024; 14:1436547. [PMID: 39027136 PMCID: PMC11254619 DOI: 10.3389/fcimb.2024.1436547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction In this study, the seasonal differences in the intestinal microbiota of Chinese mitten crab (Eriocheir sinensis) larvae were investigated at different sites in the intertidal zone of the Yangtze River Estuary. Methods 16S rRNA high-throughput sequencing technology was used to compare and analyze the microbial community structure in the intestines of juvenile crab from different seasons. Results The results showed that the main microbial phyla in all seasons and sites were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, which accounted for 97.1% of the total microbiota. Composition analysis revealed that the relative abundance of Proteobacteria decreased from summer to winter at each station, whereas Bacteroidetes showed the opposite trend. Alpha diversity analysis showed that species richness increased from summer to winter at the upstream site (P < 0.05), but decreased at the downstream site (P < 0.05), with no significant differences observed in other comparisons. Biomarker species analysis showed that juvenile crab exhibited a more specialized microbial community in summer compared with autumn and winter. Co-occurrence network analysis revealed that microbial interaction network complexity was lower in autumn compared with summer and autumn. Functional prediction analysis showed that the microbial community only exhibited seasonal differences in amino acid biosynthesis, cofactor, prosthetic group, electron carrier, and vitamin biosynthesis, aromatic compound degradation, nucleotide and nucleoside degradation, and tricarboxylic acid cycle pathways. Discussion The results indicated that the microbiota did not significantly differ among sites, and seasonal variation was a main factor influencing the differences in intestinal microbiota of Chinese mitten juvenile crab. Moreover, the microbial community was more complex in summer compared with autumn and winter.
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Affiliation(s)
- Ze Qin
- College of Fisheries, Tianjin Agricultural University, Tianjin, China
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Sikai Wang
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Shanghai Yangtze River Estuary Fishery Resources Enhancement and Ecological Restoration Engineering and Technology Research, Shanghai, China
| | - Yeling Wu
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Shanghai Yangtze River Estuary Fishery Resources Enhancement and Ecological Restoration Engineering and Technology Research, Shanghai, China
| | - Jinhui Sun
- College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Feng Zhao
- East China Sea Fisherises Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Shanghai Yangtze River Estuary Fishery Resources Enhancement and Ecological Restoration Engineering and Technology Research, Shanghai, China
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11
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Zhou Q, Jia L, Li Y, Wu W, Wang J. Significantly Enhanced Nitrate and Phosphorus Removal by Pyrite/Sawdust Composite-Driven Mixotrophic Denitrification with Boosted Electron Transfer: Comprehensive Evaluation of Water-Gas-Biofilm Phases during a Long-Term Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10149-10161. [PMID: 38808456 DOI: 10.1021/acs.est.4c03677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Further reducing total nitrogen (TN) and total phosphorus (TP) in the secondary effluent needs to be realized effectively and in an eco-friendly manner. Herein, four pyrite/sawdust composite-based biofilters were established to treat simulated secondary effluent for 304 days. The results demonstrated that effluent TN and TP concentrations from biofilters under the optimal hydraulic retention time (HRT) of 3.5 h were stable at <2.0 and 0.1 mg/L, respectively, and no significant differences were observed between inoculated sludge sources. The pyrite/sawdust composite-based biofilters had low N2O, CH4, and CO2 emissions, and the effluent's DOM was mainly composed of five fluorescence components. Moreover, mixotrophic denitrifiers (Thiothrix) and sulfate-reducing bacteria (Desulfosporosinus) contributing to microbial nitrogen and sulfur cycles were enriched in the biofilm. Co-occurrence network analysis deciphered that Chlorobaculum and Desulfobacterales were key genera, which formed an obvious sulfur cycle process that strengthened the denitrification capacity. The higher abundances of genes encoding extracellular electron transport (EET) chains/mediators revealed that pyrite not only functioned as an electron conduit to stimulate direct interspecies electron transfer by flagella but also facilitated EET-associated enzymes for denitrification. This study comprehensively evaluates the water-gas-biofilm phases of pyrite/sawdust composite-based biofilters during a long-term study, providing an in-depth understanding of boosted electron transfer in pyrite-based mixotrophic denitrification systems.
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Affiliation(s)
- Qi Zhou
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing 100084, China
| | - Lixia Jia
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuanwei Li
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weizhong Wu
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jianlong Wang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing 100084, China
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Jibril SM, Yan W, Wang Y, Zhu X, Yunying Z, Wu J, Wang L, Zhang L, Li C. Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii. Front Microbiol 2024; 15:1387870. [PMID: 38903799 PMCID: PMC11188333 DOI: 10.3389/fmicb.2024.1387870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.
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Affiliation(s)
- Sauban Musa Jibril
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Wu Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Xishen Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Zhou Yunying
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Jie Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Ling Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Limin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [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: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Hidalgo-Martinez K, Giachini AJ, Schneider M, Soriano A, Baessa MP, Martins LF, de Oliveira VM. Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33663-33684. [PMID: 38687451 DOI: 10.1007/s11356-024-33304-y] [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: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.
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Affiliation(s)
- Kelly Hidalgo-Martinez
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil.
- Programa de Pós-Graduação de Genética E Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, CEP 13083-970, Brazil.
| | - Admir José Giachini
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Marcio Schneider
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Adriana Soriano
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Marcus Paulus Baessa
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Luiz Fernando Martins
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Valéria Maia de Oliveira
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil
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15
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Li D, Deng Y, Liu L, Wang J, Huang Z, Zhang X. Analysis of heavy metal and polycyclic aromatic hydrocarbon pollution characteristics of a typical metal rolling industrial site based on data mining. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:146. [PMID: 38578375 DOI: 10.1007/s10653-024-01928-1] [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: 08/09/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
With the transformation and upgrading of industries, the environmental problems caused by industrial residual contaminated sites are becoming increasingly prominent. Based on actual investigation cases, this study analyzed the soil pollution status of a remaining sites of the copper and zinc rolling industry, and found that the pollutants exceeding the screening values included Cu, Ni, Zn, Pb, total petroleum hydrocarbons and 6 polycyclic aromatic hydrocarbon monomers. Based on traditional analysis methods such as the correlation coefficient and spatial distribution, combined with machine learning methods such as SOM + K-means, it is inferred that the heavy metal Zn/Pb may be mainly related to the production history of zinc rolling. Cu/Ni may be mainly originated from the production history of copper rolling. PAHs are mainly due to the incomplete combustion of fossil fuels in the melting equipment. TPH pollution is speculated to be related to oil leakage during the industrial use period and later period of vehicle parking. The results showed that traditional analysis methods can quickly identify the correlation between site pollutants, while SOM + K-means machine learning methods can further effectively extract complex hidden relationships in data and achieve in-depth mining of site monitoring data.
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Affiliation(s)
- De'an Li
- Guangdong Laboratory of Soil Pollution Fate and Risk Management in Earth's Critical Zone and Guangdong Key Laboratory of Contaminated Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
| | - Yirong Deng
- Guangdong Laboratory of Soil Pollution Fate and Risk Management in Earth's Critical Zone and Guangdong Key Laboratory of Contaminated Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China.
