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Yao H, Shi W, Wang X, Li J, Chen M, Li J, Chen D, Zhou L, Deng Z. The root-associated Fusarium isolated based on fungal community analysis improves phytoremediation efficiency of Ricinus communis L. in multi metal-contaminated soils. CHEMOSPHERE 2023; 324:138377. [PMID: 36905995 DOI: 10.1016/j.chemosphere.2023.138377] [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: 10/26/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Phytoremediation is a widely accepted bioremediation method of treating heavy metal contaminated soils. Nevertheless, the remediation efficiency in multi-metal contaminated soils is still unsatisfactory attributable to susceptibility to different metals. To isolate root-associated fungi for improving phytoremediation efficiency in multi-metal contaminated soils, the fungal flora in root endosphere, rhizoplane, rhizosphere of Ricinus communis L. in heavy metal contaminated soils and non-heavy metal contaminated soils were compared by ITS amplicon sequencing, and then the critical fungal strains were isolated and inoculated into host plants to improve phytoremediation efficiency in Cd, Pb, and Zn-contaminated soils. The fungal ITS amplicon sequencing analysis indicated that the fungal community in root endosphere was more susceptible to heavy metals than those in rhizoplane and rhizosphere soils and Fusarium dominated the endophytic fungal community of R. communis L. roots under heavy metal stress. Three endophytic strains (Fusarium sp. F2, Fusarium sp. F8, and Fusarium sp. F14) isolated from Ricinus communis L. roots showed high resistances to multi-metals and possessed growth-promoting characteristics. Biomass and metal extraction amount of R. communis L. with Fusarium sp. F2, Fusarium sp. F8, and Fusarium sp. F14 inoculation in Cd-, Pb- and Zn-contaminated soils were significantly higher than those without the inoculation. The results suggested that fungal community analysis-guided isolation could be employed to obtain desired root-associated fungi for enhancing phytoremediation of multi-metal contaminated soils.
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Affiliation(s)
- Huaxiong Yao
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China; School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Wenguang Shi
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China; School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Xing Wang
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China; School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Junyan Li
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China; School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Meiqi Chen
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Jianbin Li
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Danting Chen
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Lin Zhou
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Zujun Deng
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China; School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
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102
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Gong X, Feng Y, Dang K, Jiang Y, Qi H, Feng B. Linkages of microbial community structure and root exudates: Evidence from microbial nitrogen limitation in soils of crop families. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163536. [PMID: 37075993 DOI: 10.1016/j.scitotenv.2023.163536] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Rhizosphere microorganisms are critical for crop nutrient cycling and soil ecological functions in agroecosystem soils; however, there is limited information regarding the role of root exudates in determining soil microbial communities and functions in plant-soil systems, especially for microbial nutrient limitations. In the present study, rhizosphere soil samples were collected from the main food crop families, including maize, soybean, potato, and buckwheat, representing the cereals, Leguminosae, Solanaceae, and Polygonaceae families, in the northern Loess Plateau, China, to investigate soil microbial co-occurrences and assembly processes and the relationship between soil microbes and root exudates. The results showed that the crop families greatly regulated the soil microbial community composition and assembly, and all microorganisms of the four species were subjected to N limitation via the vector analysis. The topological properties of the soil microbial networks varied with the crop family, demonstrating that the ecological relationships of bacterial taxa are more complex than those of fungi. Stochastic processes were more important in stimulating assembly across the four crop families; the non-dominated process governed >60 % of the critical ecological turnover in community assembly, whereas dispersal limitation was the key factor influencing fungal community assembly. Furthermore, the metabolic profiles of root exudates in response to microbial N limitation varied by family. Microbial function and metabolic limitations were strongly associated with variations in root exudates, especially amino acids and organic acids, which were directly facilitated by crop families. Our results highlight the key roles of root exudates in stimulating microbial community structure and ecological functions from the perspective of microbial nutrient limitation and improve our understanding of plant-microbe interactions in agricultural ecosystems.
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Affiliation(s)
- Xiangwei Gong
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, PR China.
| | - Yu Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Ke Dang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, PR China
| | - Ying Jiang
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, PR China
| | - Hua Qi
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, PR China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
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103
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Wang Z, Hu X, Solanki MK, Pang F. A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5030-5041. [PMID: 36946724 DOI: 10.1021/acs.jafc.2c08017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.
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Affiliation(s)
- Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
| | - Xiaohu Hu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice 40-701, Poland
| | - Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
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104
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Huang H, Liu S, Du Y, Tang J, Hu L, Chen X. Carbon allocation mediated by arbuscular mycorrhizal fungi alters the soil microbial community under various phosphorus levels. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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105
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Liu J, Sun X, Zuo Y, Hu Q, He X. Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert. Microbiol Res 2023; 269:127314. [PMID: 36724560 DOI: 10.1016/j.micres.2023.127314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity. However, little is known about the identities and communities of phyllosphere epiphytic microorganisms inhabiting the xerophyte leaf surface in the hot and dry environment. The diversity and community composition of phyllosphere epiphytes on different desert plants in Gansu, China, was investigated using the next-generation sequencing technique, revealing the diversity and community composition of the phyllosphere epiphytic bacteria associated with desert xerophytes. In addition, the ecological functions of the bacterial communities were investigated by combining the sequence classification information and prokaryotic taxonomic function annotation (FAPROTAX). This study determined the phyllosphere bacterial community composition, microbial interactions, and their functions. Despite harsh environments in the arid desert, we found that there are still diverse epiphytic bacteria on the leaves of desert plants. The bacterial communities mainly included Actinobacteria (52.79%), Firmicutes (31.62%), and Proteobacteria (12.20%). Further comparisons revealed different microbial communities, including Firmicutes at the phylum and Paenibacillaceae at the family level, in the phyllosphere among different plants, suggesting that the host plants had strong filter effects on bacteria. Co-occurrence network analysis revealed positive relationships were dominant among different bacterial taxa. The abundance of Actinobacteria and Proteobacteria was positively correlated, demonstrating their mutual relationship. On the other hand, the abundance of Firmicutes was negatively correlated, which suggested that they inhibit the growth of other bacterial taxa. FAPROTAX prediction revealed that chemoheterotrophy (accounting for 39.02% of the community) and aerobic chemoheterotrophy (37.01%) were the main functions of the leaf epiphytic bacteria on desert plants. This study improves our understanding of the community composition and ecological functions of plant-associated microbial communities inhabiting scattered niches in the desert ecosystem. In addition, the study provides insight into the biodiversity assessment in the desert region.
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Affiliation(s)
- Jiaqiang Liu
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xiang Sun
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Yiling Zuo
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Qiannan Hu
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xueli He
- School of Life Sciences, Hebei University, Baoding 071002, China.
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106
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Michl K, Berg G, Cernava T. The microbiome of cereal plants: The current state of knowledge and the potential for future applications. ENVIRONMENTAL MICROBIOME 2023; 18:28. [PMID: 37004087 PMCID: PMC10064690 DOI: 10.1186/s40793-023-00484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
The plant microbiota fulfils various crucial functions related to host health, fitness, and productivity. Over the past years, the number of plant microbiome studies continued to steadily increase. Technological advancements not only allow us to produce constantly increasing datasets, but also to extract more information from them in order to advance our understanding of plant-microbe interactions. The growing knowledge base has an enormous potential to improve microbiome-based, sustainable agricultural practices, which are currently poorly understood and have yet to be further developed. Cereal plants are staple foods for a large proportion of the world's population and are therefore often implemented in microbiome studies. In the present review, we conducted extensive literature research to reflect the current state of knowledge in terms of the microbiome of the four most commonly cultivated cereal plants. We found that currently the majority of available studies are targeting the wheat microbiome, which is closely followed by studies on maize and rice. There is a substantial gap, in terms of published studies, addressing the barley microbiome. Overall, the focus of most microbiome studies on cereal plants is on the below-ground microbial communities, and there is more research on bacteria than on fungi and archaea. A meta-analysis conducted in the frame of this review highlights microbiome similarities across different cereal plants. Our review also provides an outlook on how the plant microbiota could be harnessed to improve sustainability of cereal crop production.
