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Liu Z, Guo Z, Zhou J, Guo X, Chen Y. Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability. Comput Struct Biotechnol J 2024; 23:2717-2726. [PMID: 39040687 PMCID: PMC11260581 DOI: 10.1016/j.csbj.2024.05.047] [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: 12/24/2023] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/24/2024] Open
Abstract
Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.
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Affiliation(s)
- Zhidong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuecheng Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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2
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Zhou J, Liu J, Wang D, Ruan Y, Gong S, Gou J, Zou X. Fungal communities are more sensitive to mildew than bacterial communities during tobacco storage processes. Appl Microbiol Biotechnol 2024; 108:88. [PMID: 38194134 DOI: 10.1007/s00253-023-12882-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]
Abstract
Mildew poses a significant threat to tobacco production; however, there is limited information on the structure of the abundant and rare microbial subcommunities in moldy tobacco leaves. In this study, we employed high-throughput sequencing technology to discern the disparities in the composition, diversity, and co-occurrence patterns of abundant and rare fungal and bacterial subcommunities between moldy and normal tobacco leaves collected from Guizhou, Shanghai, and Jilin provinces, China. Furthermore, we explored the correlation between microorganisms and metabolites by integrating the metabolic profiles of moldy and normal tobacco leaves. The results showed that the fungi are more sensitive to mildew than bacteria, and that the fungal abundant taxa exhibit greater resistance and environmental adaptability than the rare taxa. The loss of rare taxa results in irreversible changes in the diversity, richness, and composition of the fungal community. Moreover, rare fungal taxa and abundant bacterial taxa played crucial roles in maintaining the stability and functionality of the tobacco microecosystem. In moldy tobacco, however, the disappearance of rare taxa as key nodes resulted in reduced connectivity and stability within the fungal network. In addition, metabolomic analysis showed that the contents of indoles, pyridines, polyketones, phenols, and peptides were significantly enriched in the moldy tobacco leaves, while the contents of amino acids, carbohydrates, lipids, and other compounds were significantly reduced in these leaves. Most metabolites showed negative correlations with Dothideomycetes, Alphaproteobacteria, and Gammaproteobacteria, but showed positive correlations with Eurotiales and Bacilli. This study has demonstrated that abundant fungal taxa are the predominant biological agents responsible for tobacco mildew, while bacteria may indirectly contribute to this process through the production and degradation of metabolites. KEY POINTS: • Fungi exhibited greater sensitivity to mildew of tobacco leaf compared to bacteria • Rare fungal taxa underwent significant damage during the mildew process • Mildew may damage the defense system of the tobacco leaf microecosystem.
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Affiliation(s)
- Jiaxi Zhou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China
- Postdoctoral Research Workstation of China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jing Liu
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Dongfei Wang
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Yibin Ruan
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Shuang Gong
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jianyu Gou
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Xiao Zou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China.
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Lin L, Huang Y, Jia W, Zhou S, Gan C, Wu WM, Xu M. Microbiomes on microplastics versus natural microcarriers: Stability and transformation during aquatic travel from aquaculture ponds to adjacent stream. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135241. [PMID: 39032183 DOI: 10.1016/j.jhazmat.2024.135241] [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: 04/09/2024] [Revised: 07/01/2024] [Accepted: 07/16/2024] [Indexed: 07/22/2024]
Abstract
Microplastics (MPs) with different physical-chemical properties are considered as vectors for the propagation of microbes in aquatic environments. It remains unclear how plastic types impact on the plastisphere and whether different MPs spread microbes more rapidly than natural materials in microbes across distinct water bodies as proposed previously. We used in-situ incubation to investigate the microbes attached on MPs of polyethylene (PE), polypropylene (PP), and polyvinyl chloride (PVC), versus that on two natural microcarriers (quartz sands and bamboo) during the travel from aquaculture ponds with impacted by fish farming to adjacent freshwater stream. The results showed that the microbial communities on the carriers were shaped not only by environmental conditions, which were primary determinants but also by carrier types. All the tested plastics did not carry more microbes than the natural carriers during the journey. The biofilm community composition on PVC is distinct from that on PE and PP MPs and natural carriers. The plastisphere of PE and PP kept microbial proportions as natural materials did but PVC retained less than nature materials. Bamboo carried more potential pathogens than plastic polymers and quartz. The results indicated that the communities of plastisphere is polymer-type dependent, and, compared with the natural materials, MPs did not show enhanced propagation of microbes, including pathogens, cross distinct environments.
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Affiliation(s)
- Lizhou Lin
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Environmental Protection Key Laboratory of Microbiology and Regional Eco-Safety, Guangzhou 510070, China
| | - Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Environmental Protection Key Laboratory of Microbiology and Regional Eco-Safety, Guangzhou 510070, China
| | - Weibin Jia
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Environmental Protection Key Laboratory of Microbiology and Regional Eco-Safety, Guangzhou 510070, China
| | - Shaofeng Zhou
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Environmental Protection Key Laboratory of Microbiology and Regional Eco-Safety, Guangzhou 510070, China
| | - Cuifen Gan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Environmental Protection Key Laboratory of Microbiology and Regional Eco-Safety, Guangzhou 510070, China
| | - Wei-Min Wu
- Department of Civil and Environmental Engineering, William & Cloy Codiga Resource Recovery Center, Stanford University, Stanford, CA 94305, USA
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Environmental Protection Key Laboratory of Microbiology and Regional Eco-Safety, Guangzhou 510070, China.
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4
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Chen J, Zhuang J, Dai T, Zhang R, Zeng Y, Jiang B, Guo H, Guo X, Yang Y. Enhancing soil petrochemical contaminant remediation through nutrient addition and exogenous bacterial introduction. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135078. [PMID: 38964043 DOI: 10.1016/j.jhazmat.2024.135078] [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: 05/04/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/06/2024]
Abstract
Biostimulation (providing favorable environmental conditions for microbial growth) and bioaugmentation (introducing exogenous microorganisms) are effective approaches in the bioremediation of petroleum-contaminated soil. However, uncertainty remains in the effectiveness of these two approaches in practical application. In this study, we constructed mesocosms using petroleum hydrocarbon-contaminated soil. We compared the effects of adding nutrients, introducing exogenous bacterial degraders, and their combination on remediating petroleum contamination in the soil. Adding nutrients more effectively accelerated total petroleum hydrocarbon (TPH) degradation than other treatments in the initial 60 days' incubation. Despite both approaches stimulating bacterial richness, the community turnover caused by nutrient addition was gentler than bacterial degrader introduction. As TPH concentrations decreased, we observed a succession in microbial communities characterized by a decline in copiotrophic, fast-growing bacterial r-strategists with high rRNA operon (rrn) copy numbers. Ecological network analysis indicated that both nutrient addition and bacterial degrader introduction enhanced the complexity and stability of bacterial networks. Compared to the other treatment, the bacterial network with nutrient addition had more keystone species and a higher proportion of negative associations, factors that may enhance microbial community stability. Our study demonstrated that nutrient addition effectively regulates community succession and ecological interaction to accelerate the soil TPH degradation.
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Affiliation(s)
- Jiayu Chen
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jugui Zhuang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tianjiao Dai
- School of Environment, Tsinghua University, Beijing 100084, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China.
| | - Ruihuan Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yufei Zeng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Bo Jiang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Huaming Guo
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xue Guo
- School of Environment, Tsinghua University, Beijing 100084, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing 100084, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
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5
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Zhou M, Ma L, Wang Z, Li S, Cai Y, Li M, Zhang L, Wang C, Wu B, Yan Q, He Z, Shu L. Nano- and microplastics drive the dynamic equilibrium of amoeba-associated bacteria and antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134958. [PMID: 38905974 DOI: 10.1016/j.jhazmat.2024.134958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
As emerging pollutants, microplastics have become pervasive on a global scale, inflicting significant harm upon ecosystems. However, the impact of these microplastics on the symbiotic relationship between protists and bacteria remains poorly understood. In this study, we investigated the mechanisms through which nano- and microplastics of varying sizes and concentrations influence the amoeba-bacterial symbiotic system. The findings reveal that nano- and microplastics exert deleterious effects on the adaptability of the amoeba host, with the magnitude of these effects contingent upon particle size and concentration. Furthermore, nano- and microplastics disrupt the initial equilibrium in the symbiotic relationship between amoeba and bacteria, with nano-plastics demonstrating a reduced ability to colonize symbiotic bacteria within the amoeba host when compared to their microplastic counterparts. Moreover, nano- and microplastics enhance the relative abundance of antibiotic resistance genes and heavy metal resistance genes in the bacteria residing within the amoeba host, which undoubtedly increases the potential transmission risk of both human pathogens and resistance genes within the environment. In sum, the results presented herein provide a novel perspective and theoretical foundation for the study of interactions between microplastics and microbial symbiotic systems, along with the establishment of risk assessment systems for ecological environments and human health.