| | - LiLi Liu
- Guangdong Laboratory of Soil Pollution Fate and Risk Management in Earth's Critical Zone and Guangdong Key Laboratory of Contaminated Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
| | - Jun Wang
- Guangdong Laboratory of Soil Pollution Fate and Risk Management in Earth's Critical Zone and Guangdong Key Laboratory of Contaminated Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
| | - Zaoquan Huang
- Guangdong Laboratory of Soil Pollution Fate and Risk Management in Earth's Critical Zone and Guangdong Key Laboratory of Contaminated Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
| | - Xiaolu Zhang
- Guangdong Laboratory of Soil Pollution Fate and Risk Management in Earth's Critical Zone and Guangdong Key Laboratory of Contaminated Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
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16
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Li X, Ren X, Su Y, Zhou X, Wang Y, Ruan S, Yan J, Li B, Guo K. Differential effects of winter cold stress on soil bacterial communities, metabolites, and physicochemical properties in two varieties of Tetrastigma hemsleyanum Diels & Gilg in reclaimed land. Microbiol Spectr 2024; 12:e0242523. [PMID: 38470484 PMCID: PMC10994721 DOI: 10.1128/spectrum.02425-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
Tetrastigma hemsleyanum Diels & Gilg (TDG) has been recently planted in reclaimed lands in Zhejiang Province, China, to increase reclaimed land use. Winter cold stress seriously limits the growth and development of TDG and has become the bottleneck limiting the TDG planting industry. To investigate the defense mechanisms of TDG toward winter cold stress when grown on reclaimed land, a combined analysis of soil bacterial communities, metabolites, and physicochemical properties was conducted in this study. Significant differences were observed in the composition of soil bacterial communities, metabolites, and properties in soils of a cold-tolerant variety (A201201) compared with a cold-intolerant variety (B201810). The fresh weight (75.8% of tubers) and dry weight (73.6%) of A201201 were significantly higher than those of B201810. The 16S rRNA gene amplicon sequencing of soil bacteria showed that Gp5 (25.3%), Gemmatimonas (19.6%), Subdivision3 (16.7%), Lacibacterium (11.9%), Gp4 (11.8%), Gp3 (10.4%), Gp6 (7.0%), and WPS-1 (1.2%) were less common, while Chryseolinea (10.6%) were more common in A201201 soils than B201810 soils. Furthermore, linear discriminant analysis of effect size identified 35 bacterial biomarker taxa for both treatments. Co-occurrence network analyses also showed that the structures of the bacterial communities were more complex and stable in A201201 soils compared to B201810 soils. In addition, ultra-high-performance liquid chromatography coupled to mass spectrometry analysis indicated the presence of significantly different metabolites in the two soil treatments, with 10 differentially expressed metabolites (DEMs) (8 significantly upregulated by 9.2%-391.3% and 2 significantly downregulated by 25.1%-73.4%) that belonged to lipids and lipid-like molecules, organic acids and derivatives, and benzenoids. The levels of those DEMs were significantly correlated with the relative abundances of nine bacterial genera. Also, redundancy discriminant analysis revealed that the main factors affecting changes in the bacterial community composition were available potassium (AK), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC), alkaline hydrolysis nitrogen (AHN), total nitrogen (TN), available phosphorus (AP), and soil organic matter (SOM). The main factors affecting changes in the metabolite profiles were AK, MBC, MBN, AHN, pH, SOM, TN, and AP. Overall, this study provides new insights into the TDG defense mechanisms involved in winter cold stress responses when grown on reclaimed land and practical guidelines for achieving optimal TDG production.IMPORTANCEChina has been undergoing rapid urbanization, and land reclamation is regarded as a viable option to balance occupation and compensation. In general, the quality of reclaimed land cannot meet plant or even cultivation requirements due to poor soil fertility and high gravel content. However, Tetrastigma hemsleyanum Diels & Gilg (TDG), extensively used in Chinese herbal medicine, can grow well in stony soils with few nutrients. So, to increase reclaimed land use, TDG has been cultivated on reclaimed lands in Zhejiang Province, China, recently. However, the artificial cultivation of TDG is often limited by winter cold stress. The aim of this study was to find out how TDG on reclaimed land deal with winter cold stress by looking at the bacterial communities, metabolites, and physicochemical properties of the soil, thereby guiding production in practice.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yao Su
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiang Zhou
- Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou, China
| | - Yu Wang
- Qingliangfeng Lvyuan Vegetable Professional Cooperative, Hangzhou, China
| | - Songlin Ruan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Guo
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Piloto‐Sardiñas E, Abuin‐Denis L, Maitre A, Foucault‐Simonin A, Corona‐González B, Díaz‐Corona C, Roblejo‐Arias L, Mateos‐Hernández L, Marrero‐Perera R, Obregon D, Svobodová K, Wu‐Chuang A, Cabezas‐Cruz A. Dynamic nesting of Anaplasma marginale in the microbial communities of Rhipicephalus microplus. Ecol Evol 2024; 14:e11228. [PMID: 38571811 PMCID: PMC10985379 DOI: 10.1002/ece3.11228] [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: 01/12/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
Interactions within the tick microbiome involving symbionts, commensals, and tick-borne pathogens (TBPs) play a pivotal role in disease ecology. This study explored temporal changes in the microbiome of Rhipicephalus microplus, an important cattle tick vector, focusing on its interaction with Anaplasma marginale. To overcome limitations inherent in sampling methods relying on questing ticks, which may not consistently reflect pathogen presence due to variations in exposure to infected hosts in nature, our study focused on ticks fed on chronically infected cattle. This approach ensures continuous pathogen exposure, providing a more comprehensive understanding of the nesting patterns of A. marginale in the R. microplus microbiome. Using next-generation sequencing, microbiome dynamics were characterized over 2 years, revealing significant shifts in diversity, composition, and abundance. Anaplasma marginale exhibited varying associations, with its increased abundance correlating with reduced microbial diversity. Co-occurrence networks demonstrated Anaplasma's evolving role, transitioning from diverse connections to keystone taxa status. An integrative approach involving in silico node removal unveils the impact of Anaplasma on network stability, highlighting its role in conferring robustness to the microbial community. This study provides insights into the intricate interplay between the tick microbiome and A. marginale, shedding light on potential avenues for controlling bovine anaplasmosis through microbiome manipulation.
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Affiliation(s)
- Elianne Piloto‐Sardiñas
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
- Direction of Animal Health, National Center for Animal and Plant HealthCarretera de Tapaste y Autopista NacionalSan José de las LajasCuba
| | - Lianet Abuin‐Denis
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
- Animal Biotechnology DepartmentCenter for Genetic Engineering and BiotechnologyHavanaCuba
| | - Apolline Maitre
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET‐LRDE)CorteFrance
- EA 7310, Laboratoire de Virologie, Université de CorseCorteFrance
| | - Angélique Foucault‐Simonin
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
| | - Belkis Corona‐González
- Direction of Animal Health, National Center for Animal and Plant HealthCarretera de Tapaste y Autopista NacionalSan José de las LajasCuba
| | - Cristian Díaz‐Corona
- Direction of Animal Health, National Center for Animal and Plant HealthCarretera de Tapaste y Autopista NacionalSan José de las LajasCuba
| | - Lisset Roblejo‐Arias
- Direction of Animal Health, National Center for Animal and Plant HealthCarretera de Tapaste y Autopista NacionalSan José de las LajasCuba
| | - Lourdes Mateos‐Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
| | - Roxana Marrero‐Perera
- Direction of Animal Health, National Center for Animal and Plant HealthCarretera de Tapaste y Autopista NacionalSan José de las LajasCuba
| | - Dasiel Obregon
- School of Environmental SciencesUniversity of GuelphGuelphOntarioCanada
| | - Karolína Svobodová
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Alejandra Wu‐Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
| | - Alejandro Cabezas‐Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé AnimaleMaisons‐AlfortFrance
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18
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Li Y, Jin L, Wu M, Wang B, Qu N, Zhou H, Chen T, Liu G, Yue M, Zhang G. Forest management positively reshapes the phyllosphere bacterial community and improves community stability. ENVIRONMENT INTERNATIONAL 2024; 186:108611. [PMID: 38603812 DOI: 10.1016/j.envint.2024.108611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Research has shown that forest management can improve the post-drought growth and resilience of Qinghai spruce in the eastern Qilian Mountains, located on the northeastern Tibetan Plateau. However, the impact of such management on the tree-associated phyllosphere microbiome is not yet fully understood. This study provides new evidence of positive forest management effects on the phyllosphere microbiome after extreme drought, from the perspectives of community diversity, structure, network inference, keystone species, and assembly processes. In managed Qinghai spruce forest, the α-diversity of the phyllosphere bacterial communities increased, whereas the β-diversity decreased. In addition, the phyllosphere bacterial community became more stable and resistant, yet less complex, following forest management. Keystone species inferred from a bacterial network also changed under forest management. Furthermore, forest management mediated changes in community assembly processes, intensifying the influence of determinacy, while diminishing that of stochasticity. These findings support the hypothesis that management can re-assemble the phyllosphere bacterial community, enhance community stability, and ultimately improve tree growth. Overall, the study highlights the importance of forest management on the phyllosphere microbiome and furnishes new insights into forest conservation from the perspective of managing microbial processes and effects.