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Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Golm, OT Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, Southampton, SO17 1BJ UK
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107
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Lan G, Wei Y, Li Y, Wu Z. Diversity and assembly of root-associated microbiomes of rubber trees. FRONTIERS IN PLANT SCIENCE 2023; 14:1136418. [PMID: 37063173 PMCID: PMC10102524 DOI: 10.3389/fpls.2023.1136418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Understanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees. METHODS We investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes. RESULTS We show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant-soil-environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil. DISCUSSION Our study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.
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Affiliation(s)
- Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Forestry Ecology Group, Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, China
| | - Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- College of Ecology and Environment, Hainan University, Haikou, Hainan, China
| | - Yuwu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Forestry Ecology Group, Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, China
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108
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Schultz CR, Johnson M, Wallace JG. Effects of Inbreeding on Microbial Community Diversity of Zea mays. Microorganisms 2023; 11:microorganisms11040879. [PMID: 37110300 PMCID: PMC10145435 DOI: 10.3390/microorganisms11040879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.
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109
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Shang S, Li L, Xiao H, Chen J, Zang Y, Wang J, Tang X. Studies on the Composition and Diversity of Seagrass Ruppia sinensis Rhizosphere Mmicroorganisms in the Yellow River Delta. PLANTS (BASEL, SWITZERLAND) 2023; 12:1435. [PMID: 37050062 PMCID: PMC10097283 DOI: 10.3390/plants12071435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Seagrass is a significant primary producer of coastal ecosystems; however, the continued degradation of seagrass beds is a serious problem that has attracted widespread attention from researchers. Rhizosphere microorganisms affect seagrass and participate in many life activities of seagrass. This study explored the relationship between the composition of microbes in the rhizosphere and the surrounding environment of Ruppia sinensis by using High-throughput sequencing methods. The dominant bacterial groups in the rhizosphere surface sediments of R. sinensis and the surrounding environment are Proteobacteria, Bacteroidota, and Firmicutes. Moreover, the dominant fungal groups are Ascomycota, Basidiomycota, and Chytridiomycota. Significant differences (p < 0.05) were identified in microbial communities among different groups (rhizosphere, bulk sediment, and surrounding seawater). Seventy-four ASVs (For bacteria) and 48 ASVs (For fungal) were shared among seagrass rhizosphere, surrounding sediment, and seawater. The rhizosphere was enriched in sulfate-reducing bacteria and nitrogen-fixing bacteria. In general, we obtained the rhizosphere microbial community of R. sinensis, which provided extensive evidence of the relative contribution of the seagrass rhizosphere and the surrounding environment.
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Affiliation(s)
- Shuai Shang
- School of Biological and Environmental Engineering, Binzhou University, Binzhou 256600, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
| | - Liangyu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
| | - Yu Zang
- First Institute of Oceanography, Department of Natural Resources, Qingdao 266061, China
| | - Jun Wang
- School of Biological and Environmental Engineering, Binzhou University, Binzhou 256600, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
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110
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Du XD, Wang J, Shen C, Wang J, Jing Z, Huang LN, Luo ZH, Ge Y. Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion? PLANTS (BASEL, SWITZERLAND) 2023; 12:1406. [PMID: 36987094 PMCID: PMC10052042 DOI: 10.3390/plants12061406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions. We established a two-year field biodiversity experiment with a native plant species richness gradient (1, 2, 4, or 8 species) and analyzed the effects of community structure and network complexity of leaf bacteria on invasion success. Our results indicated a positive relationship between invasibility and network complexity of leaf bacteria of the invader. Consistent with previous studies, we also found that native plant species richness increased the leaf bacterial diversity and network complexity. Moreover, the results of the leaf bacteria community assembly of the invader suggested that the complex bacteria community resulted from higher native diversity rather than higher invader biomass. We concluded that increased leaf bacterial network complexity along the native plant diversity gradient likely facilitated plant invasion. Our findings provided evidence of a potential mechanism by which microbes may affect the plant community invasibility, hopefully helping to explain the non-negative relationship between native diversity and invasibility.
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Affiliation(s)
- Xiang-Deng Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Wang
- School of Life Science, Taizhou University, Taizhou 318000, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongwang Jing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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111
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Zhu C, Lin Y, Wang Z, Luo W, Zhang Y, Chu C. Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem. Front Microbiol 2023; 14:1147285. [PMID: 37007520 PMCID: PMC10064055 DOI: 10.3389/fmicb.2023.1147285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant–epiphyte and plant–endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant–endophyte network, plant–epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.
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Affiliation(s)
- Chunchao Zhu
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
- *Correspondence: Chunchao Zhu,
| | | | - Zihui Wang
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Yonghua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
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112
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Wen Z, Yang M, Han H, Fazal A, Liao Y, Ren R, Yin T, Qi J, Sun S, Lu G, Hu S, Yang Y. Mycorrhizae Enhance Soybean Plant Growth and Aluminum Stress Tolerance by Shaping the Microbiome Assembly in an Acidic Soil. Microbiol Spectr 2023; 11:e0331022. [PMID: 36916950 PMCID: PMC10100836 DOI: 10.1128/spectrum.03310-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/16/2023] [Indexed: 03/15/2023] Open
Abstract
Strongly acidic soils are characterized by high aluminum (Al) toxicity and low phosphorus (P) availability, which suppress legume plant growth and nodule development. Arbuscular mycorrhizal fungi (AMF) stimulate rhizobia and enhance plant P uptake. However, it is unclear how this symbiotic soybean-AMF-rhizobial trio promotes soybean growth in acidic soils. We examined the effects of AMF and rhizobium addition on the growth of two soybean genotypes, namely, Al-tolerant and Al-sensitive soybeans as well as their associated bacterial and fungal communities in an acidic soil. With and without rhizobial addition, AMF significantly increased the fresh shoot and root biomass of Al-tolerant soybean by 47%/87% and 37%/24%, respectively. This increase in plant biomass corresponded to the enrichment of four plant growth-promoting rhizobacteria (PGPR) in the rhizospheric soil, namely, Chitinophagaceae bacterium 4GSH07, Paraburkholderia soli, Sinomonas atrocyanea, and Aquincola tertiaricarbonis. For Al-sensitive soybean, AMF addition increased the fresh shoot and root biomass by 112%/64% and 30%/217%, respectively, with/without rhizobial addition. Interestingly, this significant increase coincided with a decrease in the pathogenic fungus Nigrospora oryzae as well as an increase in S. atrocyanea, A. tertiaricarbonis, and Talaromyces verruculosus (a P-solubilizing fungus) in the rhizospheric soil. Lastly, the compartment niche along the soil-plant continuum shaped microbiome assembly, with pathogenic/saprotrophic microbes accumulating in the rhizospheric soil and PGPR related to nitrogen fixation or stress resistance (e.g., Rhizobium leguminosarum and Sphingomonas azotifigens) accumulating in the endospheric layer. IMPORTANCE Taken together, this study examined the effects of arbuscular mycorrhizal fungi (AMF) and rhizobial combinations on the growth of Al-tolerant and Al-sensitive soybeans as well as their associated microbial communities in acidic soils and concluded that AMF enhances soybean growth and Al stress tolerance by recruiting PGPR and altering the root-associated microbiome assembly in a host-dependent manner. In the future, these findings will help us better understand the impacts of AMF on rhizosphere microbiome assembly and will contribute to the development of soybean breeding techniques for the comprehensive use of PGPR in sustainable agriculture.