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Affiliation(s)
- Min Zhou
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lu Ma
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zihe Wang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Shicheng Li
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Yijun Cai
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Meicheng Li
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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6
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Mougi A. Ecosystem engineering and food web stability. Sci Rep 2024; 14:19400. [PMID: 39169231 PMCID: PMC11339392 DOI: 10.1038/s41598-024-70626-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: 02/12/2024] [Accepted: 08/19/2024] [Indexed: 08/23/2024] Open
Abstract
Ecosystem engineering, which involves organism-triggered physical modification of the environment, is a widespread phenomenon. Despite this, the role of engineering in ecological communities remains poorly understood. This study employs a food web model to uncover the key roles of ecosystem engineering in maintaining food webs. While engineers facilitating population growth and suppressing consumers' foraging activity can help maintain complex communities with diverse species, engineering effects that suppress population growth and facilitate consumers' foraging activity can largely destabilize community dynamics. Furthermore, in the middle levels of engineering-related species within a community, an increase in species richness can increase community stability, contrary to classical ecological prediction. The study findings suggest that ecosystem engineering can explain biodiversity persistence in nature, but it depends on the proportion of engineering-related species and how engineering affects organisms.
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Affiliation(s)
- Akihiko Mougi
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu-cho, Matsue, 690-8504, Japan.
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7
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Gapp C, Dijamentiuk A, Mangavel C, Callon C, Theil S, Revol-Junelles AM, Chassard C, Borges F. Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization. mSystems 2024; 9:e0044524. [PMID: 39041801 PMCID: PMC11334471 DOI: 10.1128/msystems.00445-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping, which consists of using part of the previous production to inoculate a new one, can be used as a model engineering approach to investigate community dynamics during serial propagations. In this study, 26 raw milk samples were serially propagated 6 times each, giving rise to 26 community lineages. Bacterial community structures were analyzed by metabarcoding, and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high variability of structure and diverse acidification properties between community lineages. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure. IMPORTANCE Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.
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Affiliation(s)
- Chloé Gapp
- Université de Lorraine, LIBio, Nancy, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | | | | | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | | | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
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Tang J, Zuo W, Guo L, Han Z, Yang C, Han B, Dai L, Zhang X, Zhou X. Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Nat Commun 2024; 15:6937. [PMID: 39138170 PMCID: PMC11322527 DOI: 10.1038/s41467-024-51365-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it is unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two honeybee gut bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro and in vivo, Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established. This positive interaction vanishes when Bifidobacterium is not required on a non-methylated diet. Results from biochemical and gene expression analyses combined with model simulation further suggest that the ratio change of the two major homogalacturonan breakdown products, galacturonic acid (GalA) and di-GalA, determines the bacterial interaction. This study unravels how glycan metabolism may shape the interactions between honeybee gut bacteria.
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Affiliation(s)
- Junbo Tang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Zhihao Han
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Chengfeng Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Benfeng Han
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Department of Microbiology and Immunology, College of Biological Science, China Agricultural University, Beijing, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Hainan, China.
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9
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Jiao Y, Sun X, Dong X, Yin J, Li Z, Zhang K, Altaf MM, Li D, Zhu Z. Enhancing mango yield and soil health with organic and slow-release fertilizers: A multifaceted evaluation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175297. [PMID: 39127209 DOI: 10.1016/j.scitotenv.2024.175297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/04/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Excessive utilization of chemical fertilizers in mango orchards not only hampers the attainment of sustainable harvests but also poses significant ecological detriments. This investigation proposes a promising solution by advocating the judicious replacement of chemical fertilizers with organic fertilizer (OF) and slow-release fertilizer (SRF), with potential to bolster soil health and augment crop productivity. In light of the promise held by these alternatives, it is imperative to establish detailed fertilization protocols for enhanced sustainable practices in mango farming. This two-year field study employed a comprehensive suite of seven fertilization strategies, unveiling that a 25 % chemical fertilizers substitution with OF and SRF improved mango yields by 12.5 % and 11.3 %, respectively, over standard practices. Additionally, these approaches substantially augmented the nutritional quality of mangoes, evident from Vitamin C enhancements of 53.9 % to 56.9 %, and improvements in sugar-to-acid ratio (19.2 %-30.3 %) and solid-to-acid ratio (12.1 %-25.3 %). Notably, the application of OF and SRF led to increased leaf nitrogen and phosphorus concentrations, while simultaneously reducing soil phosphorus and potassium levels. Furthermore, these fertilizers fostered the growth of beneficial soil microorganisms, namely Actinobacteria and Proteobacteria, and strengthened the synergy within the soil bacterial community, hence optimizing bacterial competition and nutrient cycling. The study proposes that the adoption of OF or SRF can effectively regulate soil nutrient balance, promote resilient and functional soil bacterial ecosystems, and ultimately improve mango yield and fruit quality. It recommends a fertilization scheme incorporating 25 % organic or slow-release nitrogen to align with ecological sustainability goals, promoting a more vigorous and resilient soil and crop system.
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Affiliation(s)
- Yangqiu Jiao
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Jincheng Association for Science and Technology, Jincheng 048000, Shanxi Province, China
| | - Xiaoyan Sun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Xuezhi Dong
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Jing Yin
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Shandong Vicome Greenland Chemical Co., Ltd, Jinan 250204, Shandong Province, China
| | - Zhidong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Kailu Zhang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Shenzhen 518000, Guangdong Province, China
| | - Muhammad Mohsin Altaf
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Dong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China.
| | - Zhiqiang Zhu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China.
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10
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Zhou Y, Liu D, Li F, Dong Y, Jin Z, Liao Y, Li X, Peng S, Delgado-Baquerizo M, Li X. Superiority of native soil core microbiomes in supporting plant growth. Nat Commun 2024; 15:6599. [PMID: 39097606 PMCID: PMC11297980 DOI: 10.1038/s41467-024-50685-3] [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: 12/13/2023] [Accepted: 07/18/2024] [Indexed: 08/05/2024] Open
Abstract
Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Donghui Liu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Fengqiao Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhili Jin
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Yangwenke Liao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaohui Li
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Shuguang Peng
- Hunan Province Company of China Tobacco Corporation, Changsha, 410004, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China.
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11
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Qi J, Gao T, Zhou Q, Huang S, Lin J, Xu R, Tang CY, Meng F. Activating Biocake Communities Retards Jumps of Transmembrane Pressure in Membrane Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39078411 DOI: 10.1021/acs.est.4c03038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Sudden jump of transmembrane pressure (TMP) in membrane bioreactors (MBRs), associated with abrupt aggravation of membrane fouling, limits practical applications of MBRs and calls for effective mitigation strategies. While the TMP jump is generally related to the bacterial activity of biocakes, the mechanisms underlying the TMP jump remain unclear. Herein, we conducted various backwash protocols with different nutrient (e.g., nitrate and sodium acetate) loadings on fouled membranes in MBRs to reveal the critical role of bacterial activity of biocakes for the TMP jump. The filtration tests showed a lower TMP jump rate for the membrane backwashed with a nutrient solution (a mixture of 180 mg/L NaNO3 and 200 mg/L NaAc, averaged at 1.40 kPa/d) than that backwashed with tap water (averaged at 3.56 kPa/d), implying that TMP jump could be efficiently mitigated by providing sufficient nutrients to biocake bacteria. The characterization of biocakes showed that high-nutrient solution backwash considerably increased bacterial viability and activity, while considerably reducing biomolecule accumulation on membranes. The keystone taxa (e.g., g_Aeromonas and o_Chitinophagaceae) in the network of nutrient-enriched biocake communities were involved in nitrate reduction and biomolecule degradation. Ecological null model analyses revealed that the deterministic manner mainly shaped biocake communities with high-nutrient availability. Overall, this study highlights the significance of the bacterial activity of biocakes for TMP development and provides potential alternatives for controlling membrane fouling.
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Affiliation(s)
- Ji Qi
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Tianyu Gao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qicheng Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Siqian Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jingtong Lin
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chuyang Y Tang
- Department of Civil Engineering, University of Hong Kong, Pokfulam, Hong Kong
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
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12
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Kang H, Xue Y, Cui Y, Moorhead DL, Lambers H, Wang D. Nutrient limitation mediates soil microbial community structure and stability in forest restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173266. [PMID: 38759924 DOI: 10.1016/j.scitotenv.2024.173266] [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: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Soil microorganisms are often limited by nutrients, representing an important control of heterotrophic metabolic processes. However, how nutrient limitations relate to microbial community structure and stability remains unclear, which creates a knowledge gap to understanding microbial biogeography and community changes during forest restoration. Here, we combined an eco-enzymatic stoichiometry model and high-throughput DNA sequencing to assess the potential roles of nutrient limitation on microbial community structure, assembly, and stability along a forest restoration sequence in the Qinling Mountains, China. Results showed that nutrient limitations tended to decrease during the oak forest restoration. Carbon and phosphorus limitations enhanced community dissimilarity and significantly increased bacterial alpha diversity, but not fungal diversity. Stochastic assembly processes primarily structured both bacterial (average contribution of 74.73 % and 74.17 % in bulk and rhizosheath soils, respectively) and fungal (average contribution of 77.23 % and 72.04 % in bulk and rhizosheath soils, respectively) communities during forest restoration, with nutrient limitation also contributing to the importance of stochastic processes in the bacterial communities. The migration rate (m) for bacteria was 0.19 and 0.23, respectively in both bulk soil and rhizosheath soil, and was greater than that for the fungi (m was 1.19 and 1.41, respectively), indicating a stronger dispersal limitation for fungal communities. Finally, nutrient limitations significantly affected bacterial and fungal co-occurrence with more interconnections occurring among weakly nutrient-limited microbial taxa and nutrient limitations reducing community stability when nutrient availability changed during forest restoration. Our findings highlight the fundamental effects of nutrient limitations on microbial communities and their self-regulation under changing environmental resources.