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Affiliation(s)
- Yunshi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Xi'an 710069, China; Department of Life Science, Northwest University, Xi'an 710069, China
| | - Ling Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Minghui Wu
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Bo Wang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Na Qu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Xi'an 710069, China; Department of Life Science, Northwest University, Xi'an 710069, China
| | - Huaizhe Zhou
- Test Center, National University of Defense Technology, Xi'an 710106, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Xi'an 710069, China; Department of Life Science, Northwest University, Xi'an 710069, China.
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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19
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Osborne MG, Simons AL, Molano G, Tolentino B, Singh A, Arismendi GJM, Alberto F, Nuzhdin SV. Investigating the relationship between microbial network features of giant kelp "seedbank" cultures and subsequent farm performance. PLoS One 2024; 19:e0295740. [PMID: 38536857 PMCID: PMC10971754 DOI: 10.1371/journal.pone.0295740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/28/2023] [Indexed: 05/01/2024] Open
Abstract
Microbial inoculants can increase the yield of cultivated crops and are successful in independent trials; however, efficacy drops in large-scale applications due to insufficient consideration of microbial community dynamics. The structure of microbiomes, in addition to the impact of individual taxa, is an important factor to consider when designing growth-promoting inoculants. Here, we investigate the microbial network and community assembly patterns of Macrocystis pyrifera gametophyte germplasm cultures (collectively referred to as a "seedbank") used to cultivate an offshore farm in Santa Barbara, California, and identify network features associated with increased biomass of mature sporophytes. We found that [1] several network features, such as clustering coefficient and edge ratios, significantly vary with biomass outcomes; [2] gametophytes that become low- or high-biomass sporophytes have different hub taxa; and [3] microbial community assembly of gametophyte germplasm cultures is niche-driven. Overall, this study describes microbial community dynamics in M. pyrifera germplasm cultures and ultimately supports the development of early life stage inoculants that can be used on seaweed cultivars to increase biomass yield.
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Affiliation(s)
- Melisa G. Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Ariel Levi Simons
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Gary Molano
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Bernadeth Tolentino
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Anupam Singh
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States of America
| | | | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America
| | - Sergey V. Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States of America
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20
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Chang B, Zhang W, Wang Y, Zhang Y, Zhong S, Gao P, Wang L, Zhao Z. Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome. BMC Microbiol 2024; 24:73. [PMID: 38443783 PMCID: PMC10916198 DOI: 10.1186/s12866-024-03211-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Undernutrition (UN) is a critical public health issue that threatens the lives of children under five in developing countries. While evidence indicates the crucial role of the gut microbiome (GM) in UN pathogenesis, the strain-level inspection and bacterial co-occurrence network investigation in the GM of UN children are lacking. RESULTS This study examines the strain compositions of the GM in 61 undernutrition patients (UN group) and 36 healthy children (HC group) and explores the topological features of GM co-occurrence networks using a complex network strategy. The strain-level annotation reveals that the differentially enriched species between the UN and HC groups are due to discriminated strain compositions. For example, Prevotella copri is mainly composed of P. copri ASM1680343v1 and P. copri ASM345920v1 in the HC group, but it is composed of P. copri ASM346549v1 and P. copri ASM347465v1 in the UN group. In addition, the UN-risk model constructed at the strain level demonstrates higher accuracy (AUC = 0.810) than that at the species level (AUC = 0.743). With complex network analysis, we further discovered that the UN group had a more complex GM co-occurrence network, with more hub bacteria and a higher clustering coefficient but lower information transfer efficiencies. Moreover, the results at the strain level suggested the inaccurate and even false conclusions obtained from species level analysis. CONCLUSIONS Overall, this study highlights the importance of examining the GM at the strain level and investigating bacterial co-occurrence networks to advance our knowledge of UN pathogenesis.
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Affiliation(s)
- Bingmei Chang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Wenjie Zhang
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Yinan Wang
- Peking University Shenzhen Hospital, Shenzhen, People's Republic of China
| | - Yuanzheng Zhang
- Shenzhen Byoryn Technology Co., Ltd, Shenzhen, People's Republic of China
| | - Shilin Zhong
- Peking University Shenzhen Hospital, Shenzhen, People's Republic of China
| | - Peng Gao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, People's Republic of China.
| | - Lili Wang
- Department of Anesthesiology, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China.
| | - Zicheng Zhao
- Shenzhen Byoryn Technology Co., Ltd, Shenzhen, People's Republic of China.
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21
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Yao R, Ai B, Wang Z, Shen B, Xue G, Yu D. Uncovering Microbial Composition of the Tissue Microenvironment in Bladder Cancer using RNA Sequencing Data. J Cancer 2024; 15:2431-2441. [PMID: 38495492 PMCID: PMC10937280 DOI: 10.7150/jca.93055] [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: 12/08/2023] [Accepted: 01/27/2024] [Indexed: 03/19/2024] Open
Abstract
Purpose: Bladder cancer (BC) is one of the top 10 common tumors in the world. It has been reported that microbiota can colonize tissues and play important roles in tumorigenesis and progression. However, the current understanding of microorganisms in the BC tissue microenvironment remains unclear. Methods: In this study, we integrated the RNA-seq data of 479 BC tissue samples from seven datasets combined with a range of bioinformatics tools to explore the landscape of microbiome in the BC tissue microenvironment. Results: The pan-microbiome was estimated to surpass 1,400 genera. A total of seven core microbiota (Bacillus, Corynebacterium, Cutibacterium, Escherichia, Halomonas, Pasteurella, and Streptomyces) were identified. Among them, Bacillus was widely distributed in all datasets with a high relative abundance (10.11% of all samples on average). Moreover, some biological factors, including tissue source and tumor grade, were found significant effects on the microbial composition of the bladder tissue. Pseudomonas, Porphyrobacter, and Acinetobacter were enriched in tumor tissues, while Mycolicibacterium and Streptomyces were enriched in patients who showed durable response to BCG therapy. In addition, we established microbial co-occurrence networks and found that the BCG therapy may attenuate the microbiological interactions. Conclusions: This study clearly provided a microbial landscape of the BC tissue microenvironment, which was important for exploring the interactions between microorganisms and BC tissues. The identified specific taxa might be potential biomarkers for BC.
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Affiliation(s)
- Ruiqian Yao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Department of Medical Genetics, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
| | - Bin Ai
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Zeyi Wang
- Department of Urology, Huadong Hospital, Fudan University, Shanghai, China
| | - Bing Shen
- Department of Urology, Shanghai General Hospital Affiliated to Nanjing Medical University, Shanghai, 200080, China
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China
| | - Geng Xue
- Department of Medical Genetics, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
| | - Dong Yu
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
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22
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Wang X, Li J, Zheng J, Zhao L, Ruan C, Zhang D, Pan X. Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169976. [PMID: 38199380 DOI: 10.1016/j.scitotenv.2024.169976] [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: 11/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.