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Affiliation(s)
- Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hongwei Han
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yonghui Liao
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ran Ren
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shucun Sun
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, China
| | - Shuijin Hu
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Huang Y, Huang Y, Hou J, Wu L, Christie P, Liu W. Microbial community assembly of the hyperaccumulator plant Sedum plumbizincicola in two contrasting soil types with three levels of cadmium contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160917. [PMID: 36529394 DOI: 10.1016/j.scitotenv.2022.160917] [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: 09/27/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities are closely related to plant performance and numerous studies have shown their involvement with the growth and development of host plants, resistance to pathogen invasion and adaptation to environmental stress. Here we described in detail the ecological process of the microbial community assembly in hyperaccumulator plant Sedum plumbizincicola. We divided the microbiota into four ecological compartments (bulk soil, rhizosphere, root endosphere and aboveground endosphere). The results showed that host selection strongly controlled the aggregation of microbial community. So that microbes occupied different niches from the bulk soil to the aboveground endosphere, and bacterial diversity and network complexity decreased gradually. Soil types were the second influencing factor, especially for the microbial community in the root endosphere. The SourceTracker analysis further confirmed the vertical migration of microbes from bulk soil to aboveground endosphere. In addition, under the condition of heavy metal pollution, the microbial community of S. plumbizincicola tended to form a microbial pool dominated by Proteobacteria and Actinobacteria. Ellin6067, Sphingomonas, Ralstonia, SC-I-84_uncultured bacterium, Burkholderiaceae_Undibacterium and Pedosphaeraceae_uncultured bacterium etc. were identified as the vital biomarker taxa. Among these genera, the relative abundance of last three was significantly positively correlated with the activation and transfer of cadmium, and they mainly enriched in paddy soil. This study provides evidence for the mechanism by which the microbial community assembly occurs and experience for regulating the microbial community and increasing the accumulation efficiency of potentially toxic metals in S. plumbizincicola.
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Affiliation(s)
- Ya Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongjie Huang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China; Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu 241000, China.
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Nong H, Liu J, Chen J, Zhao Y, Wu L, Tang Y, Liu W, Yang G, Xu Z. Woody plants have the advantages in the phytoremediation process of manganese ore with the help of microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160995. [PMID: 36535473 DOI: 10.1016/j.scitotenv.2022.160995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The serious ecological damage caused by mining activities cannot be ignored. The use of an environmentally friendly restoration method to rebuild the vegetation and soil environment in the mining area has attracted more and more attention. This paper aims to study soil quality as well as vegetation characteristics of four woody species including Pinus massoniana (P. massoniana), Broussonetia papyrifera (B. papyrifera), Koelreuteria paniculata (K. paniculata), Osmanthus fragrans (O. fragrans), and two herbaceous species including Setaria viridis (S. viridis) and Cynodon dactylon (C. dactylon). In addition, we further clarified the effects of B. papyrifera and K. paniculata on soil nutrients and microbial communities after restoration. The results showed that the vegetation restoration area had better soil quality and plant community diversity, and the woody plants restoration effect were better. Compared with slag, B. papyrifera and K. paniculata remediation could improve soil pH and mitigate heavy metal contamination in mining areas, but was not effective in enhancing Soil Organic Matter (SOM), Total Nitrogen (TN), Total Potassium (TK) and Total Phosphorus (TP). In addition, the abundance and diversity of soil bacterial communities were increased. Of all the study sites, Proteobacteria had the greatest dominance. Vegetation restoration resulted in an increase in the relative abundance of Acidobacteria, while a decrease in Actinobacteria, Cyanobacteria and Firmicutes. With the restoration of vegetation, the increase of pH, the change of TN, SOM, TK, TP and the mitigation of Manganese (Mn) pollution were the main reasons affecting the soil microbial community. This study has great significance for understanding the ecological changes in the mining area after artificially mediated vegetation restoration, including changes in soil environment, plant community and microbial community, and woody plants will be more encouraged for the restoration of manganese mining areas.
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Affiliation(s)
- Huijiao Nong
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Beijing 100081, China
| | - Jun Liu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Junzhi Chen
- College of Forestry, Northwest A & F University, Yangling 712100, Shanxi, China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Liang Wu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Yongcheng Tang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Wensheng Liu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Guiyan Yang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Beijing 100081, China; College of Forestry, Northwest A & F University, Yangling 712100, Shanxi, China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; College of Forestry, Northwest A & F University, Yangling 712100, Shanxi, China.
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Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Habitats Within the Plant Root Differ in Bacterial Network Topology and Taxonomic Assortativity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:165-175. [PMID: 36463399 DOI: 10.1094/mpmi-09-22-0188-r] [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: 06/17/2023]
Abstract
The root microbiome is composed of distinct epiphytic (rhizosphere) and endophytic (endosphere) habitats. Differences in abiotic and biotic factors drive differences in microbial community diversity and composition between these habitats, though how they shape the interactions among community members is unknown. Here, we coupled a large-scale characterization of the rhizosphere and endosphere bacterial communities of 30 plant species across two watering treatments with co-occurrence network analysis to understand how root habitats and soil moisture shape root bacterial network properties. We used a novel bootstrapping procedure and null network modeling to overcome some of the limitations associated with microbial co-occurrence network construction and analysis. Endosphere networks had elevated node betweenness centrality versus the rhizosphere, indicating greater overall connectivity among core bacterial members of the root endosphere. Taxonomic assortativity was higher in the endosphere, whereby positive co-occurrence was more likely between bacteria within the same phylum while negative co-occurrence was more likely between bacterial taxa from different phyla. This taxonomic assortativity could be driven by positive and negative interactions among members of the same or different phylum, respectively, or by similar niche preferences associated with phylum rank among root inhabiting bacteria across plant host species. In contrast to the large differences between root habitats, drought had limited effects on network properties but did result in a higher proportion of shared co-occurrences between rhizosphere and endosphere networks. Our study points to fundamentally different ecological processes shaping bacterial co-occurrence across root habitats. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga L5L 1C6, Canada
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Julia Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto M5S 3B2, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto M5S 3B2, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto M5S 3B2, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto M5S 3B2, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto M5S 3B2, Canada
| | - Peter M Kotanen
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga L5L 1C6, Canada
| | - Marc T J Johnson
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga L5L 1C6, Canada
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Cheng Z, Zheng Q, Shi J, He Y, Yang X, Huang X, Wu L, Xu J. Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars. ISME COMMUNICATIONS 2023; 3:14. [PMID: 36813851 PMCID: PMC9947119 DOI: 10.1038/s43705-023-00213-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.
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Affiliation(s)
- Zhongyi Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Qiang Zheng
- Department of Mathematics and Theories, Peng Cheng Laboratory, Shenzhen, 518000, China
| | - Jiachun Shi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xueling Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xiaowei Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Laosheng Wu
- Department of Environmental Sciences, University of California, Riverside, CA, 92521, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
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Miao Y, Zhang X, Zhang G, Feng Z, Pei J, Liu C, Huang L. From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity. ENVIRONMENTAL MICROBIOME 2023; 18:11. [PMID: 36814319 PMCID: PMC9945605 DOI: 10.1186/s40793-023-00471-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism. RESULTS The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R2 = 0.29971; fungi, R2 = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite. CONCLUSIONS Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.
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Affiliation(s)
- Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Xing W, Gai X, Ju F, Chen G. Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160273. [PMID: 36460109 DOI: 10.1016/j.scitotenv.2022.160273] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.
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Affiliation(s)
- Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, PR China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China.
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Huang YH, Yang YJ, Wu X, Zhu CL, Lü H, Zhao HM, Xiang L, Li H, Mo CH, Li YW, Cai QY, Li QX. Adaptation of bacterial community in maize rhizosphere for enhancing dissipation of phthalic acid esters in agricultural soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 444:130292. [PMID: 36399821 DOI: 10.1016/j.jhazmat.2022.130292] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/19/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Rhizospheric degradation is a green and in situ strategy to accelerate dissipation of organic pollutants in soils. However, the mechanism on microbial degradation of phthalic acid esters (PAEs) in rhizosphere is still unclear. Here, the bacterial community and function genes in bulk and rhizospheric soils of maize (Zea mays L.) exposed to gradient concentrations of di-(2-ethylhexyl) phthalate (DEHP) were analyzed with 16 S rRNA, metagenomic sequencing and quantitative PCR (qPCR). Maize rhizosphere significantly increased the dissipation of DEHP by 4.02-11.5% in comparison with bulk soils. Bacterial community in rhizosphere exhibited more intensive response and shaped its beneficial structure and functions to DEHP stress than that in bulk soils. Both rhizospheric and pollution effects enriched more PAE-degrading bacteria (e.g., Bacillus and Rhizobium) and function genes in rhizosphere than in bulk soil, which played important roles in degradation of PAEs in rhizosphere. The PAE-degrading bacteria (including genera Sphingomonas, Sphingopyxis and Lysobacter) identified as keystone species participated in DEHP biodegradation. Identification of PAE intermediates and metagenomic reconstruction of PAE degradation pathways demonstrated that PAE-degrading bacteria degraded PAEs through cooperation with PAE-degrading and non-PAE-degrading bacteria. This study provides a comprehensive knowledge for the microbial mechanism on the superior dissipation of PAEs in rhizosphere.