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Affiliation(s)
- Haibin Kang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling 712100, China; School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
| | - Yue Xue
- School of Geography and Oceanography, Nanjing University, Nanjing 210023, China
| | - Yongxing Cui
- Institute of Biology, Freie Universität Berlin, Berlin 14195, Germany
| | - Daryl L Moorhead
- Department of Environmental Sciences, University of Toledo, Toledo 43606, USA
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
| | - Dexiang Wang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling 712100, China.
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13
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Cao X, Liu J, Zhang L, Mao W, Li M, Wang H, Sun W. Response of soil microbial ecological functions and biological characteristics to organic fertilizer combined with biochar in dry direct-seeded paddy fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174844. [PMID: 39029750 DOI: 10.1016/j.scitotenv.2024.174844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Biochar and organic fertilizer are commonly used to maintain soil health and sustainable agroecosystems, and the alternate wet-dry management of soil moisture in dry direct-seeded paddy fields can complicate the effects of biochar and organic fertilizer on soil microhabitats. Therefore, this study used chicken manure organic fertilizer to replace some of the inorganic fertilizer and applied biochar to explore the ability of biochar and organic fertilizer to regulate the functions of the soil microhabitat in dry direct-seeded paddy fields. The coupling effect of organic fertilizer and biochar increased the diversity and richness of soil bacteria but had no significant effect on soil fungi. Biochar and organic fertilizer affected the distribution and composition of soil bacteria and fungi, and the total number of soil bacteria and fungi increased by 1365 and -71 (5 t/hm2 biochar and no organic fertilizer), 660 and 79 (10 t/hm2 biochar and no organic fertilizer), 3121 and 7 (no biochar and 20 % organic fertilizer substitution), 1873 and -72 (5 t/hm2 biochar and 20 % organic fertilizer substitution), and -544 and -65 (10 t/hm2 biochar and 20 % organic fertilizer substitution), respectively, compared with that of the control treatment. Compared with the application of biochar alone, the coupling effect of biochar and organic fertilizer increased the average degree (0.95 and 0.16), links (190 and 32), and ratio of fungal positive links (1.651 %), and decreased the modularity (0.034 and 0.052) and ratio of bacterial positive links (6.482 %) of bacterial and fungal networks. In addition, the coupling effect resulted in a more complex association between soil microbial diversity and richness and microbial ecological functions. Random forest predictions indicated that, organic fertilizer as a random factor, changes in the abundance of bacterial Bacteroidetes and Nitrospirae and fungal Monoblepharomycota were the main factors driving the differences in soil microbial ecological functions.
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Affiliation(s)
- Xiaoqiang Cao
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources, Ministry of Agriculture and Rural affairs, Northeast Agricultural University, Harbin 150030, China
| | - Jilong Liu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources, Ministry of Agriculture and Rural affairs, Northeast Agricultural University, Harbin 150030, China.
| | - Lingling Zhang
- College of Arts and Science, Northeast Agricultural University, Harbin 150030, China.
| | - Weijia Mao
- Heilongjiang Province Corporation, China National Tobacco Corporation, Harbin 150010, China
| | - Mo Li
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources, Ministry of Agriculture and Rural affairs, Northeast Agricultural University, Harbin 150030, China
| | - Hao Wang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources, Ministry of Agriculture and Rural affairs, Northeast Agricultural University, Harbin 150030, China
| | - Weili Sun
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources, Ministry of Agriculture and Rural affairs, Northeast Agricultural University, Harbin 150030, China
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14
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Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, Vivas EI, Simcox J, Venturelli O. Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603560. [PMID: 39071283 PMCID: PMC11275832 DOI: 10.1101/2024.07.15.603560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Clostridioides difficile can transiently or persistently colonize the human gut, posing a risk factor for infections. This colonization is influenced by complex molecular and ecological interactions with human gut microbiota. By investigating C. difficile dynamics in human gut communities over hundreds of generations, we show patterns of stable coexistence, instability, or competitive exclusion. Lowering carbohydrate concentration shifted a community containing C. difficile and the prevalent human gut symbiont Phocaeicola vulgatus from competitive exclusion to coexistence, facilitated by increased cross-feeding. In this environment, C. difficile adapted via single-point mutations in key metabolic genes, altering its metabolic niche from proline to glucose utilization. These metabolic changes substantially impacted inter-species interactions and reduced disease severity in the mammalian gut. In sum, human gut microbiota interactions are crucial in shaping the long-term growth dynamics and evolutionary adaptations of C. difficile, offering key insights for developing anti-C. difficile strategies.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jaron Thompson
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jericha Mill
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Isabella James
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Simcox
- Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
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15
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Dong Y, Chen R, Graham EB, Yu B, Bao Y, Li X, You X, Feng Y. Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades. Nat Commun 2024; 15:6013. [PMID: 39019914 PMCID: PMC11255312 DOI: 10.1038/s41467-024-50368-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.
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Affiliation(s)
- Yang Dong
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ruirui Chen
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Emily B Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA, 99352, USA.
- School of Biological Sciences, Washington State University, P.O. Box 645910, Pullman, WA, 99164, USA.
| | - Bingqian Yu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yuanyuan Bao
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xin Li
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangwei You
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Youzhi Feng
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
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16
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Bittleston LS. Connecting microbial community assembly and function. Curr Opin Microbiol 2024; 80:102512. [PMID: 39018765 DOI: 10.1016/j.mib.2024.102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 07/19/2024]
Abstract
Microbial ecology is moving away from purely descriptive analyses to experiments that can determine the underlying mechanisms driving changes in community assembly and function. More species-rich microbial communities generally have higher functional capabilities depending on if there is positive selection of certain species or complementarity among different species. When building synthetic communities or laboratory enrichment cultures, there are specific choices that can increase the number of species able to coexist. Higher resource complexity or the addition of physical niches are two of the many factors leading to greater biodiversity and associated increases in functional capabilities. We can use principles from community ecology and knowledge of microbial physiology to generate improved microbiomes for use in medicine, agriculture, or environmental management.
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17
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Meroz N, Livny T, Friedman J. Quantifying microbial interactions: concepts, caveats, and applications. Curr Opin Microbiol 2024; 80:102511. [PMID: 39002491 DOI: 10.1016/j.mib.2024.102511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members - a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for.
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Affiliation(s)
- Nittay Meroz
- Institute of Environmental Sciences, Hebrew University, Rehovot
| | - Tal Livny
- Institute of Environmental Sciences, Hebrew University, Rehovot; Department of Immunology and Regenerative Biology, Weizmann Institute, Rehovot
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18
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Han H, Liu H, Zhang B, Li Y, Li C, Cao H. Competitive relationships due to similar nutrient preferences reshape soil bacterial metacommunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172956. [PMID: 38719036 DOI: 10.1016/j.scitotenv.2024.172956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024]
Abstract
Paddy soil, as an ecosystem with alternating drained and flooded conditions, microorganisms in it can maintain the stability of the ecosystem by regulating the composition and diversity of its species when disturbed by external biotic or abiotic factors, and the regulatory mechanism in this process is a controversial topic in ecological research. In this study, we investigate the effects of pigeon feces addition on bacterial communities in three textured soils, two conditions (drained and flooded) based on microcosm experiment using high-throughput sequencing techniques. Our results show that pigeon feces addition reduced environmental heterogeneity and community diversity, both under flooded and drained conditions and in all textured soils, thereby decreasing the effectiveness of environmental selection and increasing diffusion limitations among bacterial communities. Bacterial communities are altered by environmental factors including total organic carbon, available nitrogen, total phosphorus, available phosphorus and available potassium, resulting in the formation of new community structures and dominant genera. Bacteria from pigeon feces did not colonize the original soil in large numbers, and the soil bacterial community structure changed, with some species replaced the indigenous ones as new dominant genera. As nutrient diffusion increases the nutrient content of the soil, this does not lead to species extinction; however, nutrient diffusion creates new nutrient preferences of the bacterial community, which causes direct competition between species, and contributes to the extinction and immigration species. Our results suggest that species replacement is an adaptive strategy of soil bacterial community in response to dispersal of pigeon feces, and that bacterial community regulate diversity and abundance of the community by enhancing species extinction and immigration, thereby preventing bacteria in pigeon feces from colonizing paddy soils and maintaining ecosystem stability.
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Affiliation(s)
- Heming Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yue Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanhai Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; School of Public Health, Qingdao University, Qingdao, Shandong 266071, China.
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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19
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Liu Y, Liu L, Hou M. Sheep dung deposition disrupted the soil microbiome in degraded grassland but not in non-degraded grassland. ENVIRONMENTAL RESEARCH 2024; 252:118922. [PMID: 38614202 DOI: 10.1016/j.envres.2024.118922] [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: 01/06/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Grazing is the most extensive land use in grassland worldwide, wherein the soil microbiome is known to support multiple ecosystem functions. Yet, the experimental impact of livestock grazing and dung deposits on the soil microbiome in degraded grassland remains poorly understood. We examined the effects of sheep dung depositions on the bacterial and fungal microbiome of two grasslands: non-degraded and degraded (long-term overgrazing) in northern China. Specifically, sheep dung was experimentally added to the soil and its effects on the soil microbial community were determined 3 months later (corresponding to livestock excreta deposited throughout the entire growing season of grassland, June to September). Our results showed that sheep dung additions showed negative effects on the soil microbiome of already degraded grassland, while with a diminished impact on the non-degraded grassland. In particular, dung deposition decreased soil microbial Shannon index, notably significantly reducing fungal diversity in degraded grassland. Moreover, sheep dung deposition modifies soil bacterial community structure and diminishes bacterial community network complexity. The alteration of soil pH caused by sheep dung deposition partially explains the decline in microbial diversity in degraded grassland. However, sheep dung did not alter the relative abundance and community composition of bacterial and fungal dominant phyla either in the non-degraded or in the degraded grassland. In conclusion, the short-term deposition of sheep dung exerted a detrimental influence on the microbial community in degraded grassland soil. It contributes new experimental evidence regarding the adverse effects of livestock grazing, particularly through dung deposition, on the soil microbiome in degraded grassland. This knowledge is crucial for guiding managers in conserving the soil microbiome in grazed grasslands.