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Affiliation(s)
- Xiaonan Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Hangzhou 310015, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou 221116, China; Shaoxing Research Institute of Zhejiang University of Technology, Shaoxing 312000, China
| | - Jiahao Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jieyan Zheng
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lanxin Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenghao Ruan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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Ren A, Yao M, Fang J, Dai Z, Li X, van der Meer W, Medema G, Rose JB, Liu G. Bacterial communities of planktonic bacteria and mature biofilm in service lines and premise plumbing of a Megacity: Composition, Diversity, and influencing factors. ENVIRONMENT INTERNATIONAL 2024; 185:108538. [PMID: 38422875 DOI: 10.1016/j.envint.2024.108538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Although simulated studies have provided valuable knowledge regarding the communities of planktonic bacteria and biofilms, the lack of systematic field studies have hampered the understanding of microbiology in real-world service lines and premise plumbing. In this study, the bacterial communities of water and biofilm were explored, with a special focus on the lifetime development of biofilm communities and their key influencing factors. The 16S rRNA gene sequencing results showed that both the planktonic bacteria and biofilm were dominated by Proteobacteria. Among the 15,084 observed amplicon sequence variants (ASVs), the 33 core ASVs covered 72.8 %, while the 12 shared core ASVs accounted for 62.2 % of the total sequences. Remarkably, it was found that the species richness and diversity of biofilm communities correlated with pipe age. The relative abundance of ASV2 (f_Sphingomonadaceae) was lower for pipe ages 40-50 years (7.9 %) than for pipe ages 10-20 years (59.3 %), while the relative abundance of ASV10 (f_Hyphomonadaceae) was higher for pipe ages 40-50 years (19.5 %) than its presence at pipe ages 20-30 years (1.9 %). The community of the premise plumbing biofilm had significantly higher species richness and diversity than that of the service line, while the steel-plastics composite pipe interior lined with polyethylene (S-PE) harbored significantly more diverse biofilm than the galvanized steel pipes (S-Zn). Interestingly, S-PE was enriched with ASV27 (g_Mycobacterium), while S-Zn pipes were enriched with ASV13 (g_Pseudomonas). Moreover, the network analysis showed that five rare ASVs, not core ASVs, were keystone members in biofilm communities, indicating the importance of rare members in the function and stability of biofilm communities. This manuscript provides novel insights into real-world service lines and premise plumbing microbiology, regarding lifetime dynamics (pipe age 10-50 years), and the influences of pipe types (premise plumbing vs. service line) and pipe materials (S-Zn vs. S-PE).
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Affiliation(s)
- Anran Ren
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands; University of Chinese Academy of Sciences, Beijing, China
| | - Mingchen Yao
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands; University of Chinese Academy of Sciences, Beijing, China
| | - Jiaxing Fang
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Science and Technology, University of Twente, P.O. Box 217, 7500AE Enschede, The Netherlands
| | - Zihan Dai
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Xiaoming Li
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Walter van der Meer
- Science and Technology, University of Twente, P.O. Box 217, 7500AE Enschede, The Netherlands; Oasen Drinkwater, PO Box 122, 2800 AC, Gouda, The Netherlands
| | - Gertjan Medema
- Oasen Drinkwater, PO Box 122, 2800 AC, Gouda, The Netherlands; KWR Watercycle Research Institute, P.O. Box 1072, 3430 BB Nieuwegein, The Netherlands; Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
| | - Gang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands; University of Chinese Academy of Sciences, Beijing, China.
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24
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Khatri-Chhetri U, Banerjee S, Thompson KA, Quideau SA, Boyce MS, Bork EW, Carlyle CN. Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169353. [PMID: 38104847 DOI: 10.1016/j.scitotenv.2023.169353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.
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Affiliation(s)
- Upama Khatri-Chhetri
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Karen A Thompson
- Trent School of Environment, Trent University, Peterborough, ON K9L 0G2, Canada
| | - Sylvie A Quideau
- Department of Renewable Resources, Earth Science Building University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Mark S Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Edward W Bork
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Cameron N Carlyle
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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25
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Liao L, Yu D, Xu L, Hu Q, Liang T, Chen L, Zhu Q, Liu S, Zhong A. Submersed macrophytes Vallisneria natans and Vallisneria spinulosa improve water quality and affect microbial communities in sediment and water columns. Heliyon 2024; 10:e25942. [PMID: 38371958 PMCID: PMC10873746 DOI: 10.1016/j.heliyon.2024.e25942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024] Open
Abstract
Healthy aquatic ecosystems are essential for human beings. However, anthropogenic activities severely worsen water quality. In this study, using assembling mesocosms, we developed an efficient and easy-to-handle method to monitor the water quality by measuring the electrical conductivity (EC) of water. Our data demonstrate that the growth of two submersed macrophytes, Vallisnerianatans and Vallisneria spinulosa, improves water quality by decreasing EC. Furthermore, using high-throughput DNA sequencing, we analyzed the microbial community abundance and structure in sediment and water columns with or without plant growth. We generated 33,775 amplicon sequence variants from 69 samples of four sediment groups (BkM, CtM, VnR, and VsR) and three water column sample groups (CtW, VnW, and VsW). The results show that the relative abundance of bacteria was higher in the sediment than in the water column. Moreover, the diversity and composition of microbiomes were altered by Vallisneria spp. growth, and the α-diversity of the microbial communities decreased due to submersed macrophytes in both the sediment and water columns. The β-diversity of the microbial communities also varied significantly with or without Vallisneria spp. growth for both the sediment and water columns.
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Affiliation(s)
| | | | - Lei Xu
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
| | - Qian Hu
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
| | - Tongjun Liang
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
| | - Ludan Chen
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
| | - Qiuping Zhu
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
| | - Songping Liu
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
| | - Aiwen Zhong
- Lushan Botanical Garden, Chinese Academy of Science, Jiujiang, 332900, Jiangxi, China
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26
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Yang M, Zhao L, Yu X, Shu W, Cao F, Liu Q, Liu M, Wang J, Jiang Y. Microbial community structure and co-occurrence network stability in seawater and microplastic biofilms under prometryn pollution in marine ecosystems. MARINE POLLUTION BULLETIN 2024; 199:115960. [PMID: 38159383 DOI: 10.1016/j.marpolbul.2023.115960] [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: 10/06/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Prometryn has been extensively detected in marine environment because of its widespread usage in agriculture and aquaculture and has been concerns since its serious effects on aquatic organisms. However, its impact on the microbial community in the marine ecosystem including seawater and biofilm is still unclear. Therefore, a short-term indoor microcosm experiment of prometryn exposure was conducted. This study found that prometryn had a more significant impact on the structure and stability of the microbial community in seawater compared to microplastic biofilms. Additionally, we observed that the assembly of the microbial community in biofilms was more affected by stochastic processes than in seawater under the exposure of prometryn. Our study provided evidence for the increasing impact of the microbial communities under the stress of prometryn and microplastics.
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Affiliation(s)
- Mengyao Yang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lingchao Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wangxinze Shu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jun Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Wang Y, Wang B, Chen J, Sun L, Hou Y, Wang Y, Wang J, Gan J, Barmukh R, Li S, Fan Z, Bao P, Cao B, Cai C, Jing X, Singh BK, Varshney RK, Zhao H. Dynamics of rhizosphere microbial structure and function associated with the biennial bearing of moso bamboo. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119977. [PMID: 38160549 DOI: 10.1016/j.jenvman.2023.119977] [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: 08/27/2023] [Revised: 12/10/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Moso bamboo (Phyllostachys edulis) is a valuable nontimber forestry product with a biennial cycle, producing abundant bamboo shoots within one year (on-year) and few shoots within the following year (off-year). Moso bamboo plants undergo clonal reproduction, resulting in similar genetic backgrounds. However, the number of moso bamboo shoots produced each year varies. Despite this variation, the impact of soil nutrients and the root microbiome on the biennial bearing of moso bamboo is poorly understood. We collected 139 soil samples and determined 14 major physicochemical properties of the rhizosphere, rhizoplane, and bulk soil in different seasons (i.e., the growing and deciduous seasons) and different years (i.e., on- and off-years). Based on 16S rRNA and metagenomic sequencing, major variations were found in the rhizospheric microbial composition during different seasons and years in the moso bamboo forest. Environmental driver analysis revealed that essential nutrients (i.e., SOC, TOC, TN, P, and NH4+) were the main drivers of the soil microbial community composition and were correlated with the on- and off-year cycles. Moreover, 19 MAGs were identified as important biomarkers that could distinguish on- and off-years. We found that both season and year influenced both the microbial community structure and functional pathways through the biosynthesis of nutrients that potentially interact with the moso bamboo growth rhythm, especially the on-year root-associated microbiome, which had a greater abundance of specific nutrients such as gibberellins and vitamin B6. This work provides a dynamic perspective of the differential responses of various on- and off-year microbial communities and enhances our understanding of bamboo soil microbiome biodiversity and stability.
