1
|
Todorović I, Moënne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D. Microbial diversity in soils suppressive to Fusarium diseases. FRONTIERS IN PLANT SCIENCE 2023; 14:1228749. [PMID: 38111879 PMCID: PMC10726057 DOI: 10.3389/fpls.2023.1228749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.
Collapse
Affiliation(s)
- Irena Todorović
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Daniel Muller
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| |
Collapse
|
2
|
Bautista D, García D, Dávila L, Caro‐Quintero A, Cotes AM, González A, Zuluaga AP. Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana). ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:757-768. [PMID: 37675926 PMCID: PMC10667652 DOI: 10.1111/1758-2229.13195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023]
Abstract
Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.
Collapse
Affiliation(s)
- Daniel Bautista
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
- Department of Biological SciencesUniversidad de Los AndesBogotáColombia
| | - Diana García
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| | - Lorena Dávila
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| | | | - Alba Marina Cotes
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| | - Adriana González
- Department of BiologyUniversidad Nacional de ColombiaBogotáColombia
| | - A. Paola Zuluaga
- Corporación Colombiana de Investigación Agropecuaria, Agrosavia, Centro de Investigación TibaitatáBogotáColombia
| |
Collapse
|
3
|
Xu G, Wu Z, Tian Y, Wang J, Wang X, Cao Y. Effect of in situ vermicomposting combined with biochar application on soil properties and crop yields in the tomato monoculture system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:87721-87733. [PMID: 37428324 DOI: 10.1007/s11356-023-28572-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/29/2023] [Indexed: 07/11/2023]
Abstract
Vermicompost and biochar have been widely used to improve soil conditions. However, little information is available regarding the efficiency and effectiveness of in situ vermicomposting with biochar (IVB) in monoculture soils. In this study, we estimated the effects of IVB on soil physiochemical and microbial properties, crop yields, and fruit quality under the tomato monoculture system. The soil treatments considered were (i) untreated monoculture soil (MS, control), (ii) MS plus 1.5 t/ha biochar applied to soil surface (MS+1.5BCS), (iii) MS plus 3 t/ha biochar applied to soil surface (MS+3BCS), (iv) MS mixed with 1.5 t/ha biochar (MS+1.5BCM), (v) MS mixed with 3 t/ha biochar (MS+3BCM), (vi) in situ vermicomposting (VC), (vii) VC plus 1.5 t/ha biochar applied to VC surface (VC+1.5BCS), (viii) VC plus 3 t/ha biochar applied to VC surface (VC+3BCS), (ix) VC mixed with 1.5 t/ha biochar (VC+1.5BCM), and (x) VC mixed with 3 t/ha biochar (VC+3BCM). In general, soil pH varied from 7.68 to 7.96 under VC-related treatments. The microbial diversity was much higher in bacterial communities (OTU: 2284-3194, Shannon index: 8.81-9.91) than in fungal communities (OTU: 392-782, Shannon index: 4.63-5.71) in VC-related treatments. Specifically, Proteobacteria was the dominant bacterial phylum, followed by Bacteroidota, Chloroflexi, Patescibacteria, Acidobacteriota, Firmicutes, and Myxococcota. It is worth noting that IVB-related treatments could increase the relative abundance of Acidobacteria and reduced the relative abundance of Bacteroidetes. In addition, the VC+1.5BCM treatment exhibited the greatest yield (9377.6 kg/667m2) and simultaneously showed higher fruit quality (vitamin C, 28.94 mg/100g; soluble sugar, 20.15%) as compared to other treatments. Our results suggested that in situ vermicomposting with biochar can improve soil properties and enhance both crop yields and fruit quality under the tomato monoculture system.
Collapse
Affiliation(s)
- Guangya Xu
- School of Agronomy, Ningxia University, Yinchuan, Ningxia, 750021, People's Republic of China
| | - Zeshuai Wu
- School of Agronomy, Ningxia University, Yinchuan, Ningxia, 750021, People's Republic of China
| | - Yongqiang Tian
- School of Agronomy, Ningxia University, Yinchuan, Ningxia, 750021, People's Republic of China
- College of Horticulture, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jitao Wang
- Station of Ningxia Horticulture Technical Extension, Yinchuan, 750001, People's Republic of China
| | - Xiaozhuo Wang
- School of Agronomy, Ningxia University, Yinchuan, Ningxia, 750021, People's Republic of China
| | - Yune Cao
- School of Agronomy, Ningxia University, Yinchuan, Ningxia, 750021, People's Republic of China.
| |
Collapse
|
4
|
Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Wang X, Li W. Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum. Microbiol Spectr 2023; 11:e0533322. [PMID: 37222589 PMCID: PMC10269492 DOI: 10.1128/spectrum.05333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.
Collapse
Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
5
|
Yang F, Jiang H, Chang G, Liang S, Ma K, Cai Y, Tian B, Shi X. Effects of Rhizosphere Microbial Communities on Cucumber Fusarium wilt Disease Suppression. Microorganisms 2023; 11:1576. [PMID: 37375078 DOI: 10.3390/microorganisms11061576] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Cucumber Fusarium wilt is a worldwide soil-borne disease that seriously restricts the yield and quality of cucumber. The rhizosphere soil microbiome, as the first line of defense against pathogens invading plant roots, plays a key role in rhizosphere immune formation and function. The purpose of this study was to reveal the key microecological factors and dominant microbial flora affecting cucumber resistance and susceptibility to Fusarium wilt by analyzing the physical and chemical properties and microbial flora of rhizosphere soil with different degrees of susceptibility and resistance to cucumber Fusarium wilt, thereby laying a foundation to establish cucumber resistance to the Fusarium wilt rhizosphere core microbiome. Firstly, Illumina Miseq sequencing technology was used to evaluate the physical and chemical properties and microbial groups of cucumber rhizosphere soil at different health levels, and the key environmental factors and microbial factors related to cucumber Fusarium wilt were screened out. Subsequently, PICRUSt2 and FUNGuild were used to predict the functions of rhizosphere bacteria and fungi. Combined with functional analysis, the possible interactions among soil physical and chemical properties, cucumber rhizosphere microorganisms, and Fusarium wilt were summarized. The results showed that the available potassium content in the rhizosphere soil of healthy cucumber decreased by 10.37% and 0.56%, respectively, compared with the rhizosphere soil of severely susceptible cucumber and mildly susceptible cucumber. Exchangeable calcium content increased by 25.55% and 5.39%; the α diversity Chao1 index of bacteria and fungi in the rhizosphere soil of healthy cucumber was significantly lower than that in the rhizosphere soil of seriously infected cucumber, and the MBC content of its physical and chemical properties was also significantly lower than that in the rhizosphere soil of seriously infected cucumber. There was no significant difference in the Shannon and Simpson diversity indexes between healthy cucumber rhizosphere soil and seriously infected cucumber rhizosphere soil. The results of the β diversity analysis showed that the bacterial and fungal community structure of healthy cucumber rhizosphere soil was significantly different from that of severely and mildly infected cucumber rhizosphere soil. At the genus level, through statistical analysis, LEfSe analysis, and RDA analysis, the key bacterial and fungal genera with potential biomarker values were screened out as SHA_26, Subgroup_22, MND1, Aeromicrobium, TM7a, Pseudorhodoplanes, Kocuria, Chaetomium, Fusarium, Olpidium, and Scopulariopsis, respectively. The bacteria SHA_26, Subgroup_22, and MND1 related to cucumber Fusarium wilt inhibition belong to Chloroflexi, Acidobacteriota, and Proteobacteria, respectively. Chaetomiacea belongs to Sordariomycates. The results of functional prediction showed that changes to the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in the bacterial microbiota were concentrated in tetracycline biosynthesis, selenocompound metabolism, lipopolysaccharide biosynthesis, etc., which were mainly involved in the metabolism of terpenoids and polyketides, energy metabolism, metabolism of other amino acids, glycan biosynthesis and metabolism, lipid metabolism, cell growth and death, transcription, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The difference in fungi was mainly dung saprotroph-ectomycorrhizal-soil saprotroph-wood saprotroph. Through the correlation analysis and functional predictions of the key environmental factors, microbial flora, and cucumber health index in cucumber rhizosphere soil, we determined that the inhibition of cucumber Fusarium wilt was a synergistic effect of environmental factors and microbial flora, and a model diagram was drawn to briefly explain its mechanism. This work will provide a basis for the biological control of cucumber Fusarium wilt in the future.
Collapse
Affiliation(s)
- Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Huayan Jiang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gaozheng Chang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Shen Liang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Kai Ma
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yuxin Cai
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Baoming Tian
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xuanjie Shi
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| |
Collapse
|
6
|
Wen T, Xie P, Penton CR, Hale L, Thomashow LS, Yang S, Ding Z, Su Y, Yuan J, Shen Q. Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin. MICROBIOME 2022; 10:177. [PMID: 36271396 PMCID: PMC9587672 DOI: 10.1186/s40168-022-01375-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning. RESULTS Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.