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Affiliation(s)
- Yinghao Liu
- Institute of Grassland Research of CAAS, Hohhot, 010010, China.
| | - Liying Liu
- Inner Mongolia Autonomous Region Forestry Research Institute, China.
| | - Meiling Hou
- College of Life Science, Baicheng Normal University, Baicheng, 137000, China.
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20
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Jin R, Song J, Liu C, Lin R, Liang D, Aweya JJ, Weng W, Zhu L, Shang J, Yang S. Synthetic microbial communities: Novel strategies to enhance the quality of traditional fermented foods. Compr Rev Food Sci Food Saf 2024; 23:e13388. [PMID: 38865218 DOI: 10.1111/1541-4337.13388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/27/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Consumers are attracted to traditional fermented foods due to their unique flavor and nutritional value. However, the traditional fermentation technique can no longer accommodate the requirements of the food industry. Traditional fermented foods produce hazardous compounds, off-odor, and anti-nutritional factors, reducing product stability. The microbial system complexity of traditional fermented foods resulting from the open fermentation process has made it challenging to regulate these problems by modifying microbial behaviors. Synthetic microbial communities (SynComs) have been shown to simplify complex microbial communities and allow for the targeted design of microbial communities, which has been applied in processing traditional fermented foods. Herein, we describe the theoretical information of SynComs, particularly microbial physiological processes and their interactions. This paper discusses current approaches to creating SynComs, including designing, building, testing, and learning, with typical applications and fundamental techniques. Based on various traditional fermented food innovation demands, the potential and application of SynComs in enhancing the quality of traditional fermented foods are highlighted. SynComs showed superior performance in regulating the quality of traditional fermented foods using the interaction of core microorganisms to reduce the hazardous compounds of traditional fermented foods and improve flavor. Additionally, we presented the current status and future perspectives of SynComs for improving the quality of traditional fermented foods.
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Affiliation(s)
- Ritian Jin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Jing Song
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Chang Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Rong Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Duo Liang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Jude Juventus Aweya
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Wuyin Weng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Longji Zhu
- Institute of Urban Environment, Chinese Academy of Science, Xiamen, China
| | - Jiaqi Shang
- Key Laboratory of Bionic Engineering, College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Shen Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
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21
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Li K, Chen A, Sheng R, Hou H, Zhu B, Wei W, Zhang W. Long-term chemical and organic fertilization induces distinct variations of microbial associations but unanimous elevation of soil multifunctionality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172862. [PMID: 38705286 DOI: 10.1016/j.scitotenv.2024.172862] [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: 02/05/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
Intricate microbial associations contribute greatly to the multiple functions (multifunctionality) of natural ecosystems. However, the relationship between microbial associations and soil multifunctionality (SMF) in artificial ecosystems, particularly in agricultural ecosystem with frequent fertilization, remains unclear. In this study, based on a 28-year paddy field experiment, high-throughput sequencing and networks analysis was performed to investigate changes in soil microbial (archaea, bacteria, fungi, and protists) associations and how these changes correlate with SMF under long-term fertilization. Compared to no fertilization (CK), both chemical fertilization with N, P, and K (CF) and chemical fertilization plus rice straw retention (CFR) treatments showed significantly higher soil nutrient content, grain yield, microbial abundance, and SMF. With the exception of archaeal diversity, the CF treatment exhibited the lowest bacterial, fungal, and protist diversity, and the simplest microbial co-occurrence network. In contrast, the CFR treatment had the lowest archaeal diversity, but the highest bacterial, fungal, and protist diversity. Moreover, the CFR treatment exhibited the most complex microbial co-occurrence network with the highest number of nodes, edges, and interkingdom edges. These results highlight that both chemical fertilization with and without straw retention caused high ecosystem multifunctionality while changing microbial association oppositely. Furthermore, these results indicate that rice straw retention contributes to the development of the soil microbiome and ensures the sustainability of high-level ecosystem multifunctionality.
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Affiliation(s)
- Ke Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; College of Resource and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anlei Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Rong Sheng
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Haijun Hou
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Baoli Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
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22
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Liu C, Liu Z, Cui B, Yang H, Gao C, Chang M, Liu Y. Effects of returning peach branch waste to fields on soil carbon cycle mediated by soil microbial communities. Front Microbiol 2024; 15:1406661. [PMID: 38957617 PMCID: PMC11217190 DOI: 10.3389/fmicb.2024.1406661] [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: 03/25/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
In recent years, the rise in greenhouse gas emissions from agriculture has worsened climate change. Efficiently utilizing agricultural waste can significantly mitigate these effects. This study investigated the ecological benefits of returning peach branch waste to fields (RPBF) through three innovative strategies: (1) application of peach branch organic fertilizer (OF), (2) mushroom cultivation using peach branches as a substrate (MC), and (3) surface mulching with peach branches (SM). Conducted within a peach orchard ecosystem, our research aimed to assess these resource utilization strategies' effects on soil properties, microbial community, and carbon cycle, thereby contributing to sustainable agricultural practices. Our findings indicated that all RPBF treatments enhance soil nutrient content, enriching beneficial microorganisms, such as Humicola, Rhizobiales, and Bacillus. Moreover, soil AP and AK were observed to regulate the soil carbon cycle by altering the compositions and functions of microbial communities. Notably, OF and MC treatments were found to boost autotrophic microorganism abundance, thereby augmenting the potential for soil carbon sequestration and emission reduction. Interestingly, in peach orchard soil, fungal communities were found to contribute more greatly to SOC content than bacterial communities. However, SM treatment resulted in an increase in the presence of bacterial communities, thereby enhancing carbon emissions. Overall, this study illustrated the fundamental pathways by which RPBF treatment affects the soil carbon cycle, providing novel insights into the rational resource utilization of peach branch waste and the advancement of ecological agriculture.
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Affiliation(s)
- Chenyu Liu
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, China
| | - Zhiling Liu
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, China
| | - Bofei Cui
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, China
| | - Haiqing Yang
- Fruit Industry Serve Center of Pinggu District, Beijing, China
| | - Chengda Gao
- College of Humanities and Urban-Rural Development, Beijing University of Agriculture, Beijing, China
| | - Mingming Chang
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, China
| | - Yueping Liu
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
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23
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Qiao Y, Wang Z, Sun H, Guo H, Song Y, Zhang H, Ruan Y, Xu Q, Huang Q, Shen Q, Ling N. Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects. MICROBIOME 2024; 12:101. [PMID: 38840214 DOI: 10.1186/s40168-024-01814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community. RESULTS Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria. CONCLUSIONS Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.
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Affiliation(s)
- Yizhu Qiao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhendong Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Sun
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hanyue Guo
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Song
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - He Zhang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Ruan
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qicheng Xu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qiwei Huang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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24
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Duan Z, Huang K, Huang W, Wang B, Shi J, Xia H, Li F. Bacterial dispersal enhances the elimination of active fecal coliforms during vermicomposting of fruit and vegetable wastes: The overlooked role of earthworm mucus. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134280. [PMID: 38636233 DOI: 10.1016/j.jhazmat.2024.134280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024]
Abstract
Earthworms play a pivotal role in the elimination of fecal coliforms during vermicomposting of fruit and vegetable waste (FVWs). However, the specific mechanisms underlying the action of earthworm mucus remain unclear. This study investigated the mechanisms of fecal coliform reduction related to earthworm mucus during FVWs vermicomposting by comparing treatments with and without earthworms. The results show that the secretion of earthworm mucus decreased by 13.93 % during the startup phase, but significantly (P < 0.001) increased by 57.80 % during the degradation phase. Compared to the control without earthworms, vermicomposting led to a significant (P < 0.05) 1.22 -fold increase in the population of active bacteria, with a strong positive correlation between mucus characteristics and dominant bacterial phyla. As the dominant fecal coliforms, Escherichia coli and Klebsiella pneumoniae significantly (P < 0.05) declined by 86.20 % and 93.38 %, respectively, in the vermi-reactor relative to the control. Bacterial dispersal limitation served as a key factor constraining the elimination of E. coli (r = 0.73, P < 0.01) and K. pneumoniae (r = 0.77, P < 0.001) during vermicomposting. This study suggests that earthworm mucus increases the active bacterial abundance and cooperation by weakening the bacterial dispersal limitation, thus intensifying competition and antagonism between fecal coliforms and other bacteria.