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Affiliation(s)
- Yu-Hong Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yu-Jie Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaolian Wu
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Cui-Lan Zhu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huixiong Lü
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Qing X Li
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Wang L, Liu J, Zhang M, Wu T, Chai B. Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development. Microbiol Spectr 2023; 11:e0505122. [PMID: 36688664 PMCID: PMC9927475 DOI: 10.1128/spectrum.05051-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.
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Affiliation(s)
- Lixiao Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
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Yin Y, Wang YF, Cui HL, Zhou R, Li L, Duan GL, Zhu YG. Distinctive Structure and Assembly of Phyllosphere Microbial Communities between Wild and Cultivated Rice. Microbiol Spectr 2023; 11:e0437122. [PMID: 36625666 PMCID: PMC9927517 DOI: 10.1128/spectrum.04371-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Wild rice has been demonstrated to possess enriched genetic diversity and multiple valuable traits involved in disease/pest resistance and abiotic stress tolerance, which provides a potential resource for sustainable agriculture. However, unlike the plant compartments such as rhizosphere, the structure and assembly of phyllosphere microbial communities of wild rice remain largely unexplored. Through amplicon sequencing, this study compared the phyllosphere bacterial and fungal communities of wild rice and its neighboring cultivated rice. The core phyllosphere microbial taxa of both wild and cultivated rice are dominated with Pantoea, Methylobacterium, Nigrospora, and Papiliotrema, which are potentially beneficial to rice growth and health. Compared to the cultivated rice, Methylobacterium, Sphingomonas, Phaeosphaeria, and Khuskia were significantly enriched in the wild rice phyllosphere. The potentially nitrogen-fixing Methylobacterium is the dominated wild-enriched microbe; Sphingomonas is the hub taxon of wild rice networks. In addition, the microbiota of wild rice was more governed by deterministic assembly with a more complicated and stable community network than the cultivated rice. Our study provides a list of the beneficial microbes in the wild rice phyllosphere and reveals the microbial divergence between wild rice and cultivated rice in the original habitats, which highlights the potential selective role of wild rice in recruiting specific microbiomes for enhancing crop performance and promoting sustainable food production. IMPORTANCE Plant microbiota are being considered a lever to increase the sustainability of food production under a changing climate. In particular, the microbiomes associated with ancestors of modern cultivars have the potential to support their domesticated cultivars. However, few efforts have been devoted to studying the biodiversity and functions of microbial communities in the native habitats of ancestors of modern crop species. This study provides a list of the beneficial microbes in the wild rice phyllosphere and explores the microbial interaction patterns and the functional profiles of wild rice. This information could be useful for the future utilization of the plant microbiome to enhance crop performance and sustainability, especially in the framework of sustainable agroecosystems.
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Affiliation(s)
- Yue Yin
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Fei Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui-Ling Cui
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhou
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lv Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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122
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Busato S, Gordon M, Chaudhari M, Jensen I, Akyol T, Andersen S, Williams C. Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102326. [PMID: 36538837 PMCID: PMC9925409 DOI: 10.1016/j.pbi.2022.102326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The plant-associated microbiome is a key component of plant systems, contributing to their health, growth, and productivity. The application of machine learning (ML) in this field promises to help untangle the relationships involved. However, measurements of microbial communities by high-throughput sequencing pose challenges for ML. Noise from low sample sizes, soil heterogeneity, and technical factors can impact the performance of ML. Additionally, the compositional and sparse nature of these datasets can impact the predictive accuracy of ML. We review recent literature from plant studies to illustrate that these properties often go unmentioned. We expand our analysis to other fields to quantify the degree to which mitigation approaches improve the performance of ML and describe the mathematical basis for this. With the advent of accessible analytical packages for microbiome data including learning models, researchers must be familiar with the nature of their datasets.
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Affiliation(s)
- Sebastiano Busato
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA
| | - Max Gordon
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA
| | - Meenal Chaudhari
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA
| | - Ib Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Turgut Akyol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Stig Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA.
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123
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Li G, Liu P, Zhao J, Su L, Zhao M, Jiang Z, Zhao Y, Yang X. Correlation of microbiomes in "plant-insect-soil" ecosystem. Front Microbiol 2023; 14:1088532. [PMID: 36793880 PMCID: PMC9922863 DOI: 10.3389/fmicb.2023.1088532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Introduction Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance. Methods Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters. Results and Discussion Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.
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Affiliation(s)
- Guomeng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Peng Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Liangyinan Su
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Mengyu Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Zhengjie Jiang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,*Correspondence: Yang Zhao,
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,Xiping Yang,
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124
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Biget M, Wang T, Mony C, Xu Q, Lecoq L, Chable V, Theis KR, Ling N, Vandenkoornhuyse P. Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants. iScience 2023; 26:106031. [PMID: 36824281 PMCID: PMC9941212 DOI: 10.1016/j.isci.2023.106031] [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: 06/12/2022] [Revised: 09/07/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.
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Affiliation(s)
- Marine Biget
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Tingting Wang
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lucie Lecoq
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Véronique Chable
- UMR BAGAP INRAE, Centre Bretagne-Normandie, Domaine de la Motte, BP35327, 35653 Le Rheu Cedex, France
| | - Kevin R. Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China,Corresponding author
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France,Corresponding author
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125
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Lin Y, Fang L, Chen H, Sun X, He Y, Duan B, Li R, Cao C, Chen J. Sex-specific competition differently regulates the response of the rhizosphere fungal community of Hippophae rhamnoides-A dioecious plant, under Mn stress. Front Microbiol 2023; 14:1102904. [PMID: 36744096 PMCID: PMC9892859 DOI: 10.3389/fmicb.2023.1102904] [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: 11/19/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
In this study, we investigated the soil physicochemical parameters and responses of rhizospheric fungal communities of Hippophae rhamnoides to Mn stress under different sexual competition patterns. The results showed that competition significantly affects soil physicochemical properties, enzyme activity, and rhizosphere-associated fungal community structures. Under Mn stress, soils with intersexual competition had higher levels of N supply than those with the intrasexual competition. Moreover, fungal communities under intersexual interaction were more positive to Mn stress than intrasexual interaction. Under intrasexual competition, female plants had higher total phosphorus content, neutral phosphatase activity, and relative abundance of symbiotic fungi in soils to obtain phosphorus nutrients to alleviate Mn stress. In contrast, male plants had relatively stable fungal communities in soils. In the intersexual competition, rhizosphere fungal diversity and relative abundance of saprophytic fungi in male plants were significantly higher than in female plants under Mn stress. In addition, female plants showed greater plasticity in the response of rhizosphere microorganisms to their neighbors of different sexes. The microbial composition in soils of female plants varied more than male plants between intrasexual and intersexual competition. These results indicated that sex-specific competition and neighbor effects regulate the microbial community structure and function of dioecious plants under heavy metal stress, which might affect nutrient cycling and phytoremediation potential in heavy metal-contaminated soils.
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Affiliation(s)
- Yuhu Lin
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,School of Resources and Environmental Engineering, Mianyang Teachers’ College, Mianyang, China
| | - Ling Fang
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,School of Resources and Environmental Engineering, Mianyang Teachers’ College, Mianyang, China
| | - Hao Chen
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,School of Resources and Environmental Engineering, Mianyang Teachers’ College, Mianyang, China
| | - Xudong Sun
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China
| | - Yunxiao He
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China
| | - Baoli Duan
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Rui Li
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China
| | - Chuntao Cao
- Northwest Sichuan Geological Team, Sichuan Provincial Bureau of Geology and Mineral Resources Exploration and Development, Mianyang, China
| | - Juan Chen
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,*Correspondence: Juan Chen, ✉
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Zhang Y, Li X, Lu L, Huang F, Liu H, Zhang Y, Yang L, Usman M, Li S. Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees. Microorganisms 2023; 11:microorganisms11020233. [PMID: 36838198 PMCID: PMC9966171 DOI: 10.3390/microorganisms11020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R2 = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.
