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Pantinople DJ, Conner R, Sutton-Dauber S, Broussard K, Siniscalchi CM, Engle-Wrye NJ, Jordan HR, Folk RA. Continental sampling reveals core bacterial and environmentally driven fungal leaf endophytes in Heuchera. AMERICAN JOURNAL OF BOTANY 2024:e16428. [PMID: 39449649 DOI: 10.1002/ajb2.16428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 10/26/2024]
Abstract
PREMISE Endophytic plant-microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to root-associated endophytes, the role of environmental and host-related factors in the acquisition of leaf endophyte communities at broad spatial and phylogenetic scales remains sparsely studied. We assessed endofoliar diversity to test the hypothesis that membership in these microbial communities is driven primarily by abiotic environment and host phylogeny. METHODS We used a broad geographic coverage of North America in the genus Heuchera L. (Saxifragaceae), representing 32 species and varieties across 161 populations. Bacterial and fungal communities were characterized using 16S and ITS amplicon sequencing, respectively, and standard diversity metrics were calculated. We assembled environmental predictors for microbial diversity at collection sites, including latitude, elevation, temperature, precipitation, and soil parameters. RESULTS Assembly patterns differed between bacterial and fungal endophytes. Host phylogeny was significantly associated with bacteria, while geographic distance was the best predictor of fungal community composition. Species richness and phylogenetic diversity were consistent across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root-associated microbial communities, in this system microbes show no relationship with pH or other soil factors. CONCLUSIONS Overall, this work improves our understanding of the large-scale patterns of diversity and community composition in leaf endophytes and highlights the relative significance of environmental and host-related factors in driving different microbial communities within the leaf microbiome.
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Affiliation(s)
- Dexcem J Pantinople
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Reagan Conner
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Stephanie Sutton-Dauber
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Kelli Broussard
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
- General Libraries, 395 Hardy Road, Mississippi, 39762, Mississippi State, USA
| | - Nicholas J Engle-Wrye
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Heather R Jordan
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Ryan A Folk
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
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2
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Wang L, Yu L, Cai B. Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:427. [PMID: 39316269 DOI: 10.1007/s10653-024-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 09/16/2024] [Indexed: 09/25/2024]
Abstract
Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.
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Affiliation(s)
- Lei Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Lina Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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3
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Yu F, He Z, Xin X, Shi X, Chen L, He X, Huang Y, Li Y. Evidence that beneficial microbial inoculation enhances heavy metal-contaminated soil remediation: Variations in plant endophyte communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135883. [PMID: 39303617 DOI: 10.1016/j.jhazmat.2024.135883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/23/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Microbial remediation of heavy metal (HM)-contaminated soil is a sustainable approach; however, the impact of microbial inoculation on the internal environment of plants remains understudied. Thus, Enterobacter sp. FM-1 (Enterobacter sp.) and the hyperaccumulator Bidens pilosa L. (B. pilosa L.) were used to study these effects. Through analyses of plant physiological and biochemical characteristics, the endophytic microbial community composition, microbial co-occurrence networks and functional predictions, the potential mechanisms by which Enterobacter sp. benefits the phytoremediation of HM-contaminated soil by B. pilosa L. were elucidated. Inoculation with Enterobacter sp. promoted the growth of B. pilosa L. and influenced the endophytic microbial community diversity in B. pilosa L. Interactions among endophytes facilitated the formation of microbial networks, with endophytic fungi playing a more prominent role than endophytic bacteria as the level of HM contamination increased. Functional predictions via PICRUSt2 revealed that endophytic bacteria are involved primarily in processes related to carbohydrate metabolism, ABC transporters, and amino acid metabolism. In conclusion, this study provides evidence for the beneficial role of microbes in improving the plant endosphere environment.
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Affiliation(s)
- Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Ziang He
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Xiaomin Xin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China
| | - Xinwei Shi
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Lixing Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China
| | - Xinying He
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China
| | - Yueying Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China.