Collapse
Affiliation(s)
- Tao Wen
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Penghao Xie
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - C Ryan Penton
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Faculty of Science and Mathematics, College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, USA
| | - Lauren Hale
- Agricultural Research Service, USDA, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Linda S Thomashow
- Agricultural Research Service, US Department of Agriculture, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164, USA
| | - Shengdie Yang
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhexu Ding
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaqi Su
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
7
|
Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Li W. Long-term cultivation drives dynamic changes in the rhizosphere microbial community of blueberry. FRONTIERS IN PLANT SCIENCE 2022; 13:962759. [PMID: 36212276 PMCID: PMC9539842 DOI: 10.3389/fpls.2022.962759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Rhizosphere microbial communities profoundly affect plant health, productivity, and responses to environmental stress. Thus, it is of great significance to comprehensively understand the response of root-associated microbes to planting years and the complex interactions between plants and rhizosphere microbes under long-term cultivation. Therefore, four rabbiteye blueberries (Vaccinium ashei Reade) plantations established in 1988, 2004, 2013, and 2017 were selected to obtain the dynamic changes and assembly mechanisms of rhizosphere microbial communities with the increase in planting age. Rhizosphere bacterial and fungal community composition and diversity were determined using a high-throughput sequencing method. The results showed that the diversity and structure of bacterial and fungal communities in the rhizosphere of blueberries differed significantly among planting ages. A total of 926 operational taxonomic units (OTUs) in the bacterial community and 219 OTUs in the fungal community were identified as the core rhizosphere microbiome of blueberry. Linear discriminant analysis effect size (LEfSe) analysis revealed 36 and 56 distinct bacterial and fungal biomarkers, respectively. Topological features of co-occurrence network analysis showed greater complexity and more intense interactions in bacterial communities than in fungal communities. Soil pH is the main driver for shaping bacterial community structure, while available potassium is the main driver for shaping fungal community structure. In addition, the VPA results showed that edaphic factors and blueberry planting age contributed more to fungal community variations than bacterial community. Notably, ericoid mycorrhizal fungi were observed in cultivated blueberry varieties, with a marked increase in relative abundance with planting age, which may positively contribute to nutrient uptake and coping with environmental stress. Taken together, our study provides a basis for manipulating rhizosphere microbial communities to improve the sustainability of agricultural production during long-term cultivation.
Collapse
Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
8
|
Shen Z, Thomashow LS, Ou Y, Tao C, Wang J, Xiong W, Liu H, Li R, Shen Q, Kowalchuk GA. Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt. Research (Wash D C) 2022; 2022:9818073. [PMID: 36204250 PMCID: PMC9513836 DOI: 10.34133/2022/9818073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/22/2022] [Indexed: 11/08/2022] Open
Abstract
Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.
Collapse
Affiliation(s)
- Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Jiabao Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - George A. Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
| |
Collapse
|
9
|
Xiong J, Peng S, Liu Y, Yin H, Zhou L, Zhou Z, Tan G, Gu Y, Zhang H, Huang J, Meng D. Soil properties, rhizosphere bacterial community, and plant performance respond differently to fumigation and bioagent treatment in continuous cropping fields. Front Microbiol 2022; 13:923405. [PMID: 35935223 PMCID: PMC9354655 DOI: 10.3389/fmicb.2022.923405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/27/2022] [Indexed: 11/15/2022] Open
Abstract
Continuous cropping barriers lead to huge agriculture production losses, and fumigation and biological agents are developed to alleviate the barriers. However, there is a lack of literature on the differences between strong chemical fumigant treatment and moderate biological agent treatment. In this study, we investigated those differences and attempted to establish the links between soil properties, rhizosphere microbial community, and plant performance in both fumigation- and bioagent-treated fields. The results showed that the fumigation had a stronger effect on both soil functional microbes, i.e., ammonia oxidizers and soil-borne bacterial pathogens, and therefore, led to a significant change in soil properties, higher fertilizer efficiency, lower disease infections, and improved plant growth, compared with untreated control fields. Biological treatment caused less changes to soil properties, rhizosphere bacterial community, and plant physiology. Correlation and modeling analyses revealed that the bioagent effect was mainly direct, whereas fumigation resulted in indirect effects on alleviating cropping barriers. A possible explanation would be the reconstruction of the soil microbial community by the fumigation process, which would subsequently lead to changes in soil characteristics and plant performance, resulting in the effective alleviation of continuous cropping barriers.
Collapse
Affiliation(s)
- Jing Xiong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Shuguang Peng
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Yongjun Liu
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing, China
| | - Zhicheng Zhou
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Ge Tan
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hetian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jingyi Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- *Correspondence: Delong Meng,
| |
Collapse
|
10
|
Yang C, Tang W, Sun J, Guo H, Sun S, Miao F, Yang G, Zhao Y, Wang Z, Sun J. Weeds in the Alfalfa Field Decrease Rhizosphere Microbial Diversity and Association Networks in the North China Plain. Front Microbiol 2022; 13:840774. [PMID: 35418969 PMCID: PMC8998637 DOI: 10.3389/fmicb.2022.840774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 11/16/2022] Open
Abstract
The competition between weeds and crops for soil nutrients is affected by soil microorganisms, which drive diverse ecological processes and are critical in maintaining the stability of agroecosystems. However, the effects of plant species identity, particularly between forage and weed, on soil microbial diversity, composition, and association are not well understood. Here, we investigate the soil physicochemical properties and bacterial/fungal communities in an agroecosystem with native alfalfa [Medicago stativa (Ms)] and five common weed species (Digitaria sanguinalis, Echinochloa crusgalli, Acalypha australis, Portulaca oleracea, and Chenopodium album) in the North China Plain. The five weeds had a lower plant carbon content than Ms. while the opposite was true for plant nitrogen and phosphorus concentrations. The Shannon diversity of bacterial and fungal communities of the five weeds were significantly lower than in Ms. Soil pH and PO43−-P were identified as the most important factors in shaping the relative abundances of bacteria (Sphingomonadaceae) and fungi (Pleosporaceae), respectively. Importantly, the weeds greatly inhibited the growth of pathogenic fungi (Nectriaceae and Pleosporaceae). Bacterial co-occurrence networks depended on specific species, indicating that Ms. harbored co-occurrence networks that were more complex than those in the bacterial communities of other weed groups. Our study examines how soil nutrients and the soil microbial community structure of five weed species changed in an Ms. field. This analysis of the microbial ecological network enhances our understanding of the influence of weeds on the soil microbiome in agroecosystems.
Collapse
Affiliation(s)
- Chao Yang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Wei Tang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Junqi Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Haipeng Guo
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Shusheng Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Fuhong Miao
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Guofeng Yang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Yiran Zhao
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Zengyu Wang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Juan Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
- *Correspondence: Juan Sun,
| |
Collapse
|
11
|
Zhang Y, Zhang Y, Xu W, Hu J, Zhang Z. Possible effects of temperature on bacterial communities in the rhizosphere of rice under different climatic regions. Arch Microbiol 2022; 204:212. [PMID: 35296917 DOI: 10.1007/s00203-022-02812-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/21/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Global warming is an indisputable fact. However, the effect of warming on the rhizosphere bacterial community of crops is not well understood. Therefore, we carried out pot experiments with three rice (Oryza sativa L.) varieties in black soil across three climatic regions of northeast China to simulate temperature change, and analyzed the response of the rhizosphere bacterial community to different temperatures. Results showed that climate had stronger effects on rhizosphere bacterial communities than rice variety. The rhizosphere bacterial diversity differed significantly among the three climatic regions and positively correlated with the mean daily average temperature (MAveT), mean daily maximum temperature (MMaxT), and mean daily minimum temperature (MMinT), and negatively correlated with the daily temperature range (DTR). Principal co-ordinate analysis revealed that bulk soil bacterial communities maintained a high similarity across the three climatic regions, while rhizosphere bacterial communities notably varied. This change was significantly correlated with MAveT, MMaxT, MMinT, and DTR. Compared with bulk soil, Proteobacteria and Bacteroidetes were enriched in the rhizosphere, while Actinobacteria was depleted. Moreover, these changes were strengthened by increasing the temperature and decreasing DTR. Additionally, correlation analysis revealed that changes in rhizosphere bacterial communities were closely related to the formation of rice yields. Our study revealed that the increasing temperature indirectly reshapes the rhizosphere bacterial community that may promote rice production in areas with lower temperatures.
Collapse
Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Yujie Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Wenjie Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, People's Republic of China.
| | - Zujian Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture/Key Laboratory of Crop Genetic and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China.
| |
Collapse
|
12
|
Different soil salinity imparts clear alteration in rhizospheric bacterial community dynamics in rice and peanut. Arch Microbiol 2021; 204:36. [PMID: 34927211 DOI: 10.1007/s00203-021-02695-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in the overall health of the hostplant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN, whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community structure is related to both the adjoining soil characters and the type of the hosts.