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Affiliation(s)
- Zihao Duan
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Kui Huang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Wenqi Huang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Bangchi Wang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Jiwei Shi
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Hui Xia
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Fusheng Li
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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25
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You L, Yang C, Jin H, Kwok LY, Lv R, Ma T, Zhao Z, Zhang H, Sun Z. Shotgun metagenomic analysis of microbiota dynamics during long-term backslopping fermentation of traditional fermented milk in a controlled laboratory environment. J Dairy Sci 2024:S0022-0302(24)00826-9. [PMID: 38825103 DOI: 10.3168/jds.2023-23710] [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: 05/07/2023] [Accepted: 04/08/2024] [Indexed: 06/04/2024]
Abstract
Traditional fermented milks are produced through an inoculation process that involves the deliberate introduction of microorganisms that have been adapted and perpetuated across successive generations. However, the changes in the microbiota of traditional fermented milk during long-term inoculation fermentation in a laboratory environment remain unclear. In this study, we collected 5 samples of traditional fermented milk samples from 5 different counties in Tibet (3 kurut products) and Xinjiang (2 tarag products) of China, which served as starter cultures for a 9-mo continuous inoculation fermentation experiment. We analyzed the inter- and intra-population variations in the microbial communities of the collected samples, representing their macrodiversity and microdiversity, using shotgun metagenomic sequencing. Across all samples, we obtained a total of 186 high-quality metagenomic-assembled genomes, including 7 genera and 13 species with a relative abundance of more than 1%. The majority of these genomes were annotated as Lactobacillus helveticus (60.46%), Enterococcus durans (9.52%), and Limosilactobacillus fermentum (6.23%). We observed significant differences in species composition and abundance among the 5 initial inoculants. During the long-term inoculation fermentation, we found an overall increasing trend in species diversity, composition, and abundances of carbohydrate metabolism module-encoding genes in the fermented milk bacterial metagenome, while the fermented milk virome exhibited a relatively narrow range of variation. Lactobacillus helveticus, a dominant species in traditional fermented milk, displayed high stability during the long-term inoculation fermentation. Our study provides valuable insights for the industrial production of traditional fermented milk.
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Affiliation(s)
- Lijun You
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Chengcong Yang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Ruirui Lv
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Teng Ma
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
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26
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Zhao M, Jiang M, Qin L, Hu N, Meng J, Wang M, Wang G. The recovery of soil eukaryotic alpha and beta diversity after wetland restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171814. [PMID: 38508279 DOI: 10.1016/j.scitotenv.2024.171814] [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: 11/14/2023] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Soil eukaryotes play an important role in regulating the ecological processes and ecosystem functioning. However, the recovery potential of soil eukaryotic diversity during wetland restoration is largely unknown. We compared the alpha and beta diversity of soil eukaryotes of farmlands and natural and restored wetlands to explore the underlying abiotic and biotic driving forces in the Sanjiang Plain, China. We found that there was no significant difference of the alpha diversity of soil eukaryotes, while the beta diversity of soil eukaryotes differed significantly between the three land use types, with the mean values in the restored wetlands in between those in the natural wetlands and farmlands. The composition of soil eukaryotic communities were less diverse in farmlands compared to restored and natural wetlands. Network property of soil eukaryotes community (positive: negative edges) increased from farmlands to restored wetlands to natural wetlands, indicating enhanced species positive: negative interactions during restoration. The structural equation modeling indicated that species positive: negative interactions and soil nutrients directly affected soil eukaryotic beta diversity. Soil pH and soil water content indirectly affected soil eukaryotic beta diversity by directly affecting species interactions. Our findings suggest that wetland restoration could change soil environment, strengthen microbial cooperation, and increase eukaryotic beta diversity. However, it may take a very long time to reach the original level of soil eukaryotic structure and diversity.
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Affiliation(s)
- Meiling Zhao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Jiang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Qin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Nanlin Hu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingci Meng
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Ming Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun 130024, China
| | - Guodong Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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27
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Choudhary R, Mahadevan R. DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities. Biophys J 2024:S0006-3495(24)00320-5. [PMID: 38733081 DOI: 10.1016/j.bpj.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
There have been a growing number of computational strategies to aid in the design of synthetic microbial consortia. A framework to identify regions in parametric space to maximize two essential properties, evenness and stability, is critical. In this study, we introduce DyMMM-LEAPS (dynamic multispecies metabolic modeling-locating evenness and stability in large parametric space), an extension of the DyMMM framework. Our method explores the large parametric space of genetic circuits in synthetic microbial communities to identify regions of evenness and stability. Due to the high computational costs of exhaustive sampling, we utilize adaptive sampling and surrogate modeling to reduce the number of simulations required to map the vast space. Our framework predicts engineering targets and computes their operating ranges to maximize the probability of the engineered community to have high evenness and stability. We demonstrate our approach by simulating five cocultures and one three-strain culture with different social interactions (cooperation, competition, and predation) employing quorum-sensing-based genetic circuits. In addition to guiding circuit tuning, our pipeline gives an opportunity for a detailed analysis of pockets of evenness and stability for the circuit under investigation, which can further help dissect the relationship between the two properties. DyMMM-LEAPS is easily customizable and can be expanded to a larger community with more complex interactions.
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Affiliation(s)
- Ruhi Choudhary
- University of Toronto, Department of Chemical Engineering and Applied Chemistry, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- University of Toronto, Department of Chemical Engineering and Applied Chemistry, Toronto, ON, Canada.
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28
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Hu Y, Cai J, Song Y, Li G, Gong Y, Jiang X, Tang X, Shao K, Gao G. Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake. MICROBIAL ECOLOGY 2024; 87:68. [PMID: 38722447 PMCID: PMC11082002 DOI: 10.1007/s00248-024-02365-4] [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: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 05/12/2024]
Abstract
It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.
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Affiliation(s)
- Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jian Cai
- Xiangyang Polytechnic, Xiangyang, 441000, Hubei Province, China
| | - Yifu Song
- Nanjing Forestry University, Nanjing, 210008, China
| | | | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingyu Jiang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China.
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29
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Li JD, Gao YY, Stevens EJ, King KC. Dual stressors of infection and warming can destabilize host microbiomes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230069. [PMID: 38497264 PMCID: PMC10945407 DOI: 10.1098/rstb.2023.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/02/2024] [Indexed: 03/19/2024] Open
Abstract
Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- J. D. Li
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - Y. Y. Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
- School of Ecology and Nature Conservation, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, People's Republic of China
| | - E. J. Stevens
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - K. C. King
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
- Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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Li X, Qin H, Tang N, Li X, Xing W. Microplastics enhance the invasion of exotic submerged macrophytes by mediating plant functional traits, sediment properties, and microbial communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134032. [PMID: 38492389 DOI: 10.1016/j.jhazmat.2024.134032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/25/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Plant invasions and microplastics (MPs) have significantly altered the structure and function of aquatic habitats worldwide, resulting in severe damage to aquatic ecosystem health. However, the effects of MPs on plant invasion and the underlying mechanisms remain largely unknown. In this study, we conducted mesocosm experiments over a 90-day period to assess the effects of polystyrene microplastics on the invasion of exotic submerged macrophytes, sediment physicochemical properties, and sediment bacterial communities. Our results showed that PS-MPs significantly promoted the performance of functional traits and the invasive ability of exotic submerged macrophytes, while native plants remained unaffected. Moreover, PS-MPs addition significantly decreased sediment pH while increasing sediment carbon and nitrogen content. Additionally, MPs increased the diversity of sediment bacterial community but inhibited its structural stability, thereby impacting sediment bacterial multifunctionality to varying degrees. Importantly, we identified sediment properties, bacterial composition, and bacterial multifunctionality as key mediators that greatly enhance the invasion of exotic submerged macrophytes. These findings provide compelling evidence that the increase in MPs may exacerbate the invasion risk of exotic submerged macrophytes through multiple pathways. Overall, this study enhances our understanding of the ecological impacts of MPs on aquatic plant invasion and the health of aquatic ecosystems.
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Affiliation(s)
- Xiaowei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hongjie Qin
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Na Tang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaolu Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wei Xing
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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Wang X, Wang Z, Su S, Wu Y, Fan J, Hou X, Zhang K, Salama ES, Kulshrestha S, Ling Z, Liu P, Li X. Probiotics Pediococcus acidilactici GR-1 promotes the functional strains and remodels gut microbiota to reduce the Cr(VI) toxicity in a dual-chamber simulated intestinal system. CHEMOSPHERE 2024; 356:141927. [PMID: 38593954 DOI: 10.1016/j.chemosphere.2024.141927] [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: 09/05/2023] [Revised: 02/29/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Abstract
Numerous animal studies have demonstrated the toxicity of hexavalent chromium [Cr(VI)] and the bioremediative effects of probiotics on the composition and functions of gut microbiota. Since the precise mechanisms of Cr(VI) detoxification and its interactions with human gut microbiota were unknown, a novel dual-chamber simulated intestinal (DCSI) system was developed to maintain both the stability of the simulated system and the composition of the gut microbiota. Probiotic GR-1 was found to regulate intestinal gut microbiota, thereby reducing the toxicity of Cr(VI) within the DCSI system. The results indicate that Cr(VI) levels were reduced from 2.260 ± 0.2438 μg/g to 1.7086 ± 0.1950 μg/g in the gut microbiota cell pellet, and Cr(VI) permeability decreased from 0.5521 ± 0.1132 μg/L to 0.3681 ± 0.0178 μg/L after 48 h in simulated gut fluid. Additionally, the removal rate of 1,1-Diphenyl-2-picrylhydrazyl (DPPH), reducibility (Vitamin C), and total antioxidant capacity (T-AOC) increased by 50.83%, 31.70%, and 27.56%, respectively, following probiotic treatment. The increase in antioxidant capacity correlated with total Cr removal (P < 0.05, r from -0.80 to 0.73). 16S rRNA sequencing analysis showed that gut microbiota composition was reshaped by the addition of probiotics, which regulated the recovery of the functional gut microbiota to normal levels, rather than restoring the entire gut microbiota composition for community function. Thus, this study not only demonstrates the feasibility and stability of culturing gut microbiota but also offers a new biotechnological approach to synthesizing functional communities with functional strains for environmental risk management.