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Affiliation(s)
- Yifang Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaomin Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Correspondence: (L.L.); (S.L.)
| | - Fuyi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Yu Zhang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Luhua Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Muhammad Usman
- PEIE Research Chair for the Development of Industrial Estates and Free Zones, Center for Environmental Studies and Research, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Shun Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence: (L.L.); (S.L.)
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Sun Y, Li X, Ding C, Pan Q, Wang J. Host species and microplastics differentiate the crop root endophytic antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130091. [PMID: 36206714 DOI: 10.1016/j.jhazmat.2022.130091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/18/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The increasing One-Health concept calls for a more in-depth understanding of the dissemination of antibiotic resistance in plant microbiomes. While there is considerable published evidence that microplastics can promote the spread of antibiotic resistance genes (ARGs) in the environment, whether and how microplastics impact the plant endophytic resistome are largely unknown. Here we examined the ARGs along the soil-root continuum of maize and wheat under the pressure of microplastics. Amendment with heavy metals was also included as they can apply the selective pressure for ARG spread as well. The crop species and genotypes had significant effects on the root endophytic ARG abundance and diversity. The greatest ARG abundance was observed in the maize ZD958 endophytes (0.215 copies per 16S rRNA gene), followed by the maize XY335 (0.092 copies per 16S rRNA gene). For each crop genotype, amendment with microplastics and heavy metals significantly increased the ARG abundances and changed their profiles in root endophytes. The endophytic ARG variances were closely associated with the endophytic microbiome, the rhizosphere bacterial communities and resistome. Additionally, the level of endophytic ARGs was positively relevant to the abundance of mobile genetic elements (MGEs). These findings suggested that the root endophytic resistome was primarily affected by the crop species, and microplastics might show enhancement effects on the endophytic resistome via changing the root-associated microbiome and facilitating the MGE mediation. Overall, this study, for the first time, highlights the root endophytic ARG emergence and dissemination induced by microplastics.
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Affiliation(s)
- Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xinfei Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Changfeng Ding
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingchun Pan
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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128
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Bai L, Wang Y, Li Y, Zhang X, Lu Z, Zhang D, Sun F, Zhao X. Changes in the Microbial Community in Maize ( Zea mays L.) Root Spatial Structure Following Short-Term Nitrogen Application. ACS OMEGA 2023; 8:208-218. [PMID: 36643453 PMCID: PMC9835084 DOI: 10.1021/acsomega.2c01711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
The beneficial interactions between crop roots and microbiomes play a key role in crop nutrient availability, growth promotion, and disease suppression. Recent research, however, rarely reported the effects of nitrogen (N) application rate on microbial community composition at different spatial structures in the maize root zone. Therefore, one experiment was conducted to examine the influence of three N-application levels (0, 180, and 360 kg N ha-1) on microbial community composition in three root-associated compartments of maize (bulk soil, rhizoplane, and endosphere). The microbial diversity and community composition differed significantly among the various compartments. The effects of N application on fungal composition decreased in the order bulk soil > rhizosphere > endosphere at different sampling positions. Also, the fungal composition was more sensitive to the N-fertilizer rate in the bulk soil and the rhizosphere than the bacterial community. A total of 14.42, 9.46, and 3.55% of all taxonomic groups were sensitive to N fertilizer, respectively. The keystone species fungal groups were Humicola (bulk soil), Gibberella (rhizosphere soil), and Humicola (endosphere). Together, our results demonstrate that compared with that of the bacterial community, the fungal community composition was more susceptible to different N-application rates. N fertilization affected the distribution of microflora by changing soil physicochemical properties and enzyme activities. There were strong correlations between microbial communities in maize under the N180 treatment. Moreover, the N180 treatment had the maximum fresh yield and biomass at 64.5 and 24.3 kg·ha-1, respectively.
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Affiliation(s)
- Lanfang Bai
- Faculty
of Agronomy College, Inner Mongolia Agricultural
University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Yufen Wang
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Yahua Li
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Xiangqian Zhang
- Faculty
of Agronomy College, Inner Mongolia Agricultural
University, Hohhot, Inner Mongolia 010070, P. R. China
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
| | - Zhanyuan Lu
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
| | - Dejian Zhang
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Fengcheng Sun
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
| | - Xiaoqing Zhao
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
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129
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Wang Z, Hu X, Qu Q, Hao W, Deng P, Kang W, Feng R. Dual regulatory effects of microplastics and heat waves on river microbial carbon metabolism. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129879. [PMID: 36084464 DOI: 10.1016/j.jhazmat.2022.129879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Rivers play a critical role in the global carbon cycle, but the processes can be affected by widespread microplastic (MP) pollution and the increasing frequency of heat waves (HWs) in a warming climate. However, little is known about the role of river microbes in regulating the carbon cycle under the combined action of MP pollution and HWs. Here, through seven-day MP exposure and three cycles of HW simulation experiments, we found that MPs inhibited the thermal adaptation of the microbial community, thus regulating carbon metabolism. The CO2 release level increased, while the carbon degradation ability and the preference for stable carbon were inhibited. Metabonomic, 16 S rRNA and ITS gene analyses further revealed that the regulation of carbon metabolism was closely related to the microbial r-/K- strategy, community assembly and transformation of keystone taxa. The random forest model revealed that dissolved oxygen and ammonia-nitrogen were important variables influencing microbial carbon metabolism. The above findings regarding microbe-mediated carbon metabolism provide insights into the effect of climate-related HWs on the ecological risks of MPs.
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Affiliation(s)
- Zhongwei Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Qian Qu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Weidan Hao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Peng Deng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Ruihong Feng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education),Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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130
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Arnault G, Mony C, Vandenkoornhuyse P. Plant microbiota dysbiosis and the Anna Karenina Principle. TRENDS IN PLANT SCIENCE 2023; 28:18-30. [PMID: 36127241 DOI: 10.1016/j.tplants.2022.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/19/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.
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Affiliation(s)
- Gontran Arnault
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
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131
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Luo Y, Wang J, Wang C, Wang D, Li C, Zhang B, Zhong X, Chen L, Li H, Su H, Zheng Q, Zhu D, Tang H, Guo L. The fecal arsenic excretion, tissue arsenic accumulation, and metabolomics analysis in sub-chronic arsenic-exposed mice after in situ arsenic-induced fecal microbiota transplantation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158583. [PMID: 36084774 DOI: 10.1016/j.scitotenv.2022.158583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Arsenic can be specifically enriched by rice, and the health hazards caused by high arsenic rice are gradually attracting attention. This study aimed to explore the potential of microbial detoxification via gut microbiome in the treatment of sub-chronic arsenic poisoning. We first exposed mice to high-dose arsenic feed (30 mg/kg, rice arsenic composition) for 60 days to promote arsenic-induced microbes in situ in the gastrointestinal tract, then transplanted their fecal microbiota (FMT) into another batch of healthy recipient mice, and dynamically monitored the microbial colonization by 16S rRNA sequencing and ITS sequencing. The results showed that in situ arsenic-induced fecal microbiome can stably colonized and interact with indigenous microbes in the recipient mice in two weeks, and established a more stable network of gut microbiome. Then, the recipient mice continued to receive high-dose arsenic exposure for 52 days. After above sub-chronic arsenic exposure, compared with the non-FMT group, fecal arsenic excretion, liver and plasma arsenic accumulation were significantly lower (P < 0.05), and that in kidney, hair, and thighbone present no significant differences. Metabolomics of feces- plasma-brain axis were also disturbed, some up-regulated metabolites in feces, plasma, and cerebral cortex may play positive roles for the host. Therefore, microbial detoxification has potential in the treatment of sub-chronic arsenic poisoning. However, gut flora is an extremely complex community with different microorganisms have different arsenic metabolizing abilities, and various microbial metabolites. Coupled with the matrix effects, these factors will have various effects on the efflux and accumulation of arsenic. The definite effects (detoxification or non-detoxification) could be not assured based on the current study, and more systematic and rigorous studies are needed in the future.