Collapse
|
13
|
Tian GL, Bi YM, Jiao XL, Zhang XM, Li JF, Niu FB, Gao WW. Application of vermicompost and biochar suppresses Fusarium root rot of replanted American ginseng. Appl Microbiol Biotechnol 2021; 105:6977-6991. [PMID: 34436649 DOI: 10.1007/s00253-021-11464-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022]
Abstract
Soil sterilization integrated with agronomic measures is an effective method to reduce soilborne replant diseases. However, the effect of vermicompost or biochar application after soil sterilization on soilborne diseases is poorly understood. A pot experiment was conducted in American ginseng to investigate the effects of vermicompost (VF), biochar (BF), and a combination of vermicompost and biochar (VBF) applied after soil sterilization on the incidence of Fusarium root rot using natural recovery (F) as control. After one growing season, the disease index of root rot, the phenolic acids, and the microbial communities of American ginseng rhizosphere soil were analyzed. The disease index of VF, BF, and VBF decreased by 33.32%, 19.03%, and 80.96%, respectively, compared with F. The highest bacterial richness and diversity were observed in the rhizosphere soil of VBF. Besides, VF and VBF significantly increased the relative abundance of beneficial bacteria (Pseudomonas, Lysobacter, and Chryseolinea) in the rhizosphere soil. Higher concentrations of vanillin, one of the phenolic acids in the roots exudates, were recorded in the rhizosphere soils of BF and VBF. The vanillin concentration showed a significant negative correlation with the disease index. To conclude, vermicompost improved the beneficial bacteria of the rhizosphere soil, while biochar regulated the allelopathic effect of the phenolic acids. The study proposes a combined application of biochar and vermicompost to the rhizosphere soil to control Fusarium root rot of replanted American ginseng effectively. KEY POINTS: Vermicompost improves the relative abundance of rhizosphere beneficial bacteria. Biochar inhibits the degradation of phenolic acids by adsorption. The combination of vermicompost and biochar enhances the disease control effect.
Collapse
Affiliation(s)
- Gei-Lin Tian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- College of Agricultural and Biological Engineering, Heze University, Shandong Province, Heze, 274000, China
| | - Yan-Meng Bi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin, 300384, China
| | - Xiao-Lin Jiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xi-Mei Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Jun-Fei Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Fang-Bing Niu
- College of Business Administration, Heze University, Shandong Province, Heze, 274000, China
| | - Wei-Wei Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|
14
|
Zhu S, Lei Y, Wang C, Wei Y, Wang C, Sun Y. Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang. BMC Microbiol 2021; 21:170. [PMID: 34090353 PMCID: PMC8180054 DOI: 10.1186/s12866-021-02222-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The unique climatic conditions of the Xinjiang region nurture rich melon and fruit resources, the melon and fruit sugar sources provide sufficient nutrients for the survival of yeast, and the diverse habitats accompanied by extreme climatic conditions promote the production of yeast diversity and strain resources. However, the relationship between yeast species and their relationship with environmental factors in the soil of Xinjiang specialty cash crop Hami melon is not clear. Here, we aimed to characterize the diversity, community structure, and relationship between yeast species and environmental factors in Hami melon orchards soils in different regions of Xinjiang, China. RESULTS Based on Illumina MiSeq high-throughput sequencing analysis of the D1 domain of the LSU rRNA genes, the community richness of yeast in the soil of Northern Xinjiang was higher than in the Southern and Eastern Xinjiang, but the community diversity was significantly lower in the Northern Xinjiang than in the Southern and Eastern Xinjiang. A total of 86 OTUs were classified into 59 genera and 86 species. Most OTUs (90.4%) belonged to the Basidiomycota; only a few (9.6%) belonged to Ascomycota. The most dominant species in the Southern, Eastern and Northern Xinjiang were Filobasidium magnum (17.90%), Solicoccozyma aeria (35.83%) and Filobasidium magnum (75.36%), respectively. Principal coordinates analysis (PCoA) showed that the yeast community composition in the soils of the three regions were obviously different, with the Southern and Eastern Xinjiang having more similar yeast community. Redundancy analysis (RDA) showed that soil factors such as conductivity (CO), total phosphorus (TP) and Total potassium (TK) and climate factors such as average annual precipitation (PRCP), relative humidity (RH) and net solar radiation intensity (SWGNT) were significantly correlated with yeast communities (P < 0.05). CONCLUSION There are abundant yeast resources in the rhizosphere soil of Hami melon orchard in Xinjiang, and there are obvious differences in the diversity and community structure of yeast in the three regions of Xinjiang. Differences in climatic factors related to precipitation, humidity and solar radiation intensity and soil factors related to conductivity, total phosphorus and total potassium are key factors driving yeast diversity and community structure.
Collapse
Affiliation(s)
- ShanShan Zhu
- College of life Science / Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, North 4 Street, College of life Science, Shihezi University, Shihezi, 832003, People's Republic of China
| | - YongHui Lei
- Department of Plant protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Chong Wang
- Urumqi Customs technique center, Urumqi, 830063, China
| | - YuMei Wei
- College of life Science / Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, North 4 Street, College of life Science, Shihezi University, Shihezi, 832003, People's Republic of China
| | - ChunCheng Wang
- College of life Science / Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, North 4 Street, College of life Science, Shihezi University, Shihezi, 832003, People's Republic of China
| | - YanFei Sun
- College of life Science / Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, North 4 Street, College of life Science, Shihezi University, Shihezi, 832003, People's Republic of China.
| |
Collapse
|
15
|
The Coevolution of Plants and Microbes Underpins Sustainable Agriculture. Microorganisms 2021; 9:microorganisms9051036. [PMID: 34065848 PMCID: PMC8151373 DOI: 10.3390/microorganisms9051036] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.
Collapse
|
16
|
Fei X, Lina W, Jiayang C, Meng F, Guodong W, Yaping Y, Langjun C. Variations of microbial community in Aconitum carmichaeli Debx. rhizosphere soilin a short-term continuous cropping system. J Microbiol 2021; 59:481-490. [PMID: 33779961 DOI: 10.1007/s12275-021-0515-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Aconitum carmichaeli Debx. (Ranunculaceae) is a potential source of an important herbal drug named "Fuzi", which is derived from the lateral root of the plant. Increased therapeutic usage resulted in the great demand for artificial cultivation of A. carmichaeli, however, the obstacles caused by continuous cropping is a serious problem. Continuous cropping has shown to affect the soil biological and non-biological factors. The current study attempted to discover the variations of microbial communities and soil properties in short-term continuous cropping of A. carmichaeli. An experimental procedure with A. carmichaeli planted two years continuously was established. The variation of the soil microbial community, disease incidence, soil properties, and the correlation between soil microbe and disease incidence were investigated. The disease incidence increased during the continuous cropping of A. carmichaeli. The PCoA and LefSe results indicated that fungal communities in rhizosphere soil were altered during the short-term continuous croppingand the bacterial community was disturbed by the cultivation of A. carmichaeli, however, in the following two years of continuous cropping period, the soil bacterial community has not changed obviously. Proportions of some fungal and bacterial genera were varied significantly (p < 0.05), and some genera of microflora showed a significant correlation with adisease incidence of A. carmichaeli. Microorganisms contributing to community composition discrepancy were also elucidated. Continuous cropping of A. carmichaeli disturbed the rhizosphere soil microbial community and altered the soil chemical parameters and soil pH. These variations in soil may be related to the occurrence of plant diseases. The current study will not only provide theoretical and experimental evidence for the A. carmichaeli continuous cropping obstacles but will also contribute to A. carmichaeli agricultural production and soil improvement.
Collapse
Affiliation(s)
- Xia Fei
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'An, 710021, China
| | - Wang Lina
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Chen Jiayang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Fu Meng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Wang Guodong
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Yan Yaping
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Cui Langjun
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| |
Collapse
|
17
|
Abstract
The continuous cropping (CC) of major agricultural, horticultural, and industrial crops is an established practice worldwide, though it has significant soil health-related concerns. However, a combined review of the effects of CC on soil health indicators, in particular omics ones, remains missing. The CC may negatively impact multiple biotic and abiotic indicators of soil health, fertility, and crop yield. It could potentially alter the soil biotic indicators, which include but are not limited to the composition, abundance, diversity, and functioning of soil micro- and macro-organisms, microbial networks, enzyme activities, and soil food web interactions. Moreover, it could also alter various soil abiotic (physicochemical) properties. For instance, it could increase the accumulation of toxic metabolites, salts, and acids, reduce soil aggregation and alter the composition of soil aggregate-size classes, decrease mineralization, soil organic matter, active carbon, and nutrient contents. All these alterations could accelerate soil degradation. Meanwhile, there is still a great need to develop quantitative ranges in soil health indicators to mechanistically predict the impact of CC on soil health and crop yield gaps. Following ecological principles, we strongly highlight the significance of inter-, mixture-, and rotation-cropping with cover crops to sustain soil health and agricultural production.