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Affiliation(s)
- Yu Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | | | - Jianwei Chen
- BGI Research, Qingdao 266555, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lei Sun
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Yinguang Hou
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | | | - Jiongliang Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Huangpu District, Guangzhou 510530, China
| | - Junwei Gan
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Rutwik Barmukh
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Shanying Li
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Zeyu Fan
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Pengfei Bao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Bingchen Cao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Chunju Cai
- Changning Bamboo Forest Ecosystem National Research Station, Yibin, Sichuan 644300, China
| | - Xiong Jing
- National Agricultural Exhibition Center/China Agricultural Museum, Beijing 100125, China
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Hawkesbury Institute for the Environment Western Sydney University, Penrith, NSW 2751, Australia
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia.
| | - Hansheng Zhao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China.
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Honjo M, Suzuki K, Katai J, Tashiro Y, Aoyagi T, Hori T, Okada T, Saito Y, Futamata H. Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity. Microbes Environ 2024; 39:ME23091. [PMID: 38538313 PMCID: PMC10982111 DOI: 10.1264/jsme2.me23091] [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: 11/09/2023] [Accepted: 12/19/2023] [Indexed: 04/04/2024] Open
Abstract
A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective. A bacterial community, formed by batch transferred cultures supplied with phenol as the sole carbon and energy source and paddy soil as the inoculum, was analyzed using a principal coordinate ana-lysis (PCoA), mathematical models, and quantitative parameters defined as growth activity, community-changing activity, community-forming activity, vulnerable force, and resilience force depending on changes in the abundance of operational taxonomic units (OTUs) using 16S rRNA gene amplicon sequences. PCoA showed succession states until the 3rd transferred cultures and stable states from the 5th to 10th transferred cultures. Quantitative parameters indicated that the bacterial community was dynamic irrespective of the succession and stable states. Three activities fluctuated under stable states. Vulnerable and resilience forces were detected under the succession and stable states, respectively. Mathematical models indicated the construction of metabolic networks, suggesting the stabilizing mechanism of the community structure. Thirteen OTUs coexisted during stable states, and were recognized as core OTUs consisting of majorities, middle-class, and minorities. The abundance of the middle-class changed, whereas that of the others did not, which indicated that core OTUs maintained metabolic networks. Some extremely low abundance OTUs were consistently exchanged, suggesting a role for scavengers. These results indicate that stable states were formed by dynamic metabolic networks with members functioning to achieve robustness and plasticity.
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Affiliation(s)
- Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Hamamatsu 432–8011, Japan
| | - Kenshi Suzuki
- Microbial Ecotechnology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 111 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Junya Katai
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, 432–8011, Japan
| | - Yosuke Tashiro
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Hamamatsu 432–8011, Japan
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, 432–8011, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1 Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1 Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Takashi Okada
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606–8507, Japan
| | - Yasuhisa Saito
- Department of Mathematics, Shimane University, Matsue, 690–8504, Japan
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Hamamatsu 432–8011, Japan
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, 432–8011, Japan
- Research Institution of Green Science and Technology, Shizuoka University, Shizuoka 422–8529, Japan
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Chalifour BN, Trifonova DI, Holzhausen EA, Bailey MJ, Schmidt KA, Babaei M, Mokhtari P, Goran MI, Alderete TL. Characterizing alterations in the gut microbiota following postpartum weight change. mSystems 2023; 8:e0080823. [PMID: 37905810 PMCID: PMC10734492 DOI: 10.1128/msystems.00808-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Previous research has reported differences in the gut microbiome associated with varying body compositions. More specifically, within populations of mothers, the focus has been on the impact of gestational weight gain. This is the first study to examine postpartum weight change and its association with changes in the gut microbiome, similarly, it is the first to use a Latina cohort to do so. The results support the idea that weight gain may be an important factor in reducing gut microbiome network connectivity, diversity, and changing abundances of specific microbial taxa, all measures thought to impact host health. These results suggest that weight gain dynamically alters mothers' gut microbial communities in the first 6 months postpartum, with comparatively little change in mothers who lost weight; further research is needed to examine the health consequences of such changes.
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Affiliation(s)
- Bridget N. Chalifour
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Diana I. Trifonova
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Elizabeth A. Holzhausen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Maximilian J. Bailey
- Stanford University School of Medicine, Leland Stanford Junior University, Stanford, California, USA
| | - Kelsey A. Schmidt
- Children’s Hospital Los Angeles, University of Southern California, Los Angeles, California, USA
| | - Mahsa Babaei
- Children’s Hospital Los Angeles, University of Southern California, Los Angeles, California, USA
| | - Pari Mokhtari
- Children’s Hospital Los Angeles, University of Southern California, Los Angeles, California, USA
| | - Michael I. Goran
- Children’s Hospital Los Angeles, University of Southern California, Los Angeles, California, USA
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, USA
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Sun D, Herath J, Zhou S, Ellepola G, Meegaskumbura M. Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts. ISME COMMUNICATIONS 2023; 3:123. [PMID: 37993728 PMCID: PMC10665332 DOI: 10.1038/s43705-023-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.
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Affiliation(s)
- Dan Sun
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Jayampathi Herath
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- School of Biomedical Sciences, International Institute of Health Sciences (IIHS), No 704 Negombo Rd, Welisara, 71722, Sri Lanka
| | - Shipeng Zhou
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, KY20400, Sri Lanka
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China.
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Niu Y, An Z, Gao D, Chen F, Zhou J, Liu B, Qi L, Wu L, Lin Z, Yin G, Liang X, Dong H, Liu M, Hou L, Zheng Y. Tidal dynamics regulates potential coupling of carbon‑nitrogen‑sulfur cycling microbes in intertidal flats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165663. [PMID: 37474052 DOI: 10.1016/j.scitotenv.2023.165663] [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: 05/05/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.
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Affiliation(s)
- Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, China
| | - Zhirui An
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Zhuke Lin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China.
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Mateos-Hernández L, Maitre A, Abuin-Denis L, Obregon D, Martin E, Luis P, Maye J, Wu-Chuang A, Valiente Moro C, Cabezas-Cruz A. Hierarchical shift of the Aedes albopictus microbiota caused by antimicrobiota vaccine increases fecundity and egg-hatching rate in female mosquitoes. FEMS Microbiol Ecol 2023; 99:fiad140. [PMID: 37898556 DOI: 10.1093/femsec/fiad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/16/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023] Open
Abstract
Recent studies show that mosquito-microbiota interactions affects vector competence and fitness. We investigated if host antibodies modifying microbiota impact mosquito physiology. We focused on three prevalent bacteria (Acinetobacter, Pantoea, and Chryseobacterium), originally isolated from the Asian tiger mosquito Aedes albopictus. Our goal was to assess the impact of host antibodies on mosquito microbiota and life traits. Female mosquitoes were fed with blood from rabbits immunized with each bacterium or a mock vaccine. We compared various factors, including feeding behavior, survival rates, and reproductive success of the mosquitoes. Interestingly, mosquitoes fed with blood from a Chryseobacterium-immunized rabbit showed a significant increase in fecundity and egg-hatching rate. This outcome correlated with a decrease in the abundance of Chryseobacterium within the mosquito microbiota. While no significant changes were observed in the alpha and beta diversity indexes between the groups, our network analyses revealed an important finding. The antimicrobiota vaccines had a considerable impact on the bacterial community assembly. They reduced network robustness, and altered the hierarchical organization of nodes in the networks. Our findings provide the basis for the rational design of antimicrobiota vaccines to reduce mosquito fitness and potentially induce infection-refractory states in the microbiota to block pathogen transmission.