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Affiliation(s)
- Yu Luo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Jiating Wang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Chenfei Wang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China; Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen 518000, China
| | - Dongbin Wang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Chengji Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Bin Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Xiaoting Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Linkang Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Hao Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Hongtian Su
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Qiuyi Zheng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Dajian Zhu
- Department of Surgery, Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan 528399, China.
| | - Huanwen Tang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Lianxian Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
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132
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Zeng Q, Man X, Huang Z, Zhuang L, Yang H, Sha Y. Effects of rice blast biocontrol strain Pseudomonas alcaliphila Ej2 on the endophytic microbiome and proteome of rice under salt stress. Front Microbiol 2023; 14:1129614. [PMID: 36960288 PMCID: PMC10027718 DOI: 10.3389/fmicb.2023.1129614] [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: 12/22/2022] [Accepted: 02/13/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction Soil salinity is a prevalent environmental stress in agricultural production. Microbial inoculants could effectively help plants to alleviate salt stress. However, there is little knowledge of the biocontrol strain Pseudomonas alcaliphila Ej2 mechanisms aiding rice plants to reduce the adverse effects caused by salt stress. Methods We performed integrated field and greenhouse experiments, microbial community profiling, and rice proteomic analysis to systematically investigate the Ej2 mechanism of action. Results The results displayed that biocontrol strain Ej2 increased shoot/root length and fresh/dry weight compared with control under salt stress. Meanwhile, strain Ej2 has the ability to control rice blast disease and promote rice growth. Furthermore, the microbial community analysis revealed that the alpha-diversity of Ej2-inoculated plants was higher than the control plants, expect the Shannon index of the bacterial microbiome and the Ej2-inoculated samples clustered and separated from the control samples based on beta-diversity analysis. Importantly, the enriched and specific OTUs after Ej2 inoculation at the genus level were Streptomyces, Pseudomonas, Flavobacterium, and Bacillus. Moreover, we observed that Ej2 inoculation influenced the rice proteomic profile, including metabolism, plant-pathogen interactions, and biosynthesis of unsaturated fatty acids. These results provide comprehensive evidence that Ej2 inoculation induced the rice endophytic microbiome and proteomic profiles to promote plant growth under salt stress. Discussion Understanding the biocontrol strain effects on the endophytic microbiome and rice proteomics will help us better understand the complex interactions between plants and microorganisms under salt stress. Furthermore, unraveling the mechanisms underlying salt tolerance will help us more efficiently ameliorate saline soils.
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Affiliation(s)
- Qingchao Zeng
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Zeyang Huang
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Lubo Zhuang
- Institute of Plant Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Hanmeng Yang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- *Correspondence: Yuexia Sha,
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133
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Tao S, Yin H, Fang Y, Zhang Y, Zhang N, Qu L. Elevated O 3 concentrations alter the compartment-specific microbial communities inhabiting rust-infected poplars. Environ Microbiol 2022; 25:990-1006. [PMID: 36582119 DOI: 10.1111/1462-2920.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Elevated ozone (O3 ) can affect the susceptivity of plants to rust pathogens. However, the collective role of microbiomes involved in such interaction remains largely elusive. We exposed two cultivated poplar clones exhibiting differential O3 sensitivities, to non-filtered ambient air (NF), NF + 40 ppb or NF + 60 ppb O3 -enriched air in field open-top chambers and then inoculated Melampsora larici-populina urediniospores to study their response to rust infection and to investigate how microbiomes inhabiting four compartments (phyllosphere, rhizosphere, root endosphere, bulk soil) are involved in this response. We found that hosts with higher O3 sensitivity had significantly lower rust severity than hosts with lower sensitivity. Furthermore, the effect of increased O3 on the diversity and composition of microbial communities was highly dependent on poplar compartments, with the microbial network complexity patterns being completely opposite between the two clones. Notably, microbial source analysis estimated that phyllosphere fungal communities predominately derived from root endosphere and vice versa, suggesting a potential transmission mechanism between plant above- and below-ground systems. These promising results suggest that further investigations are needed to better understand the interactions of abiotic and biotic stresses on plant performance and the role of the microbiome in driving these changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Haiyue Yin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yue Fang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Laiye Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, China
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134
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Li X, Jin Z, Xiong L, Tong L, Zhu H, Zhang X, Qin G. Effects of Land Reclamation on Soil Bacterial Community and Potential Functions in Bauxite Mining Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16921. [PMID: 36554801 PMCID: PMC9778865 DOI: 10.3390/ijerph192416921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Studying the characteristics of microorganisms in mine reclamation sites can provide a scientific reference basis for mine land reclamation. Soils in the plough layer (0-20 cm) of the bauxite mine plots in Pingguo city, Guangxi Zhuang Autonomous Region, China, with different reclamation years were used as the research objects. The community structure of soil bacteria was analyzed with high-throughput sequencing technology. The results show the following: (1) Reclamation significantly increased the contents of soil nutrients (p < 0.05). (2) The relative abundances of Proteobacteria were high (22.90~41.56%) in all plots, and reclamation significantly reduced the relative abundances of Firmicutes (3.42-10.77%) compared to that in the control plot (24.74%) (p < 0.05). The relative abundances of α-proteobacteria generally increased while the reclamation year increased. The relative abundances of α-proteobacteria and γ-proteobacteria showed significant positive correlations with soil carbon, nitrogen, and phosphorus nutrients (p < 0.01). The relative abundance of Acidobacteria Group 6 showed significant positive correlations with soil exchangeable Ca and Mg (p < 0.01). (3) Bacterial co-occurrence network showed more Copresence interactions in all plots (50.81-58.39%). The reclaimed plots had more nodes, higher modularity, and longer characteristic path length than the control plot, and the keystone taxa changed in different plots. (4) The chemoheterotrophy and aerobic chemoheterotrophy were the most abundant functional groups in all plots (35.66-48.26%), while reclamation reduced the relative abundance of fermentation groups (1.75-11.21%). The above findings indicated that reclamation improved soil nutrients, changed the bacterial community structure and potential functions, and accelerated the microbial stabilization of the reclaimed soil.
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Affiliation(s)
- Xuesong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Zhenjiang Jin
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin 541004, China
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Liyuan Xiong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Lingchen Tong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Hongying Zhu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Xiaowen Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Guangfa Qin
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
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135
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Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. MICROBIOME 2022; 10:217. [PMID: 36482420 PMCID: PMC9733318 DOI: 10.1186/s40168-022-01383-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND From a theoretical ecology point of view, microbiomes are far more complex than expected. Besides competition and competitive exclusion, cooperative microbe-microbe interactions have to be carefully considered. Metabolic dependencies among microbes likely explain co-existence in microbiota. METHODOLOGY In this in silico study, we explored genome-scale metabolic models (GEMs) of 193 bacteria isolated from Arabidopsis thaliana roots. We analyzed their predicted producible metabolites under simulated nutritional constraints including "root exudate-mimicking growth media" and assessed the potential of putative metabolic exchanges of by- and end-products to avoid those constraints. RESULTS We found that the genome-encoded metabolic potential is quantitatively and qualitatively clustered by phylogeny, highlighting metabolic differentiation between taxonomic groups. Random, synthetic combinations of increasing numbers of strains (SynComs) indicated that the number of producible compounds by GEMs increased with average phylogenetic distance, but that most SynComs were centered around an optimal phylogenetic distance. Moreover, relatively small SynComs could reflect the capacity of the whole community due to metabolic redundancy. Inspection of 30 specific end-product metabolites (i.e., target metabolites: amino acids, vitamins, phytohormones) indicated that the majority of the strains had the genetic potential to produce almost all the targeted compounds. Their production was predicted (1) to depend on external nutritional constraints and (2) to be facilitated by nutritional constraints mimicking root exudates, suggesting nutrient availability and root exudates play a key role in determining the number of producible metabolites. An answer set programming solver enabled the identification of numerous combinations of strains predicted to depend on each other to produce these targeted compounds under severe nutritional constraints thus indicating a putative sub-community level of functional redundancy. CONCLUSIONS This study predicts metabolic restrictions caused by available nutrients in the environment. By extension, it highlights the importance of the environment for niche potential, realization, partitioning, and overlap. Our results also suggest that metabolic dependencies and cooperation among root microbiota members compensate for environmental constraints and help maintain co-existence in complex microbial communities. Video Abstract.