Collapse
|
18
|
Qiu W, Su H, Yan L, Ji K, Liu Q, Jian H. Organic Fertilization Assembles Fungal Communities of Wheat Rhizosphere Soil and Suppresses the Population Growth of Heterodera avenae in the Field. FRONTIERS IN PLANT SCIENCE 2020; 11:1225. [PMID: 32849758 PMCID: PMC7429443 DOI: 10.3389/fpls.2020.01225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Heterodera avenae (cereal cyst nematode, CCN) infects wheat and other cereal crops and causes severe losses in their yield. Research has shown that CCN infestations can be mitigated by organic fertilization in wheat fields, but the mechanisms underlying this phenomenon are still largely unknown. In this study, the relationships among CCN, soil properties, and soil fungal communities with organic fertilizer (OF) or chemical fertilizer (CF) and without fertilizer (CK), were investigated for two years in a wheat field in Henan province, China. Our results showed that the concentrations of soil total N, total P, available P, available K, and organic matter were all promoted by the OF treatment at the jointing stage of wheat, coinciding with the peak in egg hatching and penetration of wheat root by CCNs. Soil total N correlated positively (R2 = 0.759, p < 0.05) with wheat yields but negatively (R2 = 0.663, p < 0.01) with Pf/Pi (index of cyst nematode reproduction), implying the regulated soil property contributes to suppressing CCN in the OF treatment. Furthermore, fungal community α-diversity (Shannon and Simpson) and β-diversity (PCoA) of rhizosphere soil was improved under the organic fertilizer treatment. The fungal genera negatively associated with the Pf/Pi of CCN were highly enriched, which included Mortierella and Chaetomium, two taxa already reported as being nematophagous fungi in many other studies. These two genera were heavily surrounded by much more related fungal genera in the constructs co-occurrence network. These results suggested that the OF treatment shifted soil fungal community functioning towards the suppression of CCN. Taken together, the suppressed cyst nematode reproduction with the assembly of fungal communities in the rhizosphere led to greater wheat yields under organic fertilization. These findings provide an in-depth understanding of the benefits provided by organic fertilization for developing sustainable agriculture.
Collapse
|
19
|
Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
Collapse
Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| |
Collapse
|
20
|
Li J, Chen X, Li S, Zuo Z, Zhan R, He R. Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices. BOTANICAL STUDIES 2020; 61:18. [PMID: 32542518 PMCID: PMC7295922 DOI: 10.1186/s40529-020-00295-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes of soil microbial communities are one of the main factors of continuous cropping problem. Andrographis paniculata has been reported to have replant problem in cultivation. However, little is known about the variations of rhizosphere soil microbial communities of A. paniculata under a continuous cropping system. Here, Illumina MiSeq was used to investigate the shifts of rhizospheric bacterial and fungal communities after continuous cropping of A. paniculata. RESULTS The bacterial diversity increased whereas the fungal diversity decreased in rhizosphere soil after consecutive A. paniculata monoculture; and the soil microbial community structure differed between newly plant soil and continuous cropped soil. Taxonomic analyses further revealed that the bacterial phyla Proteobacteria, Acidobacteria and Bacteroidetes and the fungal phyla Zygomycota, Ascomycota and Cercozoa were the dominant phyla across all soil samples. The relative abundance of phyla Acidobacteria and Zygomycota were significantly increased after continuous cropping. Additionally, the most abundant bacterial genus Pseudolabrys significantly decreased, while the predominant fungal genus Mortierella increased considerably in abundance after continuous cropping. CONCLUSIONS Our results revealed the changes on diversity and composition of bacterial and fungal communities in rhizospheric soil under continuous cropping of A. paniculata. These data contributed to the understanding of soil micro-ecological environments in the rhizosphere of A. paniculata.
Collapse
Affiliation(s)
- Junren Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Xiuzhen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Simin Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Zimei Zuo
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Rui He
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China.
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China.
| |
Collapse
|
21
|
Xiong W, Song Y, Yang K, Gu Y, Wei Z, Kowalchuk GA, Xu Y, Jousset A, Shen Q, Geisen S. Rhizosphere protists are key determinants of plant health. MICROBIOME 2020; 8:27. [PMID: 32127034 PMCID: PMC7055055 DOI: 10.1186/s40168-020-00799-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators-protists-are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. RESULTS We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. CONCLUSIONS We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. Video Abstract.
Collapse
Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Yuqi Song
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Keming Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yian Gu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhong Wei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Stefan Geisen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Department of Terrestrial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), 6708, PB, Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University & Research, 6700, ES, Wageningen, The Netherlands
| |
Collapse
|
22
|
Wu L, Yang B, Li M, Chen J, Xiao Z, Wu H, Tong Q, Luo X, Lin W. Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease. PLANT DISEASE 2020; 104:25-34. [PMID: 31726014 DOI: 10.1094/pdis-04-19-0833-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.
Collapse
Affiliation(s)
- Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Bo Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Manlin Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Jun Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Zhigang Xiao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Hongmiao Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Qingyu Tong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University
| | - Xiaomian Luo
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University
| |
Collapse
|
23
|
Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4943150. [PMID: 31815142 PMCID: PMC6878781 DOI: 10.1155/2019/4943150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/05/2022]
Abstract
To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.
Collapse
|
24
|
Zhou D, Jing T, Chen Y, Wang F, Qi D, Feng R, Xie J, Li H. Deciphering microbial diversity associated with Fusarium wilt-diseased and disease-free banana rhizosphere soil. BMC Microbiol 2019; 19:161. [PMID: 31299891 PMCID: PMC6626388 DOI: 10.1186/s12866-019-1531-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/26/2019] [Indexed: 11/18/2022] Open
Abstract
Background Fusarium wilt of banana (Musa spp.) caused by the fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a typical soilborne disease, that severely devastates the banana industry worldwide, and soil microbial diversity is closely related to the spread of Fusarium wilt. To understand the relationship between microbial species and Fusarium wilt, it is important to understand the microbial diversity of the Fusarium wilt-diseased and disease-free soils from banana fields. Results Based on sequencing analysis of the bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences, Foc abundance, fungal or bacterial richness and diversity were higher in the diseased soils than in the disease-free soils. Although Ascomycota and Zygomycota were the most abundant fungi phyla in all soil samples, Ascomycota abundance was significantly reduced in the disease-free soils. Mortierella (36.64%) was predominant in the disease-free soils. Regarding bacterial phyla, Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Nitrospirae, Verrucomicrobia and Planctomycetes were dominant phyla in all soil samples. In particular, Firmicutes contributed 16.20% of the total abundance of disease-free soils. At the bacterial genus level, Bacillus, Lactococcus and Pseudomonas were abundant in disease-free soils with abundances of 8.20, 5.81 and 2.71%, respectively; lower abundances, of 4.12, 2.35 and 1.36%, respectively, were found in diseased soils. The distribution characteristics of fungal and bacterial genera may contribute to the abundance decrease of Foc in the disease-free soils. Conclusion Unique distributions of bacteria and fungi were observed in the diseased and disease-free soil samples from banana fields. These specific genera are useful for constructing a healthy microbial community structure of soil.
Collapse
Affiliation(s)
- Dengbo Zhou
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Tao Jing
- Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yufeng Chen
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Fei Wang
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dengfeng Qi
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Renjun Feng
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
| | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| |
Collapse
|
25
|
Zhang M, Riaz M, Zhang L, El-Desouki Z, Jiang C. Biochar Induces Changes to Basic Soil Properties and Bacterial Communities of Different Soils to Varying Degrees at 25 mm Rainfall: More Effective on Acidic Soils. Front Microbiol 2019; 10:1321. [PMID: 31249563 PMCID: PMC6582450 DOI: 10.3389/fmicb.2019.01321] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/27/2019] [Indexed: 02/04/2023] Open
Abstract
Biochar and chemical fertilizer have been widely used in agriculture. Most studies have proved that they not only alter soil nutrient content, but also have an impact on soil microbial communities. However, the effects of biochar and chemical fertilizer application on the overall bacterial community in different soil types under rainfall conditions are not yet understood. We took rainfall as a fixed influencing factor and selected four typical soils of China to investigate the bacterial effects of biochar and chemical fertilizer at 25 mm rainfall, and to identify specific differential bacteria and their functions, and to explore the changes of the bacterial community structure of different soil types. The depth of simulated rainfall was 25 mm each time. Yellow-brown soil, fluvo-aquic soil, lou soil, and black soil were chosen for experiment and each soil was divided into four treatments, included non-biochar and non-fertilizer (CK), fertilizer alone (F), biochar alone (C), and combination of biochar and fertilizer (FC). The results indicated that biochar and fertilizer have a more significant effect on bacterial communities in acidic soils. The amendment of biochar and fertilizer alone or together identified 3 (f_Oxalobacteraceae, f_Solibacteraceae_Subgroup_3, f_Sphingomonadaceae), 5 (f_Chitinophagaceae, f_Comamonadaceae, f_Geobacteraceae, f_norank_o_SC-I-84, f_norank_c_OPB35_soil_group), 1 (f_Blastocatellaceae_Subgroup_4) and 0 differential bacteria in yellow-brown soil, fluvo-aquic soil, lou soil, and black soil by statistical test. In yellow-brown soil, the application of biochar alone increased the relative abundance of potential pathogens within the Sphingomonadaceae and reduced the relative abundance of beneficial bacteria in Solibacteraceae, but the addition of biochar and fertilizer together increased the relative abundance of some beneficial bacteria in Oxalobacteraceae. In fluvo-aquic soil, both biochar, and chemical fertilizers promoted the relative abundance of some beneficial bacteria belonging to Chitinophagaceae, Comamonadaceae, and Geobacteraceae that may be involved in nutrient cycling, degradation of plant residues and increase of metal tolerance. The interactions between acidic soil bacterial communities and measured soil parameters including pH, organic matter were found to be statistically significant. Results from this study revealed that it is necessary to formulate biochar and fertilizer application schemes based on different soil types.