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Affiliation(s)
- Xing Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Zemin Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Shaochen Su
- Healthy Examination & Management Center, First Hospital of Lanzhou University, Lanzhou, 730000, PR China.
| | - Ying Wu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Jingjing Fan
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Xiaoxiao Hou
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Kunyue Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China.
| | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Biotechnology and Management Sciences, Shoolini University, Bajhol, Solan, Himachal Pradesh, 173229, India.
| | - Zhenmin Ling
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Pu Liu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Xiangkai Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
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Yan X, Li S, Abdullah Al M, Mo Y, Zuo J, Grossart HP, Zhang H, Yang Y, Jeppesen E, Yang J. Community stability of free-living and particle-attached bacteria in a subtropical reservoir with salinity fluctuations over 3 years. WATER RESEARCH 2024; 254:121344. [PMID: 38430754 DOI: 10.1016/j.watres.2024.121344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/22/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Changes in salinity have a profound influence on ecological services and functions of inland freshwater ecosystems, as well as on the shaping of microbial communities. Bacterioplankton, generally classified into free-living (FL) and particle-attached (PA) forms, are main components of freshwater ecosystems and play key functional roles for biogeochemical cycling and ecological stability. However, there is limited knowledge about the responses of community stability of both FL and PA bacteria to salinity fluctuations. Here, we systematically explored changes in community stability of both forms of bacteria based on high-frequency sampling in a shallow urban reservoir (Xinglinwan Reservoir) in subtropical China for 3 years. Our results indicated that (1) salinity was the strongest environmental factor determining FL and PA bacterial community compositions - rising salinity increased the compositional stability of both bacterial communities but decreased their α-diversity. (2) The community stability of PA bacteria was significantly higher than that of FL at high salinity level with low salinity variance scenarios, while the opposite was found for FL bacteria, i.e., their stability was higher than PA bacteria at low salinity level with high variance scenarios. (3) Both bacterial traits (e.g., bacterial genome size and interaction strength of rare taxa) and precipitation-induced factors (e.g., changes in salinity and particle) likely contributed collectively to differences in community stability of FL and PA bacteria under different salinity scenarios. Our study provides additional scientific basis for ecological management, protection and restoration of urban reservoirs under changing climatic and environmental conditions.
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Affiliation(s)
- Xue Yan
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Mamun Abdullah Al
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jun Zuo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Lab for Water Environment and Marine Biological Resources Protection, Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin 16775, Germany; Institute of Biochemistry and Biology, Potsdam University, Potsdam 14469, Germany
| | - Hongteng Zhang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yigang Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Erik Jeppesen
- Department of Ecoscience, Aarhus University, Aarhus 8000, Denmark; Sino-Danish Centre for Education and Research, Beijing 100049, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara 06800, Turkey; Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China; Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin 33731, Turkey
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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Wang M, Lin M, Liu Q, Li C, Pang X. Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171007. [PMID: 38401731 DOI: 10.1016/j.scitotenv.2024.171007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.
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Affiliation(s)
- Min Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China; School of Ecology and Environment, Hainan University, China
| | - Mao Lin
- College of Geography and Resources, Sichuan Normal University, Chengdu 610101, China
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China
| | - Cheng Li
- School of Ecology and Environment, Hainan University, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China.
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Daval C, Tran T, Verdier F, Martin A, Alexandre H, Grandvalet C, Tourdot-Maréchal R. Identification of Key Parameters Inducing Microbial Modulation during Backslopped Kombucha Fermentation. Foods 2024; 13:1181. [PMID: 38672854 PMCID: PMC11049054 DOI: 10.3390/foods13081181] [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: 02/21/2024] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study was to assess the impact of production parameters on the reproducibility of kombucha fermentation over several production cycles based on backslopping. Six conditions with varying oxygen accessibility (specific interface surface) and initial acidity (through the inoculation rate) of the cultures were carried out and compared to an original kombucha consortium and a synthetic consortium assembled from yeasts and bacteria isolated from the original culture. Output parameters monitored were microbial populations, biofilm weight, key physico-chemical parameters and metabolites. Results highlighted the existence of phases in microbial dynamics as backslopping cycles progressed. The transitions between phases occurred faster for the synthetic consortium compared to the original kombucha. This led to microbial dynamics and fermentative kinetics that were reproducible over several cycles but that could also deviate and shift abruptly to different behaviors. These changes were mainly induced by an increase in the Saccharomyces cerevisiae population, associated with an intensification of sucrose hydrolysis, sugar consumption and an increase in ethanol content, without any significant acceleration in the rate of acidification. The study suggests that the reproducibility of kombucha fermentations relies on high biodiversity to slow down the modulations of microbial dynamics induced by the sustained rhythm of backslopping cycles.
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Affiliation(s)
- Claire Daval
- Institut Agro, Université Bourgogne Franche-Comté, Université Bourgogne, INRAE, UMR PAM 1517, 21000 Dijon, France (H.A.); (C.G.); (R.T.-M.)
| | - Thierry Tran
- Institut Agro, Université Bourgogne Franche-Comté, Université Bourgogne, INRAE, UMR PAM 1517, 21000 Dijon, France (H.A.); (C.G.); (R.T.-M.)
| | | | - Antoine Martin
- Biomère, 10B Rue du Nouveau Bêle, 44470 Carquefou, France
| | - Hervé Alexandre
- Institut Agro, Université Bourgogne Franche-Comté, Université Bourgogne, INRAE, UMR PAM 1517, 21000 Dijon, France (H.A.); (C.G.); (R.T.-M.)
| | - Cosette Grandvalet
- Institut Agro, Université Bourgogne Franche-Comté, Université Bourgogne, INRAE, UMR PAM 1517, 21000 Dijon, France (H.A.); (C.G.); (R.T.-M.)
| | - Raphaëlle Tourdot-Maréchal
- Institut Agro, Université Bourgogne Franche-Comté, Université Bourgogne, INRAE, UMR PAM 1517, 21000 Dijon, France (H.A.); (C.G.); (R.T.-M.)
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Yang C, Hu J, Su Q, Zhang Z, Du Y, Wang J, Sun H, Han B, Tang J, Guo L, Li H, Cai W, Zheng H, Zhou X, Zhang X. A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database. INSECT SCIENCE 2024. [PMID: 38594229 DOI: 10.1111/1744-7917.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/13/2024] [Accepted: 03/09/2024] [Indexed: 04/11/2024]
Abstract
Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.
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Affiliation(s)
- Chengfeng Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan Province, China
| | - Jiawei Hu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Zijing Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yating Du
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jieni Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huihui Sun
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan Province, China
| | - Benfeng Han
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junbo Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan Province, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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Zhang L, Graham N, Li G, Zhu Y, Yu W. Excessive Ozonation Stress Triggers Severe Membrane Biofilm Accumulation and Fouling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5899-5910. [PMID: 38502922 DOI: 10.1021/acs.est.3c10429] [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: 03/21/2024]
Abstract
The established benefits of ozone on microbial pathogen inactivation, natural organic matter degradation, and inorganic/organic contaminant oxidation have favored its application in drinking water treatment. However, viable bacteria are still present after the ozonation of raw water, bringing a potential risk to membrane filtration systems in terms of biofilm accumulation and fouling. In this study, we shed light on the role of the specific ozone dose (0.5 mg-O3/mg-C) in biofilm accumulation during long-term membrane ultrafiltration. Results demonstrated that ozonation transformed the molecular structure of influent dissolved organic matter (DOM), producing fractions that were highly bioavailable at a specific ozone dose of 0.5, which was inferred to be a turning point. With the increase of the specific ozone dose, the biofilm microbial consortium was substantially shifted, demonstrating a decrease in richness and diversity. Unexpectedly, the opportunistic pathogen Legionella was stimulated and occurred in approximately 40% relative abundance at the higher specific ozone dose of 1. Accordingly, the membrane filtration system with a specific ozone dose of 0.5 presented a lower biofilm thickness, a weaker fluorescence intensity, smaller concentrations of polysaccharides and proteins, and a lower Raman activity, leading to a lower hydraulic resistance, compared to that with a specific ozone dose of 1. Our findings highlight the interaction mechanism between molecular-level DOM composition, biofilm microbial consortium, and membrane filtration performance, which provides an in-depth understanding of the impact of ozonation on biofilm accumulation.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Nigel Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| | - Guibai Li
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Wei F, Xie T, Su C, He B, Shu Z, Zhang Y, Xiao Z, Hao J. Stability and Assembly Mechanisms of Butterfly Communities across Environmental Gradients of a Subtropical Mountain. INSECTS 2024; 15:230. [PMID: 38667360 PMCID: PMC11050375 DOI: 10.3390/insects15040230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024]
Abstract
Mountain ecosystems harbor evolutionarily unique and exceptionally rich biodiversity, particularly in insects. In this study, we characterized the diversity, community stability, and assembly mechanisms of butterflies on a subtropical mountain in the Chebaling National Nature Reserve, Guangdong Province, China, using grid-based monitoring across the entire region for two years. The results showed that species richness, abundance, and Faith's phylogenetic diversity decreased with increasing elevation; taxonomic diversity played a considerable role in mediating the effects of environmental changes on stability. Moreover, our results showed that stochastic processes are dominant in governing the assembly of butterfly communities across all elevational gradients, with habitats at an elevation of 416-580 m subjected to the strongest stochastic processes, whereas heterogeneous selection processes displayed stronger effects on the assembly of butterfly communities at 744-908 m, 580-744 m, and 908-1072 m, with abiotic factors inferred as the main driving forces. In addition, significant differences were detected between the barcode tree and the placement tree for the calculated β-NTI values at 416-580 m. Overall, this study provides new insights into the effects of environmental change on the stability and assembly of butterflies in Chebaling, which will be beneficial for biodiversity conservation and policy development.