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Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35000, Rennes, France
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | - Nathan Vannier
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | | | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany.
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136
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Yang M, Luo F, Song Y, Ma S, Ma Y, Fazal A, Yin T, Lu G, Sun S, Qi J, Wen Z, Li Y, Yang Y. The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities. Microb Biotechnol 2022; 15:2942-2957. [PMID: 36336802 PMCID: PMC9733649 DOI: 10.1111/1751-7915.14164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate-treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil-plant continuum largely control the composition and function of the root-associated microbiome of triple transgenic soybean.
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Affiliation(s)
- Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Fuhe Luo
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Yuchen Song
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Shenglin Ma
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Yudi Ma
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Tongming Yin
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- School of Life SciencesHuaiyin Normal UniversityHuaianChina
| | - Shucun Sun
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, College of Environmental and Resource SciencesZhejiang A&F UniversityHangzhouChina
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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137
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Li WJ, Li HZ, An XL, Lin CS, Li LJ, Zhu YG. Effects of manure fertilization on human pathogens in endosphere of three vegetable plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120344. [PMID: 36206891 DOI: 10.1016/j.envpol.2022.120344] [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: 05/06/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Pathogens can colonize plant endosphere and, be transferred into human beings through the food chain. However, our understanding of the influences of agricultural activities, such as fertilization, on endophytic microbial communities and human pathogens is still limited. Here, we conducted a microcosm experiment using the combination of 16 S rRNA gene amplicon sequencing and high-throughput qPCR array to reveal the effects of manure fertilization on microbiomes of soils and plants and how such impact is translated into endophytic pathogens. Our results showed that manure fertilization significantly altered soil microbiomes, whereas with less influence on endophytic microbial communities. Soil is a vital source of both bacterial communities and human pathogens for the plant endosphere. The abundance of pathogens was increased both in soils and endosphere under manure fertilization. These findings provide an integrated understanding of the impact of manure fertilization on endophytic pathogens.
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Affiliation(s)
- Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Chen-Shuo Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Li-Juan Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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138
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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139
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Li D, Yao H, Zhu X, Li Z, Zeng X. Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:90495-90508. [PMID: 35870064 DOI: 10.1007/s11356-022-22145-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Intestinal microbes regulate the development of diseases induced by environmental exposure. Thallium (Tl) is a highly toxic heavy metal, and its toxicity is rarely discussed in relation to gut microbes. Herein, we showed that Tl(I) exposure (10 ppm for 2 weeks) affected the alpha diversity of bacteria in the ileum, colon, and feces, but had little effect on the beta diversity of bacteria through 16S rRNA sequencing. LEfSe analysis revealed that Tl(I) exposure changed the abundance of intestinal microbiota along the digestive tract. Cecum metabolomic detection and analysis showed that Tl(I) exposure altered the abundance and composition of metabolites. In addition, the Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure impaired amino acid, lipid, purine metabolism, and G protein-coupled receptor signalling pathways. A consistency test revealed a strong correlation, and a Pearson's correlation analysis showed an extensive interaction, between microorganisms and metabolites. Analysis of the intestinal immunity revealed that Tl(I) exposure suppressed the immune responses, which also had regional differences. These results identify the perturbation of the intestinal microenvironment by Tl exposure and provide a new explanation for Tl toxicity.
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Affiliation(s)
- Dong Li
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Huan Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Xiaohua Zhu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China.
- College of Environmental and Civil Engineering, Chengdu University of Technology, Chengdu, 610059, Sichuan, China.
| | - Zeqin Li
- College of Environmental and Civil Engineering, Chengdu University of Technology, Chengdu, 610059, Sichuan, China
| | - Xianyin Zeng
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
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Alfradique Monteiro D, Fazolato CSB, Martins LF, Tavora Coelho da Costa Rachid C. The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model. FEMS Microbiol Ecol 2022; 98:6825450. [PMID: 36370453 DOI: 10.1093/femsec/fiac135] [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: 09/26/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant-microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.
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Affiliation(s)
- Douglas Alfradique Monteiro
- Laboratory of Biotechnology and Microbial Ecology, Department of General Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolline Silva Barbosa Fazolato
- Laboratory of Biotechnology and Microbial Ecology, Department of General Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Caio Tavora Coelho da Costa Rachid
- Laboratory of Biotechnology and Microbial Ecology, Department of General Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Zhang Z, Chai X, Gao Y, Zhang B, Lu Y, Du Y, Zhang Y, Ding Y, Tariq A, Ullah A, Li X, Zeng F. Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages. Microorganisms 2022; 10:microorganisms10122376. [PMID: 36557629 PMCID: PMC9785364 DOI: 10.3390/microorganisms10122376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.
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Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- Correspondence: (Z.Z.); (F.Z.)
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yan Lu
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yi Du
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Ya Ding
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Z.Z.); (F.Z.)
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Zhao J, Zhang H, Liu J, Ke Z, Xiang C, Zhang L, Li K, Lai Y, Ding X, Tan Y. Role of jellyfish in mesozooplankton community stability in a subtropical bay under the long-term impacts of temperature changes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157627. [PMID: 35907549 DOI: 10.1016/j.scitotenv.2022.157627] [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: 02/12/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
To understand zooplankton community changes in the context of climate change and anthropogenic disturbances, we analyzed mesozooplankton samples from four seasons in the subtropical Daya Bay, which is susceptible to perceived disturbances in the South China Sea. The zooplankton community was found to be divided into two clusters, namely the Outer-bay Cluster (OC) comprising Noctiluca scintillans, Temora turbinata, and Paracalanus spp., and the Inner-bay Cluster (IC) which was dominated by Pseudevadne tergestina, Oikopleura rufescens, and Paracalanus spp. The OC was recorded in waters with low Chl a concentrations and high salinity, coinciding with open seawater intrusion. The IC occurred in waters with high Chl a concentrations, low salinity, with terrestrial inputs from the Dan'ao River. The dominant cladoceran species has changed in spring from Penilia avirostris to Pseudevadne tergestina owing to suitable temperature conditions and the low wind speed in this region. Most of the keystone species recorded during all seasons were found to be copepods based on co-occurrence network analysis. Numbers of keystone jellyfish (cnidaria) species, such as Geryonia proboscidalis, Chelophyes contorta, and Aeginura grimaldi were significantly higher in summer than in other seasons due to a low-temperature seawater intrusion, which can result in the highest stability of community structures and affect coastal food webs and fishery resources. Our results highlight that zooplankton community succession may occur with long-term temperature changes in the subtropical Daya Bay under global climate change conditions.
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Affiliation(s)
- Jingjing Zhao
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Huangchen Zhang
- Guangdong Center for Marine Development Research, Guangzhou 510220, China
| | - Jiaxing Liu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhixin Ke
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Chenhui Xiang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Liming Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaizhi Li
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yanjiao Lai
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiang Ding
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yehui Tan
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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143
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Xu Y, Yang Z, Wang X, Chai H, Li S, Wu Y, Wang R. Land use differentially affects fungal communities and network complexity in northeast China. Front Microbiol 2022; 13:1064363. [DOI: 10.3389/fmicb.2022.1064363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
BackgroundThe soil fungal community is one of the most important drivers of the soil nutrient cycling that sustains plant growth. However, little research has been done on the effects of different land uses on soil fungal communities in northeast China.MethodsIn this study, we conducted a field experiment to investigate the effects of continuous cropping of grass, maize, and alfalfa on their respective fungal communities and co-occurrence networks.ResultsWe showed that the physicochemical properties of the soil, such as nitrate (NO3-N), available phosphorus, and soil pH, were the most important driving factors affecting the structure of the soil fungal community in different cropping systems. In addition, compared to the cultivation of grass and maize, the continuous cropping of alfalfa increased the abundance of several beneficial as well as pathogenic species, such as Mortierella and Gaiellales. In addition, the networks differed among plant species and according to the number of years of continuous cultivation.ConclusionThis suggests that the continuous cropping of alfalfa results in greater cooperation among fungi, which may be beneficial to the soil as well as to the development of the alfalfa.