Collapse
Affiliation(s)
- Mengyang Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Zeinab El-Desouki
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.,Department of Soil Sciences, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
26
|
Wang M, Li S, Chen S, Meng N, Li X, Zheng H, Zhao C, Wang D. Manipulation of the rhizosphere bacterial community by biofertilizers is associated with mitigation of cadmium phytotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:413-421. [PMID: 30176454 DOI: 10.1016/j.scitotenv.2018.08.174] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 05/13/2023]
Abstract
The objective of this study was to understand the effect of biofertilizers on cadmium (Cd)-induced phytotoxicity and the rhizosphere bacterial community. The crop specie rice (Oryza sativa L.) was planted in Cd-contaminated soils, and Illumina high-throughput sequencing was performed to investigate how the composition of the rhizosphere bacterial community responded to the addition of biofertilizers. Biofertilizers were effective in alleviating Cd phytotoxicity as indicated by the significant increase in plant biomass (up to 85.2% and 48.4% for roots and shoots, respectively) and decrease in tissue Cd concentration (up to 72.2% in roots) of rice receiving fertilizer treatments compared with the CK (no treatment). These positive effects were likely due to the increase in soil pH, which can be attributed primarily to Cd immobilization, and the promotion of beneficial taxa such as Proteobacteria, Bacteroidetes, Gemmatimonadetes, and Firmicutes. In addition, autoclaved biofertilizers tended to have similar beneficial effects and similar bacterial community alpha diversities as the original biofertilizer treatments. This suggests that the change in soil physicochemical properties by biofertilizer addition might drive the structure of rhizosphere bacterial community, and not the biofertilizer microbes themselves. In both the original and sterilized biofertilizer treatments, the effectiveness in mitigating of Cd phytotoxicity was found to be dependent on the type of biofertilizer applied. Comparatively, the biofertilizer denoted as DY was more effective in mitigating Cd phytotoxicity than others. These results demonstrate that biofertilizer addition could be a promising approach to immobilize soil Cd by manipulating the rhizosphere bacterial community, thus to facilitate plant growth.
Collapse
Affiliation(s)
- Meng Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shanshan Li
- School of Land Science and Technology, China University of Geosciences, Beijing 100083, PR China
| | - Shibao Chen
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
| | - Nan Meng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoyue Li
- School of Land Science and Technology, China University of Geosciences, Beijing 100083, PR China
| | - Han Zheng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Chunmei Zhao
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Duo Wang
- College of Energy, Xiamen University, Xiamen, Fujian 361102, PR China
| |
Collapse
|
27
|
Yang M, Mavrodi DV, Thomashow LS, Weller DM. Differential Response of Wheat Cultivars to Pseudomonas brassicacearum and Take-All Decline Soil. PHYTOPATHOLOGY 2018; 108:1363-1372. [PMID: 29905506 PMCID: PMC6483097 DOI: 10.1094/phyto-01-18-0024-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
2,4-Diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. in the P. fluorescens complex are primarily responsible for a natural suppression of take-all of wheat known as take-all decline (TAD) in many fields in the United States. P. brassicacearum, the most common DAPG producer found in TAD soils in the Pacific Northwest (PNW) of the United States, has biological control, growth promoting and phytotoxic activities. In this study, we explored how the wheat cultivar affects the level of take-all suppression when grown in a TAD soil, and how cultivars respond to colonization by P. brassicacearum. Three cultivars (Tara, Finley, and Buchanan) supported similar rhizosphere population sizes of P. brassicacearum when grown in a TAD soil, however they developed significantly different amounts of take-all. Cultivars Tara and Buchanan developed the least and most take-all, respectively, and Finley showed an intermediate amount of disease. However, when grown in TAD soil that was pasteurized to eliminate both DAPG producers and take-all suppression, all three cultivars were equally susceptible to take-all. The three cultivars also responded differently to the colonization and phytotoxicity of P. brassicacearum strains Q8r1-96 and L5.1-96, which are characteristic of DAPG producers in PNW TAD soils. Compared with cultivar Tara, cultivar Buchanan showed significantly reduced seedling emergence and root growth when colonized by P. brassicacearum, and the response of Finley was intermediate. However, all cultivars emerged equally when treated with a DAPG-deficient mutant of Q8r1-96. Our results indicate that wheat cultivars grown in a TAD soil modulate both the robustness of take-all suppression and the potential phytotoxicity of the antibiotic DAPG.
Collapse
Affiliation(s)
| | - Dmitri V. Mavrodi
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg 39406
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
| | | |
Collapse
|
28
|
Rilling JI, Acuña JJ, Sadowsky MJ, Jorquera MA. Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile. Front Microbiol 2018; 9:2710. [PMID: 30524385 PMCID: PMC6256256 DOI: 10.3389/fmicb.2018.02710] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/23/2018] [Indexed: 11/17/2022] Open
Abstract
Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.
Collapse
Affiliation(s)
- Joaquin I. Rilling
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Jacquelinne J. Acuña
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michael J. Sadowsky
- Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Milko A. Jorquera
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| |
Collapse
|
29
|
Li H, Wang J, Liu Q, Zhou Z, Chen F, Xiang D. Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing. J Basic Microbiol 2018; 59:181-191. [PMID: 30288775 DOI: 10.1002/jobm.201800304] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 09/11/2018] [Indexed: 11/11/2022]
Abstract
Soil bacteria play key roles in determining soil health and plant growth. In this study, four sweet potato fields that had been consecutively monocultured for 1, 2, 3, and 4 years were used to investigate the effect of monoculture on soil physicochemical properties and soil bacterial communities. The results revealed that continuous cropping led to a significant decline in soil pH, soil organic carbon, and soil bacterial abundance. Miseq pyrosequencing analysis of 16S rRNA genes revealed that Proteobacteria and Bacteroidetes were the main phyla in the sweet potato monoculture soils, comprising up to 66.24% of the total sequences. The relative abundances of beneficial bacteria, including Actinobacteria, Gemmatimonadetes, Firmicutes, Xanthomonadaceae, Rhodospirillaceae, and Syntrophobacteraceae, as well as their subgroups at the genus and operational taxonomic unit (OTU) levels, decreased considerably as the number of continuous cropping years increased. In contrast, the number of potentially pathogenic bacteria, such as Acidobacteria, Sphingomonadaceae, and Pedobacter accumulated with increasing years. The results also showed the alterations to the bacterial community in the sweet potato monoculture soils were mainly driven by soil pH and soil organic matter. Overall, the decline in soil quality after successive sweet potato monoculture can be attributed to the imbalance in soil properties and soil microbes, including the decrease in soil pH and soil organic carbon, and the enrichment of pathogenic bacteria at the expense of plant-beneficial bacteria.
Collapse
Affiliation(s)
- Huan Li
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Jinqiang Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Qing Liu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Zhengfeng Zhou
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Falin Chen
- Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Dan Xiang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
30
|
Zhou L, Wang Y, Xie Z, Zhang Y, Malhi SS, Guo Z, Qiu Y, Wang L. Effects of lily/maize intercropping on rhizosphere microbial community and yield of Lilium davidii var. unicolor. J Basic Microbiol 2018; 58:892-901. [PMID: 30101457 DOI: 10.1002/jobm.201800163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/02/2018] [Accepted: 07/25/2018] [Indexed: 11/07/2022]
Abstract
Continuous cropping of lily (Lilium davidii var. unicolor) or any other crop seriously affects yield and quality. In this study, we compared continuous cropping with lily/maize intercropping. We also examined the lily rhizosphere microbes community in both sole lily cropping and lily/maize intercropping systems, by the llumina Miseq platform. Here we refer to data of recent years field experimentation of a lily/maize intercrop system in different planting configurations in the Gaolan Ecological and Agricultural Research Station. Treatments included sole crops of lily and maize, an intercrop consisting of strips of four lily rows alternating with one maize rows. The land equivalent ratio (LER) of intercrops was 1.294. The results showed that compared to sole cropping, the yield of lily in the first year of planting increased when lily was intercropped with maize. The species annotation of the high-throughput sequencing experiment showed that there was no difference in the diversity of the lily rhizosphere soil microbes on phylum taxonomic level, but the relative abundance of some genus changed obviously. The relative abundance of harmful fungus Fusarium spp. and, Funneliformis spp., decreased, and the relative abundance of beneficial bacteria Sphingomonas spp. and, Nitrospira spp., increased. In addition, we found that Lecanicillium spp., appeared only in the intercropping lily rhizosphere soil and sole cropping maize rhizosphere soil. In conclusion, the findings indicated that lily/maize intercropping could change soil microenvironment, and affect the diversity and structure of microorganism community in lily rhizosphere, with further beneficial effect on the yield of lily.