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Affiliation(s)
- Lourdes Mateos-Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
| | - Apolline Maitre
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMETLRDE), Corte 20250, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte 20250, France
| | - Lianet Abuin-Denis
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, Havana 10600, Cuba
| | - Dasiel Obregon
- School of Environmental Sciences University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Edwige Martin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne 69622, France
| | - Patricia Luis
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne 69622, France
| | - Jennifer Maye
- SEPPIC Paris La Défense, La Garenne Colombes 92250, France
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
| | - Claire Valiente Moro
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne 69622, France
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
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Jiang H, Gao W, Lu Q, Wang S. Carbon/nitrogen flows and associated microbial communities in full-scale foodwaste treatment plants. BIORESOURCE TECHNOLOGY 2023; 388:129775. [PMID: 37722539 DOI: 10.1016/j.biortech.2023.129775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Microorganisms play key roles in the conversion of organic matter in foodwaste. However, both the microbially-mediated element (carbon/C and nitrogen/N) flows and associated microbial communities in foodwaste treatment plants (FWTPs) remain unclear. This study collected samples of different foodwaste treatment units from five full-scale FWTPs to analyze the C/N flows and microbial communities in foodwaste treatment processes. Results showed that 39.8-45.0% of organic carbon in foodwaste was converted into biogas. Hydrolytic acidogenic bacteria (e.g., Lactobacillus and Limosilactobacillus) and eukaryota (e.g., Cafeteriaceae, Saccharomycetales, and Agaricomycetes) were more abundant in feedstock and pretreatment units. Redundancy analyses showed that acidogens were major players in the transformation of foodwaste organic matter. Populations of W27 and Tepidanaerobacter were major contributors to the difference in conversion of C/N in these FWTPs. This study could support foodwaste treatment efficiencies improvement by providing insights into C/N flows and associated microbiota in FWTPs.
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Affiliation(s)
- Haihong Jiang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Weijun Gao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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Ni J, Ji J, Li YY, Kubota K. Propidium monoazide - polymerase chain reaction reveals viable microbial community shifts in anaerobic membrane bioreactors treating domestic sewage at low temperature. BIORESOURCE TECHNOLOGY 2023; 387:129564. [PMID: 37506934 DOI: 10.1016/j.biortech.2023.129564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
An anaerobic membrane bioreactor (AnMBR) treated domestic sewage at 15 °C under different hydraulic retention time (HRT) conditions (6, 12, 16, and 24 h). Propidium monoazide (PMA)-PCR excluded microorganisms without intact cell membranes, focusing on the viable microbial community in anaerobic digestion. The results showed that the 6-hour HRT had poor treatment performance: low chemical oxygen demand removal efficiency (below 80%) and high mean trans-membrane pressure and flux (15 kPa and 9.4 L/(m2 h)). Comparatively, PMA-PCR combined with next-generation sequencing improved the identification of microbial changes compared to conventional 16S rRNA gene sequencing. HRT influenced microorganisms in the hydrolysis and acid-production stages, including carbohydrate-degrading bacteria such as Bifidobacterium and Prevotella 1. Remarkably, a comparison with an AnMBR at 25 °C showed Proteobacteria to be the main cause of membrane fouling in the low-temperature AnMBR, with most operational taxonomic units negatively correlated with HRT and solids retention time.
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Affiliation(s)
- Jialing Ni
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan; Department of Frontier Sciences for Advanced Environment, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan
| | - Jiayuan Ji
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan; Institute for Future Initiatives, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan; Department of Frontier Sciences for Advanced Environment, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan; Department of Frontier Sciences for Advanced Environment, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 Japan.
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Huang Q, Zhang H, Zhang L, Xu B. Bacterial microbiota in different types of processed meat products: diversity, adaptation, and co-occurrence. Crit Rev Food Sci Nutr 2023:1-16. [PMID: 37905560 DOI: 10.1080/10408398.2023.2272770] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
As a double-edged sword, some bacterial microbes can improve the quality and shelf life of meat products, but others mainly responsible for deterioration of the safety and quality of meat products. This review aims to present a landscape of the bacterial microbiota in different types of processed meat products. After demonstrating a panoramic view of the bacterial genera in meat products, the diversity of bacterial microbiota was evaluated in two dimensions, namely different types of processed meat products and different meats. Then, the influence of environmental factors on bacterial communities was evaluated according to the storage temperature, packaging conditions, and sterilization methods. Furthermore, microbes are not independent. To explore interactions among those genera, co-occurrence patterns were examined. In these respects, this review highlighted the recent advances in fundamental principles that underlie the environmental adaption tricks and why some species tend to occur together frequently, such as metabolic cross-feeding, co-aggregate at microscale, and the intercellular signaling system. Further investigations are required to unveil the underlying molecular mechanisms that govern microbial community systems, ultimately contributing to developing new strategies to harness beneficial microorganisms and control harmful microorganisms.
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Affiliation(s)
- Qianli Huang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Huijuan Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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Zhu S, Cai Y, Li Y, Xiong J, Lei Y, Sun Y. Effects of temporal and spatial scales on soil yeast communities in the peach orchard. Front Microbiol 2023; 14:1226142. [PMID: 37795290 PMCID: PMC10546340 DOI: 10.3389/fmicb.2023.1226142] [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: 05/20/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
Shihezi Reclamation Area is located at the southern edge of the Junggar Basin, with natural, soil, and climatic conditions unique to the production of peaches. In turn, peach orchards have accumulated rich microbial resources. As an important taxon of soil fungi, the diversity and community structure changes of yeast in the soil of peach orchards on spatial and temporal scales are still unknown. Here, we aimed to investigate the changes in yeast diversity and community structure in non-rhizosphere and rhizosphere soils of peach trees of different ages in the peach orchard and the factors affecting them, as well as the changes in the yeast co-occurrence network in the peach orchard at spatial and temporal scales. High-through put sequencing results showed that a total of 114 yeast genera were detected in all soil samples, belonging to Ascomycota (60 genera) and Basidiomycota (54 genera). The most dominant genus, Cryptococcus, was present in greater than 10% abundance in each sample. Overall, the differences in yeast diversity between non-rhizosphere and rhizosphere soil of peach trees at 3, 8 and 15 years were not significant. Principal coordinate analysis (PCoA) showed that differences in yeast community structure were more pronounced at the temporal scale compared to the spatial scale. The results of soil physical and chemical analysis showed that the 15-year-old peach rhizosphere soil had the lowest pH, while the OM, TN, and TP contents increased significantly. Redundancy analysis showed that soil pH and CO were key factors contributing to changes in soil yeast community structure in the peach orchard at both spatial and temporal scales. The results of co-occurrence network analysis showed that the peach orchard soil yeast network showed synergistic effects as a whole, and the degree of interactions and connection tightness of the 15-year-old peach orchard soil yeast network were significantly higher than the 3- and 8-year-old ones on the time scale. The results reveal the distribution pattern and mechanism of action of yeast communities in peach orchard soils, which can help to develop effective soil management strategies and improve the stability of soil microecology, thus promoting crop growth.
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Affiliation(s)
- ShanShan Zhu
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - YanLi Cai
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Jie Xiong
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - YongHui Lei
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - YanFei Sun
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
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Adejoro DO, Jones EE, Ridgway HJ, Mundy DC, Vanga BR, Bulman SR. Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure. Front Microbiol 2023; 14:1231832. [PMID: 37680529 PMCID: PMC10482235 DOI: 10.3389/fmicb.2023.1231832] [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: 05/31/2023] [Accepted: 07/26/2023] [Indexed: 09/09/2023] Open
Abstract
Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach is the investigation of disease escape plants, which remain healthy under high disease pressure, likely due to their microbiome function. This study explored the microbiome of grapevines with the disease escape phenotype. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was applied to trunk tissues of GTD escape and adjacent diseased vines. Our findings showed that the GTD escape vines had a significantly different microbiome compared with diseased vines. The GTD escape vines consistently harbored a higher relative abundance of the bacterial taxa Pseudomonas and Hymenobacter. Among fungi, Aureobasidium and Rhodotorula were differentially associated with GTD escape vines, while the GTD pathogen, Eutypa, was associated with the diseased vines. This is the first report of the link between the GTD escape phenotype and the grapevine microbiome.