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Affiliation(s)
- Fanyu Wei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (F.W.); (T.X.); (C.S.); (B.H.)
| | - Tingting Xie
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (F.W.); (T.X.); (C.S.); (B.H.)
- Key Laboratory of Zoological and Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100045, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (F.W.); (T.X.); (C.S.); (B.H.)
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (F.W.); (T.X.); (C.S.); (B.H.)
| | - Zufei Shu
- Guangdong Chebaling National Nature Reserve Administration Bureau, Shaoguan 512500, China; (Z.S.); (Y.Z.)
| | - Yingming Zhang
- Guangdong Chebaling National Nature Reserve Administration Bureau, Shaoguan 512500, China; (Z.S.); (Y.Z.)
| | - Zhishu Xiao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing 100045, China
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (F.W.); (T.X.); (C.S.); (B.H.)
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Liu J, Wang J, Zhang M, Wang X, Guo P, Li Q, Ren J, Wei Y, Wu T, Chai B. Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170386. [PMID: 38280613 DOI: 10.1016/j.scitotenv.2024.170386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiayi Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Xue Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Ping Guo
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Qianru Li
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiali Ren
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Yuqi Wei
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, GA 30460-8042, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China.
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Chen X, Wang M, Luo L, An L, Liu X, Fang Y, Huang T, Nie Y, Wu XL. High immigration rates critical for establishing emigration-driven diversity in microbial communities. Cell Syst 2024; 15:275-285.e4. [PMID: 38401538 DOI: 10.1016/j.cels.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/03/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
Unraveling the mechanisms governing the diversity of ecological communities is a central goal in ecology. Although microbial dispersal constitutes an important ecological process, the effect of dispersal on microbial diversity is poorly understood. Here, we sought to fill this gap by combining a generalized Lotka-Volterra model with experimental investigations. Our model showed that emigration increases the diversity of the community when the immigration rate crosses a defined threshold, which we identified as Ineutral. We also found that at high immigration rates, emigration weakens the relative abundance of fast-growing species and thus enhances the mass effect and increases the diversity. We experimentally confirmed this finding using co-cultures of 20 bacterial strains isolated from the soil. Our model further showed that Ineutral decreases with the increase of species pool size, growth rate, and interspecies interaction. Our work deepens the understanding of the effects of dispersal on the diversity of natural communities.
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Affiliation(s)
- Xiaoli Chen
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China
| | - Miaoxiao Wang
- Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Dübendorf 8600, Switzerland
| | - Laipeng Luo
- College of Engineering, Peking University, Beijing 100871, China
| | - Liyun An
- College of Architecture and Environment, Sichuan University, Chengdu 610000, China
| | - Xiaonan Liu
- College of Engineering, Peking University, Beijing 100871, China
| | - Yuan Fang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Ting Huang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China; Institute of Ecology, Peking University, Beijing 100871, China.
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Romdhane S, Huet S, Spor A, Bru D, Breuil MC, Philippot L. Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly. ENVIRONMENTAL MICROBIOME 2024; 19:18. [PMID: 38504378 PMCID: PMC10953230 DOI: 10.1186/s40793-024-00559-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors. RESULTS We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any "home field advantage" during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering. CONCLUSIONS Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.
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Affiliation(s)
- Sana Romdhane
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France.
| | - Sarah Huet
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Aymé Spor
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - David Bru
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Marie-Christine Breuil
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Laurent Philippot
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
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Geesink P, ter Horst J, Ettema TJG. More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities. FEMS Microbiol Ecol 2024; 100:fiae029. [PMID: 38444203 PMCID: PMC10950044 DOI: 10.1093/femsec/fiae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.
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Affiliation(s)
- Patricia Geesink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jolanda ter Horst
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Zou H, He J, Chu Y, Xu B, Li W, Huang S, Guan X, Liu F, Li H. Revealing discrepancies and drivers in the impact of lomefloxacin on groundwater denitrification throughout microbial community growth and succession. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133139. [PMID: 38056273 DOI: 10.1016/j.jhazmat.2023.133139] [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: 09/20/2023] [Revised: 10/31/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The coexistence of antibiotics and nitrates has raised great concern about antibiotic's impact on denitrification. However, conflicting results in these studies are very puzzling, possibly due to differences in microbial succession stages. This study investigated the effects of the high-priority urgent antibiotic, lomefloxacin (LOM), on groundwater denitrification throughout microbial growth and succession. The results demonstrated that LOM's impact on denitrification varied significantly across three successional stages, with the most pronounced effects exhibited in the initial stage (53.8% promotion at 100 ng/L-LOM, 84.6% inhibition at 100 μg/L-LOM), followed by the decline stage (13.3-18.2% inhibition), while no effect in the stable stage. Hence, a distinct pattern encompassing susceptibility, insusceptibility, and sub-susceptibility in LOM's impact on denitrification was discovered. Microbial metabolism and environment variation drove the pattern, with bacterial numbers and antibiotic resistance as primary influencers (22.5% and 15.3%, p < 0.01), followed by carbon metabolism and microbial community (5.0% and 3.68%, p < 0.01). The structural equation model confirmed results reliability. Bacterial numbers and resistance influenced susceptibility by regulating compensation and bacteriostasis, while carbon metabolism and microbial community impacted energy, electron transfer, and gene composition. These findings provide valuable insights into the complex interplay between antibiotics and denitrification patterns in groundwater.
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Affiliation(s)
- Hua Zou
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Jiangtao He
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China.
| | - Yanjia Chu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Baoshi Xu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Wei Li
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Shiwen Huang
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Xiangyu Guan
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Haiyan Li
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
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Song Z, Li K, Li K. Integrated characterizations of intestinal bacteria and transcriptomics revealed the acute stress response to carbonate alkalinity in white shrimp Penaeusvannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109420. [PMID: 38325592 DOI: 10.1016/j.fsi.2024.109420] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
The impact of carbonate alkalinity in saline-alkaline water on aquatic organisms, particularly Penaeus vannamei, a significant species in aquaculture, remains a critical area of study. To elucidate the acute response mechanisms of P. vannamei to elevated carbonate alkalinity environments, we utilized 16S rRNA gene and transcriptome sequencing technologies to analyze intestinal bacteria and gene expressions within various tissues. Our investigation revealed notable changes in specific intestinal bacterial OTUs, whose abundances varied preceding the overall bacterial community, indicating the sensitivity to carbonate alkalinity exposure. These shifts are accompanied by a simplification in bacterial networks and alterations in pathogenic OTUs, notably Aeromonas OTU. Concurrently, gene expression variations were observed across the hepatopancreas, gills, muscles, and intestines, with decreasing numbers of DEGs in the mentioned order. Annotation of these DEGs revealed enrichments in pathways related to transport, catabolism, immune responses, circulatory functions, and lipid metabolism. Notably, correlations between specific intestinal bacterial OTUs and gene expression shifts were identified across these tissues. Several OTUs, attributed to Rhizobiales, Saccharimonadales, Acidovora, and Aeromona, exhibited a correlation with DEGs in all four tissues, primarily associated with amino acid metabolism, signal transduction, and transport and catabolism pathways. Our study provides comprehensive insights into the dynamic responses of P. vannamei to elevated carbonate alkalinity stress. These findings contribute crucial knowledge for effective P. vannamei cultivation in saline-alkaline water, advancing our understanding in this field.
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Affiliation(s)
- Zule Song
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kui Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kejun Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China.
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Li Z, Feng C, Lei J, He X, Wang Q, Zhao Y, Qian Y, Zhan X, Shen Z. Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3654-3664. [PMID: 38318812 DOI: 10.1021/acs.est.3c07717] [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: 02/07/2024]
Abstract
How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.