Collapse
Affiliation(s)
- Lijing Zhou
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Yajun Wang
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Zhongkui Xie
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Yubao Zhang
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Sukhdev S Malhi
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Zhihong Guo
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Yang Qiu
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Le Wang
- Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu, China
| |
Collapse
|
31
|
Bhattacharyya D, Duta S, Yu SM, Jeong SC, Lee YH. Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202. THE PLANT PATHOLOGY JOURNAL 2018; 34:286-296. [PMID: 30140182 PMCID: PMC6097822 DOI: 10.5423/ppj.oa.03.2018.0047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 05/28/2023]
Abstract
Maintenance of a beneficial microbial community, especially in the rhizosphere, is indispensable for plant growth and agricultural sustainability. In this sense, plant growth-promoting rhizobacteria (PGPR) have been extensively studied for their role in plant growth promotion and disease resistance. However, the impact of introducing PGPR strains into rhizosphere microbial communities is still underexplored. We previously found that the Proteus vulgaris JBLS202 strain (JBLS202) promoted growth of Kimchi cabbage and altered the relative abundance of total bacteria and Pseudomonas spp. in the treated rhizosphere. To extend these findings, we used pyrosequencing to analyze the changes in bacterial communities in the rhizosphere of Kimchi cabbage after introduction of JBLS202. The alterations were also evaluated by taxon-specific real-time PCR (qPCR). The pyrosequencing data revealed an increase in total bacteria abundance, including specific groups such as Proteobacteria, Acidobacteria, and Actinobacteria, in the treated rhizosphere. Time-course qPCR analysis confirmed the increase in the abundance of Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. Furthermore, genes involved in nitrogen cycling were upregulated by JBLS202 treatment indicating changes in ecological function of the rhizosphere soil. Overall, these results indicate that introduction of JBLS202 alters both the composition and function of the rhizosphere bacterial community, which can have direct and indirect effects on plant growth. Therefore, we propose that long-term changes in bacterial composition and community-level function need to be considered for practical use of PGPRs.
Collapse
Affiliation(s)
| | - Swarnalee Duta
- Division of Biotechnology, Chonbuk National University, Iksan 54596,
Korea
| | - Sang-Mi Yu
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju 37242,
Korea
| | - Sang Chul Jeong
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju 37242,
Korea
| | - Yong Hoon Lee
- Division of Biotechnology, Chonbuk National University, Iksan 54596,
Korea
- Advanced Institute of Environment and Bioscience, Plant Medical Research Center, and Institute of Bio-industry, Chonbuk National University, Jeonju 54896,
Korea
| |
Collapse
|
32
|
Hayden HL, Savin KW, Wadeson J, Gupta VVSR, Mele PM. Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. Front Microbiol 2018; 9:859. [PMID: 29780371 PMCID: PMC5945926 DOI: 10.3389/fmicb.2018.00859] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/13/2018] [Indexed: 11/29/2022] Open
Abstract
The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R. solani AG8. Analysis of 12 rhizosphere metatranscriptomes (six per field) was undertaken using two bioinformatic approaches involving unassembled and assembled reads. Differential expression analysis showed the dominant taxa in the rhizosphere based on mRNA annotation were Arthrobacter spp. and Pseudomonas spp. for non-suppressive samples and Stenotrophomonas spp. and Buttiauxella spp. for the suppressive samples. The assembled metatranscriptome analysis identified more differentially expressed genes than the unassembled analysis in the comparison of suppressive and non-suppressive samples. Suppressive samples showed greater expression of a polyketide cyclase, a terpenoid biosynthesis backbone gene (dxs) and many cold shock proteins (csp). Non-suppressive samples were characterised by greater expression of antibiotic genes such as non-heme chloroperoxidase (cpo) which is involved in pyrrolnitrin synthesis, and phenazine biosynthesis family protein F (phzF) and its transcriptional activator protein (phzR). A large number of genes involved in detoxifying reactive oxygen species (ROS) and superoxide radicals (sod, cat, ahp, bcp, gpx1, trx) were also expressed in the non-suppressive rhizosphere samples most likely in response to the infection of wheat roots by R. solani AG8. Together these results provide new insight into microbial gene expression in the rhizosphere of wheat in soils suppressive and non-suppressive to R. solani AG8. The approach taken and the genes involved in these functions provide direction for future studies to determine more precisely the molecular interplay of plant-microbe-pathogen interactions with the ultimate goal of the development of management options that promote beneficial rhizosphere microflora to reduce R. solani AG8 infection of crops.
Collapse
Affiliation(s)
- Helen L Hayden
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Keith W Savin
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Jenny Wadeson
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Vadakattu V S R Gupta
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia.,College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Pauline M Mele
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia
| |
Collapse
|
33
|
Svenningsen NB, Watts-Williams SJ, Joner EJ, Battini F, Efthymiou A, Cruz-Paredes C, Nybroe O, Jakobsen I. Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota. THE ISME JOURNAL 2018; 12:1296-1307. [PMID: 29382946 PMCID: PMC5931975 DOI: 10.1038/s41396-018-0059-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 12/12/2017] [Indexed: 12/03/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) colonise roots of most plants; their extra-radical mycelium (ERM) extends into the soil and acquires nutrients for the plant. The ERM coexists with soil microbial communities and it is unresolved whether these communities stimulate or suppress the ERM activity. This work studied the prevalence of suppressed ERM activity and identified main components behind the suppression. ERM activity was determined by quantifying ERM-mediated P uptake from radioisotope-labelled unsterile soil into plants, and compared to soil physicochemical characteristics and soil microbiome composition. ERM activity varied considerably and was greatly suppressed in 4 of 21 soils. Suppression was mitigated by soil pasteurisation and had a dominating biotic component. AMF-suppressive soils had high abundances of Acidobacteria, and other bacterial taxa being putative fungal antagonists. Suppression was also associated with low soil pH, but this effect was likely indirect, as the relative abundance of, e.g., Acidobacteria decreased after liming. Suppression could not be transferred by adding small amounts of suppressive soil to conducive soil, and thus appeared to involve the common action of several taxa. The presence of AMF antagonists resembles the phenomenon of disease-suppressive soils and implies that ecosystem services of AMF will depend strongly on the specific soil microbiome.
Collapse
Affiliation(s)
- Nanna B Svenningsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Erik J Joner
- Norwegian Institute for Bioeconomy Research, Ås Akershus, Norway
| | - Fabio Battini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Aikaterini Efthymiou
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Carla Cruz-Paredes
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Iver Jakobsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
| |
Collapse
|
34
|
Shen Z, Penton CR, Lv N, Xue C, Yuan X, Ruan Y, Li R, Shen Q. Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans. MICROBIAL ECOLOGY 2018; 75:739-750. [PMID: 28791467 DOI: 10.1007/s00248-017-1052-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/28/2017] [Indexed: 05/14/2023]
Abstract
The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study. The results showed that successive cropping of banana was significantly correlated with the Fusarium wilt disease incidence. Fungal communities responded more obviously and quickly to banana consecutive monoculture than bacterial community. Moreover, a higher fungal richness significantly correlated to a higher banana Fusarium wilt disease incidence but a lower yield. Banana fungal pathogenic genus of Fusarium and Phyllosticta were closely associated with banana yield depletion and disease aggravation. Potential biocontrol agents, such as Funneliformis, Mortierella, Flavobacterium, and Acidobacteria subgroups, exhibited a significant correlation to lower disease occurrence. Further networks analysis revealed that the number of functionally interrelated modules decreased, the composition shifted from bacteria- to fungi-dominated among these modules, and more resources-competitive interactions within networks were observed after banana long-term monoculture. Our results also showed that bacterial and fungal communities were mainly driven by soil organic matter. Overall, the findings indicated that the bacterial and fungal community structures altered significantly after banana long-term monoculture, and the fungal richness, abundance of Fusarium, interactions between and within bacteria and fungi in ecological networks, and soil organic matter were associated with banana soil-borne Fusarium wilt disease.
Collapse
Affiliation(s)
- Zongzhuan Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - C Ryan Penton
- College of Integrative Sciences and Arts, Julie Ann Wrigley Global Institute of Sustainability, Fundamental and Applied Microbiomics Institute, Arizona State University, Mesa, AZ, USA
| | - Nana Lv
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Xue
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianfu Yuan
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunze Ruan
- Hainan key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Agriculture, Hainan University, Haikou, 570228, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
35
|
Ye J, Liang J, Wang L, Markou G, Jia Q. Operation optimization of a photo-sequencing batch reactor for wastewater treatment: Study on influencing factors and impact on symbiotic microbial ecology. BIORESOURCE TECHNOLOGY 2018; 252:7-13. [PMID: 29306132 DOI: 10.1016/j.biortech.2017.12.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/19/2017] [Accepted: 12/25/2017] [Indexed: 06/07/2023]
Abstract
Wastewater treatment technology with better energy efficiency and recyclability is in urgent demand. Photo-Sequencing batch reactor (SBR), which introduces microalgae into conventional SBR, is considered to have more potential for resource recycling. In this study, a photo-SBR was evaluated through the manipulation of several key operational parameters, i.e., aeration strength, light supply intensity and time per cycle, and solid retention time (SRT). The algal-bacterial symbiotic system had the potential of removing COD, NH4+-N and TN with limited aeration, representing the advantage of energy-saving by low aeration requirement. Maintaining appropriate proportion of microalgae in the symbiotic system is critical for good system performance. Introducing microalgae into conventional SBR has obvious impact on the original microbial ecology. When the concentration of microalgae is too high (>4.60 mg Chl/L), the inhibition on certain phyla of bacteria, e.g., Bacteroidetes and Actinobacteria, would become prominent and not conducive to the stable operation.