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Affiliation(s)
- Damola O. Adejoro
- Department of Pest-Management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
| | - E. Eirian Jones
- Department of Pest-Management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
| | - Hayley J. Ridgway
- Department of Pest-Management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, Canterbury, New Zealand
| | - Dion C. Mundy
- The New Zealand Institute for Plant and Food Research Limited, Blenheim, Marlborough, New Zealand
| | - Bhanupratap R. Vanga
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, Canterbury, New Zealand
- Grapevine Improvement Laboratory, Bragato Research Institute, Lincoln, Canterbury, New Zealand
| | - Simon R. Bulman
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, Canterbury, New Zealand
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Mehta SD, Agingu W, Zulaika G, Nyothach E, Bhaumik R, Green SJ, van Eijk AM, Otieno FO, Phillips-Howard PA, Schneider J. Vaginal Microbial Network Analysis Reveals Novel Taxa Relationships among Adolescent and Young Women with Incident Sexually Transmitted Infection Compared with Those Remaining Persistently Negative over a 30-Month Period. Microorganisms 2023; 11:2035. [PMID: 37630595 PMCID: PMC10459434 DOI: 10.3390/microorganisms11082035] [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: 06/07/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A non-optimal vaginal microbiome (VMB) is typically diverse with a paucity of Lactobacillus crispatus and is often associated with bacterial vaginosis (BV) and sexually transmitted infections (STIs). Although compositional characterization of the VMB is well-characterized, especially for BV, knowledge remains limited on how different groups of bacteria relate to incident STIs, especially among adolescents. In this study, we compared the VMB (measured via 16S ribosomal RNA gene amplicon sequencing) of Kenyan secondary school girls with incident STIs (composite of chlamydia, gonorrhea, and trichomoniasis) to those who remained persistently negative for STIs and BV over 30 months of follow-up. We applied microbial network analysis to identify key taxa (i.e., those with the greatest connectedness in terms of linkages to other taxa), as measured by betweenness and eigenvector centralities, and sub-groups of clustered taxa. VMB networks of those who remained persistently negative reflected greater connectedness compared to the VMB from participants with STI. Taxa with the highest centralities were not correlated with relative abundance and differed between those with and without STI. Subject-level analyses indicated that sociodemographic (e.g., age and socioeconomic status) and behavioral (e.g., sexual activity) factors contribute to microbial network structure and may be of relevance when designing interventions to improve VMB health.
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Affiliation(s)
- Supriya D. Mehta
- Division of Epidemiology & Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL 60612, USA
- Division of Infectious Disease Medicine, College of Medicine, Rush University, Chicago, IL 60612, USA
| | - Walter Agingu
- Nyanza Reproductive Health Society, Kisumu P.O. Box 1764, Kenya
| | - Garazi Zulaika
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK (P.A.P.-H.)
| | | | - Runa Bhaumik
- Division of Epidemiology & Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- Division of Infectious Disease Medicine, College of Medicine, Rush University, Chicago, IL 60612, USA
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL 60612, USA
| | - Anna Maria van Eijk
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK (P.A.P.-H.)
| | | | | | - John Schneider
- Departments of Medicine and Public Health Sciences, School of Medicine, University of Chicago, Chicago, IL 60637, USA;
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Liu Z, Peng T, Ma S, Qi C, Song Y, Zhang C, Li K, Gao N, Pu M, Wang X, Bi Y, Na X. Potential benefits and risks of solar photovoltaic power plants on arid and semi-arid ecosystems: an assessment of soil microbial and plant communities. Front Microbiol 2023; 14:1190650. [PMID: 37588884 PMCID: PMC10427150 DOI: 10.3389/fmicb.2023.1190650] [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: 03/21/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Exponential increase in photovoltaic installations arouses concerns regarding the impacts of large-scale solar power plants on dryland ecosystems. While the effects of photovoltaic panels on soil moisture content and plant biomass in arid ecosystems have been recognized, little is known about their influence on soil microbial communities. Here, we employed a combination of quantitative PCR, high-throughput sequencing, and soil property analysis to investigate the responses of soil microbial communities to solar panel installation. We also report on the responses of plant communities within the same solar farm. Our findings showed that soil microbial communities responded differently to the shading and precipitation-alternation effects of the photovoltaic panels in an arid ecosystem. By redirecting rainwater to the lower side, photovoltaic panels stimulated vegetation biomass and soil total organic carbon content in the middle and in front of the panels, positively contributing to carbon storage. The shade provided by the panels promoted the co-occurrence of soil microbes but inhibited the abundance of 16S rRNA gene in the soil. Increase in precipitation reduced 18S rRNA gene abundance, whereas decrease in precipitation led to decline in plant aboveground biomass, soil prokaryotic community alpha diversity, and dehydrogenase activity under the panels. These findings highlight the crucial role of precipitation in maintaining plant and soil microbial diversities in dryland ecosystems and are essential for estimating the potential risks of large-scale solar power plants on local and global climate change in the long term.
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Affiliation(s)
- Ziyu Liu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tong Peng
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shaolan Ma
- No. 1 Middle School of Penyang, Guyuan, China
| | - Chang Qi
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yanfang Song
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Chuanji Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kaile Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Na Gao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Meiyun Pu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yurong Bi
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaofan Na
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
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Yao S, Jin T, Zhang L, Zhang Y, Chen R, Wang Q, Lv M, Hu C, Ma T, Xia W. N/S element transformation modulating lithospheric microbial communities by single-species manipulation. MICROBIOME 2023; 11:107. [PMID: 37194043 DOI: 10.1186/s40168-023-01553-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation. RESULTS Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil. CONCLUSIONS The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.
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Affiliation(s)
- Shun Yao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Tianzhi Jin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Lu Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Yong Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Qian Wang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Mingjie Lv
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Chuxiao Hu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China.
| | - Wenjie Xia
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China.
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Huang Q, Liu Y, Ranjan Dhar B. Boosting resilience of microbial electrolysis cell-assisted anaerobic digestion of blackwater with granular activated carbon amendment. BIORESOURCE TECHNOLOGY 2023; 381:129136. [PMID: 37169203 DOI: 10.1016/j.biortech.2023.129136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Poor hydrolysis and methanogenesis efficiencies remain the main challenges for blackwater anaerobic digestion. This study investigated the performance of a granular activated carbon (GAC) amended microbial electrolysis cell-assisted anaerobic digester (MEC-AD) treating blackwater. Due to hydrolysis limitation, both MEC-AD and control reactors experienced performance declines as the organic loading rate increased from 3.0 to 4.5 g COD/L-d. Then, adding GAC without mixing formed GAC-sludge aggregates that improved methane yield to 38.3% and 32.3% in the MEC-AD and control reactor, respectively, and enhanced hydrolysis efficiency. The amended MEC-AD also successfully overcame the performance deterioration due to a temperature drop. Biomarker identification revealed the crucial roles of GAC biofilms and settled sludge in promoting methanogenesis and hydrolysis, respectively. This study demonstrated the GAC addition and the electrochemical environment could have a reciprocal influence, leading to more robust syntrophic microbial interactions, which could guide the future application of conductive materials in MEC-AD systems.
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Affiliation(s)
- Qi Huang
- Department of Civil and Environmental Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB, T6G 1H9, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB, T6G 1H9, Canada.
| | - Bipro Ranjan Dhar
- Department of Civil and Environmental Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB, T6G 1H9, Canada
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Ding W, Li J, Hu B, Chu G, Tao R. Response of abundance, diversity, and network of rhizosphere fungal community to monoculture of cut chrysanthemum. Appl Microbiol Biotechnol 2023; 107:3673-3685. [PMID: 37115253 DOI: 10.1007/s00253-023-12542-z] [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: 12/18/2022] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The effects of different monoculture years on rhizosphere fungal communities (abundance, diversity, structure, and cooccurrence network) of cut chrysanthemum were determined. Three different monoculture years were (i) planting for only 1 year (Y1), (ii) continuous monoculture for 6 years (Y6), and (iii) continuous monoculture for 12 years (Y12). Compared to the Y1 treatment, the Y12 treatment significantly decreased the rhizosphere fungal gene copy numbers but increased the potential pathogen Fusarium oxysporum (P < 0.05). Both the Y6 and Y12 treatments significantly increased fungal diversity (Shannon and Simpson indices), but Y6 had great potential to enhance fungal richness (Chao1 index) relative to the Y12 treatment. Monoculture treatments decreased the relative abundance of Ascomycota but increased that of Mortierellomycota. Four ecological clusters (Modules 0, 3, 4, and 9) were observed in the fungal cooccurrence network across the Y1, Y6, and Y12 treatments, and only Module 0 was significantly enriched in the Y12 treatment and associated with soil properties (P < 0.05). RDA (redundancy analysis) and Mantel analysis showed that soil pH and soil nutrients (organic carbon, total nitrogen, and available phosphorus) were the key factors affecting fungal communities during monoculture of cut chrysanthemum. Overall, the changes in soil properties were responsible for shaping rhizospheric soil fungal communities in long-term rather than short-term monoculture systems. KEY POINTS: • Both short- and long-term monocultures reshaped the soil fungal community structure. • Long-term monoculture enhanced the network complexity of the fungal community. • Soil pH, C and N levels mainly drove modularization in the fungal community network.