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Affiliation(s)
- Zhenling Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Chenghong Feng
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Jinming Lei
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiaokang He
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Qixuan Wang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yue Zhao
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yibin Qian
- National Plot Zone for Ecological Conservation (Hainan) Research Center, Hainan Research Academy of Environmental Sciences, Haikou 571127, P. R. China
| | - Xinmin Zhan
- Civil Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
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Kumar V, Roy S, Parida SN, Bisai K, Dhar S, Jana AK, Das BK. Deciphering the impact of endoparasitic infection on immune response and gut microbial composition of Channa punctata. Front Cell Infect Microbiol 2024; 14:1296769. [PMID: 38476164 PMCID: PMC10927727 DOI: 10.3389/fcimb.2024.1296769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/19/2024] [Indexed: 03/14/2024] Open
Abstract
Intestinal parasitic infections caused by helminths are globally distributed and are a major cause of morbidity worldwide. Parasites may modulate the virulence, gut microbiota diversity and host responses during infection. Despite numerous works, little is known about the complex interaction between parasites and the gut microbiota. In the present study, the complex interplay between parasites and the gut microbiota was investigated. A total of 12 bacterial strains across four major families, including Enterobacteriaceae, Morganellaceae, Flavobacteriaceae, and Pseudomonadaceae, were isolated from Channa punctata, infected with the nematode species Aporcella sp., Axonchium sp., Tylencholaimus mirabilis, and Dioctophyme renale. The findings revealed that nematode infection shaped the fish gut bacterial microbiota and significantly affected their virulence levels. Nematode-infected fish bacterial isolates are more likely to be pathogenic, with elevated hemolytic activity and biofilm formation, causing high fish mortality. In contrast, isolates recovered further from non-parasitised C. punctata were observed to be non-pathogenic and had negligible hemolytic activity and biofilm formation. Antibiogram analysis of the bacterial isolates revealed a disproportionately high percentage of bacteria that were either marginally or multidrug resistant, suggesting that parasitic infection-induced stress modulates the gut microenvironment and enables colonization by antibiotic-resistant strains. This isolation-based study provides an avenue to unravel the influence of parasitic infection on gut bacterial characteristics, which is valuable for understanding the infection mechanism and designing further studies aimed at optimizing treatment strategies. In addition, the cultured isolates can supplement future gut microbiome studies by providing wet lab specimens to compare (meta)genomic information discovered within the gut microenvironment of fish.
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Affiliation(s)
| | | | | | | | | | | | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology (AEBN) Division, Indian Council of Agricultural Research (ICAR)-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, India
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46
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Yang M, Liu N, Wang B, Li Y, Li W, Shi X, Yue X, Liu CQ. Stepwise degradation of organic matters driven by microbial interactions in China΄s coastal wetlands: Evidence from carbon isotope analysis. WATER RESEARCH 2024; 250:121062. [PMID: 38157604 DOI: 10.1016/j.watres.2023.121062] [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: 07/21/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
The microbial "unseen majority" as drivers of carbon cycle represent a significant source of uncertain climate change. To comprehend the resilience of life forms on Earth to climate change, it is crucial to incorporate knowledge of intricate microbial interactions and their impact to carbon transformation. Combined with carbon stable isotope analysis and high-throughput sequencing technology, the underlying mechanism of microbial interactions for organic carbon degradation has been elucidated. Niche differentiation enabled archaea to coexist with bacteria mainly in a cooperative manner. Bacteria composed of specialists preferred to degrade lighter carbon, while archaea were capable of utilizing heavier carbon. Microbial resource-dependent interactions drove stepwise degradation of organic matter. Bacterial cooperation directly facilitated the degradation of algae-dominated particulate organic carbon, while competitive feeding of archaea caused by resource scarcity significantly promoted the mineralization of heavier particulate organic carbon and then the release of dissolved inorganic carbon. Meanwhile, archaea functioned as a primary decomposer and collaborated with bacteria in the gradual degradation of dissolved organic carbon. This study emphasized microbial interactions driving carbon cycle and provided new perspectives for incorporating microorganisms into carbon biogeochemical models.
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Affiliation(s)
- Meiling Yang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China
| | - Na Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Baoli Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China.
| | - Yajun Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Wanzhu Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xinjie Shi
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xinrui Yue
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China
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47
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Chen M, Zhou S, Xiang P, Wang Y, Luo X, Zhang X, Wen D. Elevated CO 2 and nitrogen addition enhance the symbiosis and functions of rhizosphere microorganisms under cadmium exposure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:120012. [PMID: 38171127 DOI: 10.1016/j.jenvman.2023.120012] [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: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
Soil microbes are fundamental to ecosystem health and productivity. How soil microbial communities are influenced by elevated atmospheric carbon dioxide (eCO2) concentration and nitrogen (N) deposition under heavy metal pollution remains uncertain, despite global exposure of terrestrial ecosystems to eCO2, high N deposition and heavy metal stress. Here, we conducted a four year's open-top chamber experiment to assess the effects of soil cadmium (Cd) treatment (10 kg hm-2 year-1) alone and combined treatments of Cd with eCO2 concentration (700 ppm) and/or N addition (100 kg hm-2 year-1) on tree growth and rhizosphere microbial community. Relative to Cd treatment alone, eCO2 concentration in Cd contaminated soil increased the complexity of microbial networks, including the number links, average degree and positive/negative ratios. The combined effect of eCO2 and N addition in Cd contaminated soil not only increased the complexity of microbial networks, but also enhanced the abundance of microbial urealysis related UreC and nitrifying related amoA1 and amoA2, and the richness of arbuscular mycorrhiza fungi (AMF), thereby improving the symbiotic functions between microorganisms and plants. Results from correlation analysis and structural equation model (SEM) further demonstrated that eCO2 concentration and N addition acted on functions and networks differently. Elevated CO2 positively regulated microbial networks and functions through phosphorus (P) and Cd concentration in roots, while N addition affected microbial functions through soil available N and soil organic carbon (SOC) concentration and microbial network through soil Cd concentration. Overall, our findings highlight that eCO2 concentration and N addition make microbial communities towards ecosystem health that may mitigate Cd stress, and provide new insights into the microbiology supporting phytoremediation for Cd contaminated sites in current and future global change scenarios.
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Affiliation(s)
- Minghao Chen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyidan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China
| | - Ping Xiang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yutao Wang
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xianzhen Luo
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China
| | - Xiaofeng Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dazhi Wen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, 341000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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48
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Vitasse Y, Pohl N, Walde MG, Nadel H, Gossner MM, Baumgarten F. Feasting on the ordinary or starving for the exceptional in a warming climate: Phenological synchrony between spongy moth ( Lymantria dispar) and budburst of six European tree species. Ecol Evol 2024; 14:e10928. [PMID: 38371870 PMCID: PMC10869895 DOI: 10.1002/ece3.10928] [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: 02/28/2023] [Revised: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 02/20/2024] Open
Abstract
Global warming is affecting the phenological cycles of plants and animals, altering the complex synchronization that has co-evolved over thousands of years between interacting species and trophic levels. Here, we examined how warmer winter conditions affect the timing of budburst in six common European trees and the hatching of a generalist leaf-feeding insect, the spongy moth Lymantria dispar, whose fitness depends on the synchrony between egg hatch and leaf emergence of the host tree. We applied four different temperature treatments to L. dispar eggs and twig cuttings, that mimicked warmer winters and reduced chilling temperatures that are necessary for insect diapause and bud dormancy release, using heated open-top chambers (ambient or +3.5°C), and heated greenhouses (maintained at >6°C or >10°C). In addition, we conducted preference and performance tests to determine which tree species the larvae prefer and benefit from the most. Budburst success and twig survival were highest for all tree species at ambient temperature conditions, whereas it declined under elevated winter temperature for Tilia cordata and Acer pseudoplatanus, likely due to a lack of chilling. While L. dispar egg hatch coincided with budburst in most tree species within 10 days under ambient conditions, it coincided with budburst only in Quercus robur, Carpinus betulus, and, to a lesser extent, Ulmus glabra under warmer conditions. With further warming, we, therefore, expect an increasing mismatch in trees with high chilling requirements, such as Fagus sylvatica and A. pseudoplatanus, but still good synchronization with trees having low chilling requirements, such as Q. robur and C. betulus. Surprisingly, first instar larvae preferred and gained weight faster when fed with leaves of F. sylvatica, while Q. robur ranked second. Our results suggest that spongy moth outbreaks are likely to persist in oak and hornbeam forests in western and central Europe.
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Affiliation(s)
- Yann Vitasse
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Nora Pohl
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesLommaSweden
| | - Manuel G. Walde
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Hannah Nadel
- United States Department of AgricultureAnimal and Plant Health Inspection Service, Forest Pest Methods LaboratoryBuzzards BayMassachusettsUSA
| | - Martin M. Gossner
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
- Department of Environmental Systems ScienceInstitute of Terrestrial Ecosystems, ETH ZürichZürichSwitzerland
| | - Frederik Baumgarten
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
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49
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Kang H, Chai A, Lin Z, Shi Y, Xie X, Li L, Fan T, Xiang S, Xie J, Li B. Deciphering Differences in Microbial Community Diversity between Clubroot-Diseased and Healthy Soils. Microorganisms 2024; 12:251. [PMID: 38399655 PMCID: PMC10893227 DOI: 10.3390/microorganisms12020251] [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: 12/26/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.
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Affiliation(s)
- Huajun Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Ali Chai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Zihan Lin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Yanxia Shi
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Xuewen Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Lei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Tengfei Fan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Sheng Xiang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
| | - Baoju Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
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50
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Qiao Y, Huang Q, Guo H, Qi M, Zhang H, Xu Q, Shen Q, Ling N. Nutrient status changes bacterial interactions in a synthetic community. Appl Environ Microbiol 2024; 90:e0156623. [PMID: 38126758 PMCID: PMC10807438 DOI: 10.1128/aem.01566-23] [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: 09/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.IMPORTANCEUnderstanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.
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Affiliation(s)
- Yizhu Qiao
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qiwei Huang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hanyue Guo
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Meijie Qi
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - He Zhang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qicheng Xu
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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