Collapse
Affiliation(s)
- Jianfeng Ye
- Water Research Institute, Shanghai Academy of Environmental Sciences, 508 Qinzhou Rd, 200233 Shanghai, China
| | - Junyu Liang
- Water Research Institute, Shanghai Academy of Environmental Sciences, 508 Qinzhou Rd, 200233 Shanghai, China; School of Environmental Science and Engineering, Donghua University, 849 West Zhongshan Rd, 200336 Shanghai, China
| | - Liang Wang
- Water Research Institute, Shanghai Academy of Environmental Sciences, 508 Qinzhou Rd, 200233 Shanghai, China.
| | - Giorgos Markou
- School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Qilong Jia
- Water Research Institute, Shanghai Academy of Environmental Sciences, 508 Qinzhou Rd, 200233 Shanghai, China; School of Environmental Science and Engineering, Donghua University, 849 West Zhongshan Rd, 200336 Shanghai, China
| |
Collapse
|
36
|
Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems. Int J Mol Sci 2018; 19:ijms19020622. [PMID: 29470429 PMCID: PMC5855844 DOI: 10.3390/ijms19020622] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/11/2018] [Accepted: 02/15/2018] [Indexed: 11/29/2022] Open
Abstract
Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS), semi-separation intercropping (SS) using a nylon net, and complete separation intercropping (CS) using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs) showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS) showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS) improved levels of soil-available nutrients (nitrogen (N) and phosphorus (P)) and enzymes (urease and acid phosphomonoesterase) as compared to intercropping without belowground interactions (CS). Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillusbrevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P) supply capacity and soil microecosystem stability.
Collapse
|
37
|
Rilling JI, Acuña JJ, Sadowsky MJ, Jorquera MA. Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile. Front Microbiol 2018. [PMID: 30524385 DOI: 10.3389/fmicb.2018.02710/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.
Collapse
Affiliation(s)
- Joaquin I Rilling
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Jacquelinne J Acuña
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Milko A Jorquera
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| |
Collapse
|
38
|
Gómez Expósito R, de Bruijn I, Postma J, Raaijmakers JM. Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils. Front Microbiol 2017; 8:2529. [PMID: 29326674 PMCID: PMC5741648 DOI: 10.3389/fmicb.2017.02529] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Disease suppressive soils offer effective protection to plants against infection by soil-borne pathogens, including fungi, oomycetes, bacteria, and nematodes. The specific disease suppression that operates in these soils is, in most cases, microbial in origin. Therefore, suppressive soils are considered as a rich resource for the discovery of beneficial microorganisms with novel antimicrobial and other plant protective traits. To date, several microbial genera have been proposed as key players in disease suppressiveness of soils, but the complexity of the microbial interactions as well as the underlying mechanisms and microbial traits remain elusive for most disease suppressive soils. Recent developments in next generation sequencing and other 'omics' technologies have provided new insights into the microbial ecology of disease suppressive soils and the identification of microbial consortia and traits involved in disease suppressiveness. Here, we review the results of recent 'omics'-based studies on the microbial basis of disease suppressive soils, with specific emphasis on the role of rhizosphere bacteria in this intriguing microbiological phenomenon.
Collapse
Affiliation(s)
- Ruth Gómez Expósito
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands
| | - Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Joeke Postma
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| |
Collapse
|
39
|
Yang H, Li J, Xiao Y, Gu Y, Liu H, Liang Y, Liu X, Hu J, Meng D, Yin H. An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease. Front Microbiol 2017; 8:2179. [PMID: 29163453 PMCID: PMC5681905 DOI: 10.3389/fmicb.2017.02179] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/24/2017] [Indexed: 12/01/2022] Open
Abstract
The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health.
Collapse
Affiliation(s)
- Hongwu Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, China.,School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Jin Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, China
| |
Collapse
|
40
|
Schlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T. Disease Suppressive Soils: New Insights from the Soil Microbiome. PHYTOPATHOLOGY 2017; 107:1284-1297. [PMID: 28650266 DOI: 10.1094/phyto-03-17-0111-rvw] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.
Collapse
Affiliation(s)
- Daniel Schlatter
- First, third, and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - Linda Kinkel
- First, third, and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - Linda Thomashow
- First, third, and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - David Weller
- First, third, and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - Timothy Paulitz
- First, third, and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| |
Collapse
|
41
|
Dong L, Xu J, Zhang L, Yang J, Liao B, Li X, Chen S. High-throughput sequencing technology reveals that continuous cropping of American ginseng results in changes in the microbial community in arable soil. Chin Med 2017; 12:18. [PMID: 28680459 PMCID: PMC5496220 DOI: 10.1186/s13020-017-0139-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND American ginseng (Panax quinquefolius L.) is renowned worldwide for its eutherapeutic effects. The replantation of American ginseng usually fails due to problems associated with continuous cropping. An imbalance in the microbial community is thought to be responsible for this, but the overall changes in microbial communities under a continuous cropping system are unclear. METHODS This study used quantitative polymerase chain reaction combined with high-throughput sequencing methods to confirm changes in a microbial community under continuous cropping of American ginseng. RESULTS Copy numbers of bacteria and fungi significantly declined by 47.7 and 45.5%, respectively, upon American ginseng cropping over 3 years. A total of 66,391 classified sequences were obtained from high-throughput sequencing analyses of 16S and 18S rRNA in six soil samples. A decline in bacterial diversity and an increase in fungal diversity were observed in the continuous cropping soils of American ginseng compared to those of traditional crops. Compared with soils used for traditional crops, the relative abundance of bacterial and fungal groups changed in soils subjected to continuous cropping with American ginseng. CONCLUSIONS Our results revealed that the diversity and composition of soil bacterial and fungal communities changed in the continuous cropping of American ginseng compared to those of traditional crops. Those data provided comprehensive insight into microbial communities at the agro-ecosystem scale and contributed to the understanding of micro-ecological environments in the rhizosphere of medicinal plants.
Collapse
Affiliation(s)
- Linlin Dong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Lianjuan Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Juan Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| |
Collapse
|
42
|
Lee CG, Iida T, Inoue Y, Muramoto Y, Watanabe H, Nakaho K, Ohkuma M. Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse. Microbes Environ 2017; 32:118-124. [PMID: 28502968 PMCID: PMC5478534 DOI: 10.1264/jsme2.me16136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 02/13/2017] [Indexed: 11/30/2022] Open
Abstract
The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA. A difference in prokaryotic community structures between soil samples with and without bacterial wilt was only observed in the upper soil layer despite apparent similarities in the communities at the phylum level. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and several Archaea were more abundant in soil samples without disease symptoms, whereas taxa in another eight phyla were more abundant in soil samples with disease symptoms. Furthermore, some prokaryotic taxa were abundant specifically in the lower layer of soil, regardless of whether disease was present. These prokaryotic taxa may suppress or accelerate the pathogenesis of bacterial wilt and are good targets for future studies on disease control.
Collapse
Affiliation(s)
- Chol Gyu Lee
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| | - Toshiya Iida
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| | - Yasuhiro Inoue
- Central Region Agricultural Research Center, National Agriculture and Food Research OrganizationTsukuba, Ibaraki, 305–8666Japan
| | - Yasunori Muramoto
- Gifu Prefectural Agricultural Technology Center729 Matamaru, Gifu 501–1152Japan
| | - Hideki Watanabe
- Gifu Prefectural Agricultural Technology Center729 Matamaru, Gifu 501–1152Japan
| | - Kazuhiro Nakaho
- Central Region Agricultural Research Center, National Agriculture and Food Research OrganizationTsukuba, Ibaraki, 305–8666Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| |
Collapse
|
43
|
de Boer W. Upscaling of fungal-bacterial interactions: from the lab to the field. Curr Opin Microbiol 2017; 37:35-41. [PMID: 28437664 DOI: 10.1016/j.mib.2017.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
Abstract
Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.
Collapse
Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Soil Quality, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
44
|
Hamid MI, Hussain M, Wu Y, Zhang X, Xiang M, Liu X. Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode. FEMS Microbiol Ecol 2017; 93:fiw222. [PMID: 27789537 DOI: 10.1093/femsec/fiw222] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 12/16/2023] Open
Abstract
One of the mechanisms of disease suppressiveness in soils is long-term monoculture (LTM) cropping to dissuade pathogen infestation. However, the linkage between monoculturing and microbial community assemblage in the rhizosphere for disease suppression remains unclear. To decipher this potential relationship, soil samples were collected from seven locations in northeastern China, where LTM (6-38 yr) and short-term monoculture (STM ≤ 5 yr) cropping of soybean showed varying degrees of soil suppressiveness to the soybean cyst nematode (SCN; Heterodera glycines). Using high-throughput pyrosequencing to examine bacterial 16S rRNA and fungal ITS1 genes, we observed substantial variation in the species richness and relative abundance of taxa in the rhizosphere across different sampling sites. At the genus level, the genera Pseudomonas, Purpureocillium and Pochonia, which have been documented to suppress SCN in earlier studies, were much more abundant in LTM soils than in STM soils. Moreover, the relative abundance of several bacterial and fungal genera with metabolic, biocidal and parasitic activities was also monitored in the rhizosphere. In this study, we provide additional evidence that plants shift the structural and functional composition of the rhizosphere microbiota to suppress pathogen infection in LTM cropping soils.