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Affiliation(s)
- Wangying Ding
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Jun Li
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Baowei Hu
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Guixin Chu
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China
| | - Rui Tao
- Department of Environmental Science and Engineering, School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, People's Republic of China.
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43
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Xing W, Gai X, Ju F, Chen G. Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160273. [PMID: 36460109 DOI: 10.1016/j.scitotenv.2022.160273] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.
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Affiliation(s)
- Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, PR China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China.
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Yu X, Gao X, Shang L, Wang X, Jiao Y, Zhang XH, Shi X. Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160321. [PMID: 36414066 DOI: 10.1016/j.scitotenv.2022.160321] [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: 09/02/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.
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Affiliation(s)
- Xiaowen Yu
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xueyu Gao
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Li Shang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiaoyu Wang
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Yutian Jiao
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China.
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Thapa A, Park JH, Shin SG, Jo HM, Kim MS, Park Y, Han U, Cho SK. Elucidation of microbial interactions, dynamics, and keystone microbes in high pressure anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159718. [PMID: 36302429 DOI: 10.1016/j.scitotenv.2022.159718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
High-pressure anaerobic digestion (HPAD) is a promising technology for producing biogas enriched with high methane content in a single-step process. To enhance HPAD performance, a comprehensive understanding of microbial community dynamics and their interactions is essential. For this, mesophilic batch high-pressurized anaerobic reactors were operated under 3 bars (H3) and 6 bars (H6). The experimental results showed that the effect of high-pressure (up to 6 bar) on acidification was negligible while methanogenesis was significantly delayed. Microbial analysis showed the predominance of Defluviitoga affiliated with the phylum Thermotogae and the reduction of Thiopseudomonas under high-pressure conditions. In addition, the microbial cluster pattern in H3 and H6 was significantly different compared to the CR, indicating a clear shift in microbial community structure. Moreover, Methanobacterium, Methanomicrobiaceae, Alkaliphilus, and Petrimonas were strongly correlated in network analysis, and they could be identified as keystone microbes in the HPAD reactor.
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Affiliation(s)
- Ajay Thapa
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Jeong-Hoon Park
- Sustainable Technology and Wellness R&D Group, Korea Institute of Industrial Technology (KITECH), Jeju-si, Republic of Korea
| | - Seung Gu Shin
- Department of Energy System Engineering, Gyeongang National University, Gyeongnam 52725, Republic of Korea
| | - Hong-Mok Jo
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Min-Sang Kim
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Yeongmi Park
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Uijeong Han
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Si-Kyung Cho
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea.
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Abiriga D, Jenkins A, Klempe H. Microbial assembly and co-occurrence network in an aquifer under press perturbation. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01698-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Thousands of aquifers worldwide have been polluted by leachate from landfills and many more remained threatened. Microbial communities from these environments play a crucial role in mediating biodegradation and maintaining the biogeochemical cycles, but their co-occurrence and assembly mechanism have not been investigated.
Method
Here, we coupled network analysis with multivariate statistics to assess the relative importance of deterministic versus stochastic microbial assembly in an aquifer undergoing intrinsic remediation, using 16S metabarcoding data generated through Illumina MiSeq sequencing of the archaeal/bacterial V3–V4 hypervariable region.
Results
Results show that both the aquifer-wide and localised community co-occurrences deviate from expectations under null models, indicating the predominance of deterministic processes in shaping the microbial communities. Further, the amount of variation in the microbial community explained by the measured environmental variables was 55.3%, which illustrates the importance of causal factors in forming the structure of microbial communities in the aquifer. Based on the network topology, several putative keystone taxa were identified which varied remarkably among the wells in terms of their number and composition. They included Nitrospira, Nitrosomonadaceae, Patulibacter, Legionella, uncharacterised Chloroflexi, Vicinamibacteriales, Neisseriaceae, Gemmatimonadaceae, and Steroidobacteraceae. The putative keystone taxa may be providing crucial functions in the aquifer ranging from nitrogen cycling by Nitrospira, Nitrosomonadaceae, and Steroidobacteraceae, to phosphorous bioaccumulation by Gemmatimonadaceae.
Conclusion
Collectively, the findings provide answers to fundamental ecological questions which improve our understanding of the microbial ecology of landfill leachate plumes, an ecosystem that remains understudied.
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Miao X, Han X, Liu C, Bai X. Intrinsic chlorine resistance of bacteria modulated by glutaminyl-tRNA biosynthesis in drinking water supply systems. CHEMOSPHERE 2022; 308:136322. [PMID: 36084827 DOI: 10.1016/j.chemosphere.2022.136322] [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: 06/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The existence of chlorine-resistant bacteria (CRB) in drinking water supply systems (DWSSs) results in significant challenges to the biological security of drinking water. However, little is known about the intrinsic chlorine-resistant molecular metabolic mechanism of bacteria in DWSSs. This research explored the microbial interactions and the key metabolic pathways that modulate the chlorine resistance of bacteria in full-scale chloraminated DWSSs. The dominant CRB, including Bdellovibrio, Bradyrhizobium, Peredibacter, Sphingomonas, and Hydrogenophaga, strongly interacted with each other to maintain basic metabolism. A total of 4.21% of the bacterial metabolic pathways were key and specific to chlorine-resistant bacteria. Glutaminyl-tRNA biosynthesis was the dominant metabolic pathway of CRB in the target DWSSs. After chloramine disinfection, the relative abundance of glutamate-tRNA ligase (GlnRS) and the related orthologous genes increased by 10.11% and 14.58%, respectively. The inactivation rate of the GlnRS overexpression strain (81.40%) was lower than that of the wild-type strain (90.11%) after exposure to chloramine. Meanwhile, the growth rate of the GlnRS overexpression strain was higher than that of the wild-type strain. Glutaminyl-tRNA biosynthesis can enhance chlorine resistance in DWSSs.
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Affiliation(s)
- Xiaocao Miao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xue Han
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Chenxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Camara M, Filloux A. Supporting the strategic pillars of translational research in biofilms. NPJ Biofilms Microbiomes 2022; 8:90. [PMID: 36372799 PMCID: PMC9659558 DOI: 10.1038/s41522-022-00354-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/14/2022] Open
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Zhang L, Yuan Y, Zhang Y, Liu Y. Exploring key factors in anaerobic syntrophic interactions: Biomass activity, microbial community, and morphology. BIORESOURCE TECHNOLOGY 2022; 363:127852. [PMID: 36067891 DOI: 10.1016/j.biortech.2022.127852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The present work evaluated the impacts of microbial communities, biomass activity and sludge morphology on anaerobic syntrophic reactions. Experiments were conducted using mature floc sludge and granular sludge under different food/microbes ratios, and with different sludge types (floc sludge, concentrated floc sludge and granular sludge) and sludge morphology (granules, vortexed granules, and granules with different particle sizes). The results show that the intact granules achieved the most effective syntrophic reaction among all sludge types. The granule structure facilitated the enrichment of syntrophic acetate oxidation bacteria (g_Syner-01 and g_Mesotoga) and methanogens, which corresponds to their superior specific methanogenic activity and high production of communication compounds. Despite the high diffusion and substrate uptake capacities, the disintegrated granules had low H2 consumption rates, which led to poor syntrophic activities. The results underline the importance of sludge spatial structures in promoting excellent syntrophic activities and the development of diverse microbial communities.
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Affiliation(s)
- Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yiyang Yuan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yingdi Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
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Wang M, Tu Q. Effective data filtering is prerequisite for robust microbial association network construction. Front Microbiol 2022; 13:1016947. [PMID: 36267180 PMCID: PMC9577025 DOI: 10.3389/fmicb.2022.1016947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.
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Affiliation(s)
- Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Xiamen University, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
- *Correspondence: Qichao Tu,
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