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May-Mutul CG, López-Garrido MA, O’Connor-Sánchez A, Peña-Ramírez YJ, Labrín-Sotomayor NY, Estrada-Medina H, Ferrer MM. Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3098. [PMID: 36432829 PMCID: PMC9699097 DOI: 10.3390/plants11223098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
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Affiliation(s)
- Carla G. May-Mutul
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miguel A. López-Garrido
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Aileen O’Connor-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
| | - Yuri J. Peña-Ramírez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Natalia Y. Labrín-Sotomayor
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Héctor Estrada-Medina
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miriam M. Ferrer
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
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Pantigoso HA, Newberger D, Vivanco JM. The rhizosphere microbiome: Plant-microbial interactions for resource acquisition. J Appl Microbiol 2022; 133:2864-2876. [PMID: 36648151 PMCID: PMC9796772 DOI: 10.1111/jam.15686] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 01/21/2023]
Abstract
While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant's own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant-microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.
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Affiliation(s)
- Hugo A. Pantigoso
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Derek Newberger
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Jorge M. Vivanco
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
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Chen X, Chen H, Zhao J, Xin Y, Li Y. Bacterial community structure and diversity in the rhizospheric soil of Robinia pseudoacacia and Juniperus sabina planted in iron tailings matrix. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:83404-83416. [PMID: 35763144 DOI: 10.1007/s11356-022-21669-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Iron tailings matrix is deficient in nutrients, and phytoremediation is one of the effective methods to improve tailings nutrients. The response of phytoremediation to tailings microorganisms remains to be studied. The present study analyzed rhizospheric soil of two kinds of plants bacterial diversity and community structure and their relationship with soil environmental factors. The results indicate that the rhizospheric soil bacteria species of Robinia pseudoacacia and Juniperus sabina were not significantly different from that of bare tailings, but rhizospheric soil bacterial community compositions and abundance were significantly different from that of bare tailings. Canonical correlation analysis (CCA) showed that soil alkali-hydrolyzable nitrogen (AN), soil total nitrogen (TN), and soil organic matter (SOM) were the main environmental factors affecting bacterial community diversity. Spearman's correlation analysis showed that AN, TN, and SOM were significantly positively correlated with the relative abundance of Gemmatimonadetes and Nitrospirae, and were significantly negatively correlated with that of Firmicutes, Fusobacteria, and Bacteroidetes. FAPROTAX function prediction showed that the functional microbial communities of rhizospheric soil of the two plants were significantly different from those of bare tailings. Overall, the findings support an increase of microbial diversity, SOM, and nitrogen in rhizospheric soil of revegetated tailings compared to bare tailings. These results provide theoretical support for the development and application of phytoremediation in abandoned mines.
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Affiliation(s)
- Xiaolin Chen
- College of Forestry, Hebei Agricultural University, No. 2596, Lekai South Street, Lianchi District, Baoding City, 071000, Hebei Province, China
| | - Haipeng Chen
- College of Forestry, Hebei Agricultural University, No. 2596, Lekai South Street, Lianchi District, Baoding City, 071000, Hebei Province, China
| | - Jiaqi Zhao
- College of Forestry, Hebei Agricultural University, No. 2596, Lekai South Street, Lianchi District, Baoding City, 071000, Hebei Province, China
| | - Yue Xin
- College of Forestry, Hebei Agricultural University, No. 2596, Lekai South Street, Lianchi District, Baoding City, 071000, Hebei Province, China
| | - Yuling Li
- College of Forestry, Hebei Agricultural University, No. 2596, Lekai South Street, Lianchi District, Baoding City, 071000, Hebei Province, China.
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Tan X, Xie H, Yu J, Wang Y, Xu J, Xu P, Ma B. Host genetic determinants drive compartment-specific assembly of tea plant microbiomes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2174-2186. [PMID: 35876474 PMCID: PMC9616527 DOI: 10.1111/pbi.13897] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Diverse host factors drive microbial variation in plant-associated environments, whereas their genetic mechanisms remain largely unexplored. To address this, we coupled the analyses of plant genetics and microbiomes in this study. Using 100 tea plant (Camellia sinensis) cultivars, the microbiomes of rhizosphere, root endosphere and phyllosphere showed clear compartment-specific assembly, whereas the subpopulation differentiation of tea cultivars exhibited small effects on microbial variation in each compartment. Through microbiome genome-wide association studies, we examined the interactions between tea genetic loci and microbial variation. Notably, genes related to the cell wall and carbon catabolism were heavily linked to root endosphere microbial composition, whereas genes related to the metabolism of metal ions and small organic molecules were overrepresented in association with rhizosphere microbial composition. Moreover, a set of tea genetic variants, including the cytoskeleton-related formin homology interacting protein 1 gene, were strongly associated with the β-diversity of phyllosphere microbiomes, implying their interactions with the overall structure of microbial communities. Our results create a catalogue of tea genetic determinants interacting with microbiomes and reveal the compartment-specific microbiome assembly driven by host genetics.
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Affiliation(s)
- Xiangfeng Tan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Hengtong Xie
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jingwen Yu
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Yuefei Wang
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
| | - Ping Xu
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
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148
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Li J, Liu YX, Lü PP, Wang YL, Li ZF, Zhang Y, Gan HY, Li XC, Mandal D, Cai J, Guo ZX, Yao H, Guo LD. Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland. Microbiol Spectr 2022; 10:e0226022. [PMID: 36135597 PMCID: PMC9604091 DOI: 10.1128/spectrum.02260-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/28/2022] [Indexed: 01/04/2023] Open
Abstract
Distinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland. IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil - plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Xuan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Peng Lü
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Yong-Long Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Zhong-Feng Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hui-Yun Gan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dipa Mandal
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Xuan Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hui Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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149
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Lin Q, Wang Y, Li M, Xu Z, Li L. Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L. FRONTIERS IN PLANT SCIENCE 2022; 13:988485. [PMID: 36340378 PMCID: PMC9632346 DOI: 10.3389/fpls.2022.988485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The plant microbiome profoundly affects many aspects of host performance; however, the ecological processes by which plant hosts govern microbiome assembly, function, and dispersal remain largely unknown. Here, we investigated the bacterial and fungal communities in multiple compartment niches (bulk soil, rhizosphere soil, root endosphere, phylloplane, and leaf endosphere) of Casuarina equisetifolia L. at three developmental stages in Hainan Province, China. We found that microbiome assemblages along the soil-plant continuum were shaped by the compartment niches. Bacterial diversity and richness decreased from the soils to roots to leaves, with the highest network complexity found in the roots and the lowest found in the phylloplane. However, fungal diversity gradually increased from the soils to roots to phyllosphere, whereas fungal richness decreased from the soils to roots but increased from the roots to phyllosphere; the greatest network complexity was found in bulk soils and the lowest was found in the roots. Different biomarker taxa occurred in the different ecological niches. Bacterial and fungal communities exhibited distinct ecological functions; the former played important roles in maintaining plant growth and providing nutrients, whereas the latter predominantly decomposed organic matter. The bacterial community of C. equisetifolia mostly originated from bulk soil, whereas the fungal community was mainly derived from rhizosphere soil and air. Leaf endophytes were positively correlated with organic carbon, and root and soil microorganisms were positively correlated with total nitrogen, total phosphorus, and total potassium. Our findings provide empirical evidence for plant-microbiome interactions and contribute to future research on non-crop management and the manipulation of non-crop microbiomes.
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150
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Lu Q, Hu C, Cai L, Wu C, Zhang H, Wei L, Zhang T, Hu H, Liu S, Lei J, Ge T, Dai L, Yang J, Chen J. Changes in soil fungal communities after onset of wheat yellow mosaic virus disease. Front Bioeng Biotechnol 2022; 10:1033991. [PMID: 36324899 PMCID: PMC9621598 DOI: 10.3389/fbioe.2022.1033991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 10/29/2023] Open
Abstract
Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 +) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 + is the most important soil physicochemical factor influencing fungal diversity and community composition.
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Affiliation(s)
- Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Cailin Hu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chuanfa Wu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Haoqing Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Liang Wei
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Haichao Hu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shuang Liu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jiajia Lei
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tida Ge
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
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