Collapse
Affiliation(s)
- M Imran Hamid
- State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China
- Department of Plant Pathology, University College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Muzammil Hussain
- State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yunpeng Wu
- State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China
| | - Xiaoling Zhang
- State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China
| | - Meichun Xiang
- State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China
| | - Xingzhong Liu
- State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Rd., Chaoyang District, Beijing 100101, China
| |
Collapse
|
45
|
Dong L, Xu J, Feng G, Li X, Chen S. Soil bacterial and fungal community dynamics in relation to Panax notoginseng death rate in a continuous cropping system. Sci Rep 2016; 6:31802. [PMID: 27549984 PMCID: PMC4994099 DOI: 10.1038/srep31802] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/26/2016] [Indexed: 11/25/2022] Open
Abstract
Notoginseng (Panax notoginseng), a valuable herbal medicine, has high death rates in continuous cropping systems. Variation in the soil microbial community is considered the primary cause of notoginseng mortality, although the taxa responsible for crop failure remains unidentified. This study used high-throughput sequencing methods to characterize changes in the microbial community and screen microbial taxa related to the death rate. Fungal diversity significantly decreased in soils cropped with notoginseng for three years. The death rate and the fungal diversity were significantly negatively correlated, suggesting that fungal diversity might be a potential bioindicator of soil health. Positive correlation coefficients revealed that Burkholderiales, Syntrophobacteraceae, Myrmecridium, Phaeosphaeria, Fusarium, and Phoma were better adapted to colonization of diseased plants. The relative abundance of Fusarium oxysporum (R = 0.841, P < 0.05) and Phaeosphaeria rousseliana (R = 0.830, P < 0.05) were positively associated with the death rate. F. oxysporum was a pathogen of notoginseng root-rot that caused seedling death. Negative correlation coefficients indicated that Thermogemmatisporaceae, Actinosynnemataceae, Hydnodontaceae, Herpotrichiellaceae, and Coniosporium might be antagonists of pathogens, and the relative abundance of Coniosporium perforans was negatively correlated with the death rate. Our findings provide a dynamic overview of the microbial community and present a clear scope for screening beneficial microbes and pathogens of notoginseng.
Collapse
Affiliation(s)
- Linlin Dong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guangquan Feng
- Wenshan Prefecture Sanqi Science and Technology Research Institute, Sanqi Research department, Yunnan province 663000, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| |
Collapse
|
46
|
Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME JOURNAL 2016; 11:56-66. [PMID: 27482928 DOI: 10.1038/ismej.2016.108] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/11/2016] [Accepted: 06/24/2016] [Indexed: 12/18/2022]
Abstract
We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspensions of the same soil. We used 16S ribosomal RNA amplicon sequencing to determine the taxonomical structure of the bacterial communities and a shotgun metagenomics approach to investigate the potential functional diversity of the communities. By comparing the bacterial communities in soil and rhizosphere, the selective power of the plant was observed both at the taxonomic and functional level, although the diversity indices of soil and rhizosphere samples showed a highly variable, irregular pattern. Lesser variation, that is, more homogenization, was found for both the taxonomic structure and the functional profile of the rhizosphere communities as compared to the communities of the bulk soil. Network analysis revealed stronger interactions among bacterial operational taxonomic units in the rhizosphere than in the soil. The enrichment processes in the rhizosphere selected microbes with particular functional genes related to transporters, the Embden-Meyerhof-Parnas pathway and hydrogen metabolism. This selection was not random across bacteria with these functional traits, but it was species specific. Overall, this suggests that functional traits are a key to the assembly of bacterial rhizosphere communities.
Collapse
|
47
|
Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y, Kwon SK, Crüsemann M, Bok Lee Y, Kim JF, Giaever G, Nislow C, Moore BS, Thomashow LS, Weller DM, Kwak YS. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. THE ISME JOURNAL 2016; 10:119-29. [PMID: 26057845 PMCID: PMC4681868 DOI: 10.1038/ismej.2015.95] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/26/2015] [Accepted: 05/03/2015] [Indexed: 01/21/2023]
Abstract
Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic's mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.
Collapse
Affiliation(s)
- Jae-Yul Cha
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Sangjo Han
- Bioinformatics Tech Lab, SK Telecom, Sungnam, Republic of Korea
| | - Hee-Jeon Hong
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hyunji Cho
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Daran Kim
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Youngho Kwon
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Max Crüsemann
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Yong Bok Lee
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - David M Weller
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - Youn-Sig Kwak
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| |
Collapse
|
48
|
Wu L, Wang J, Huang W, Wu H, Chen J, Yang Y, Zhang Z, Lin W. Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture. Sci Rep 2015; 5:15871. [PMID: 26515244 PMCID: PMC4626807 DOI: 10.1038/srep15871] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/07/2015] [Indexed: 11/11/2022] Open
Abstract
Under consecutive monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during monoculture. Prolonged monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.
Collapse
Affiliation(s)
- Linkun Wu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Juanying Wang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Weimin Huang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Hongmiao Wu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Jun Chen
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Yanqiu Yang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Zhongyi Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Wenxiong Lin
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| |
Collapse
|
49
|
Wu Z, Hao Z, Zeng Y, Guo L, Huang L, Chen B. Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng. Antonie van Leeuwenhoek 2015; 108:1059-74. [PMID: 26296378 DOI: 10.1007/s10482-015-0560-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/17/2015] [Indexed: 01/26/2023]
Abstract
Rhizosphere and root-associated microbial communities are known to be related to soil-borne disease and plant health. In the present study, the microbial communities in rhizosphere soils and roots of both healthy and diseased Panax notoginseng were analyzed by high-throughput sequencing of 16S rRNA for bacteria and 18S rRNA internal transcribed spacer for fungi, to reveal the relationship of microbial community structure with plant health status. In total, 5593 bacterial operational taxonomic units (OTUs) and 963 fungal OTUs were identified in rhizosphere soils, while 1794 bacterial and 314 fungal OTUs were identified from root samples respectively. Principal coordinate analysis separated the microbial communities both in the rhizosphere soils and roots of diseased P. notoginseng from healthy plants. Compared to those of healthy P. notoginseng, microbial communities in rhizosphere soils and roots of diseased plants showed a decrease in alpha diversity. By contrast, bacterial community dissimilarity increased and fungal community dissimilarity decreased in rhizosphere soils of diseased plants, while both bacterial and fungal community dissimilarity in roots showed no significant difference between healthy and diseased plants. Redundancy analysis at the phylum level showed that mycorrhizal colonization and soil texture significantly affected microbial community composition in rhizosphere soils, whereas shoot nutrition status had a significant effect on microbial community composition in root samples. Our study provided strong evidence for the hypothesis that microbial diversity could potentially serve as an indicator for disease outbreak of medicinal plants, and supported the ecological significance of microbial communities in maintaining plant healthy and soil fertility.
Collapse
Affiliation(s)
- Zhaoxiang Wu
- 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
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yan Zeng
- China National Group Corporation of Traditional and Herbal Medicine, Beijing, 100097, China
| | - Lanping Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| |
Collapse
|
50
|
Kyselková M, Almario J, Kopecký J, Ságová-Marečková M, Haurat J, Muller D, Grundmann GL, Moënne-Loccoz Y. Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:346-53. [PMID: 24992533 DOI: 10.1111/1758-2229.12131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/21/2013] [Indexed: 06/03/2023]
Abstract
Very few soil quality indicators include disease-suppressiveness criteria. We assessed whether 64 16S rRNA microarray probes whose signals correlated with tobacco black root rot suppressiveness in greenhouse analysis could also discriminate suppressive from conducive soils under field conditions. Rhizobacterial communities of tobacco and wheat sampled in 2 years from four farmers' fields of contrasted suppressiveness status were compared. The 64 previously identified indicator probes correctly classified 72% of 29 field samples, with nine probes for Azospirillum, Gluconacetobacter, Sphingomonadaceae, Planctomycetes, Mycoplasma, Lactobacillus crispatus and Thermodesulforhabdus providing the best prediction. The whole probe set (1033 probes) revealed strong effects of plant, field location and year on rhizobacterial community composition, and a smaller (7% variance) but significant effect of soil suppressiveness status. Seventeen additional probes correlating with suppressiveness status in the field (noticeably for Agrobacterium, Methylobacterium, Ochrobactrum) were selected, and combined with the nine others, they improved correct sample classification from 72% to 79% (100% tobacco and 63% wheat samples). Pseudomonas probes were not informative in the field, even those targeting biocontrol pseudomonads producing 2,4-diacetylphloroglucinol, nor was quantitative polymerase chain reaction for 2,4-diacetylphloroglucinol-synthesis gene phlD. This study shows that a subset of 16S rRNA probes targeting diverse rhizobacteria can be useful as suppressiveness indicators under field conditions.
Collapse
Affiliation(s)
- Martina Kyselková
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, Ecologie Microbienne, UMR5557, Villeurbanne, France; Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology, České Budějovice, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|