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4
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Shah SH, Liu H, Khan M, Muhammad R, Qadeer A, Fouad D, Chen CC. Exploration of Klebsiella aerogenes derived secondary metabolites and their antibacterial activities against multidrug-resistant bacteria. PLoS One 2024; 19:e0300979. [PMID: 39283918 PMCID: PMC11404795 DOI: 10.1371/journal.pone.0300979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/07/2024] [Indexed: 09/22/2024] Open
Abstract
As the effectiveness of current treatments against the development of antimicrobial resistance is declining, new strategies are required. A great source of novel secondary metabolites with therapeutics effects are the endophytic bacteria present in medicinal plants. In this study, Klebsiella aerogenes (an endophytic bacteria belonging to the Enterobacteriaceae family) was isolated from Kalanchoe blossfeldiana (a medicinal plant". The bacterial secondary metabolites were identified using GC-MS techniques. Furthermore, the antibacterial potentials were investigated against multi-drug resistance (MDR) Salmonella typhi and Staphylococcus aureus. The GC-MS chromatogram of K. aerogenes secondary metabolites extract displayed total of 36 compounds. Ethyl acetate extracts of K. aerogenes, showed mean zone of growth inhibition of 15.00 ± 1.00 against S. typhi and 7.00 ± 1.00mm against S. aureus, respectively. The extract demonstrated significant antibacterial effectiveness against S. typhi and moderate antibacterial efficacy against S. aureus, with minimum inhibitory concentration (MIC) values ranging from 0.089 to 0.39 mg/mL. The time-kill kinetics profile of the ethyl acetate extract against S. typhi revealed a decrease in the number of viable cells during the initial 5, 6, and 24 hours. Conversely, there was a sudden increase in viable cells up to 6 hours for S. aureus. The identified secondary metabolite with high percentage than others, benzeneethanamine exhibited favorable interactions (-7.2 kcal/mol) with the penicillin-binding protein (PBP2a) of S. aureus and (-7.5 kcal/mol) osmoporin (OmpC) of S. typhi, indicating its potential as a candidate for drug development against these MDR bacteria. This study reported for the first time, bacterial endophytes associated with K. blossfeldiana with antibacterial activities.
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Affiliation(s)
- Syed Hussain Shah
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar, Pakistan
| | - Hsien Liu
- Division of General Surgery, Department of Surgery, Ditmanson Medical Foundation, Chia-yi Christian Hospital, Chiayi, Taiwan
| | - Muddasir Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar, Pakistan
| | - Abdul Qadeer
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Dalia Fouad
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
- Ph.D. Program in Translational Medicine and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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5
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Dos Santos DFB, Herschberger JE, Subedi B, Pocius VM, Neely WJ, Greenspan SE, Becker CG, Romero GQ, Kersch-Becker MF. Leaf Shelters Facilitate the Colonisation of Arthropods and Enhance Microbial Diversity on Plants. Ecol Lett 2024; 27:e14499. [PMID: 39354894 DOI: 10.1111/ele.14499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/03/2024] [Indexed: 10/03/2024]
Abstract
Shelter-building insects are important ecosystem engineers, playing critical roles in structuring arthropod communities. Nonetheless, the influence of leaf shelters and arthropods on plant-associated microbiota remains largely unexplored. Arthropods that visit or inhabit plants can contribute to the leaf microbial community, resulting in significant changes in plant-microbe interactions. By artificially constructing leaf shelters, we provide evidence that shelter-building insects influence not only the arthropod community structure but also impact the phyllosphere microbiota. Leaf shelters exhibited higher abundance and richness of arthropods, changing the associated arthropod community composition. These shelters also altered the composition and community structure of phyllosphere microbiota, promoting greater richness and diversity of bacteria at the phyllosphere. In leaf shelters, microbial diversity positively correlated with the richness and diversity of herbivores. These findings demonstrate the critical role of leaf shelters in structuring both arthropod and microbial communities through altered microhabitats and species interactions.
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Affiliation(s)
- Danilo F B Dos Santos
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Chemical Ecology, Ecology Institute, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jacob E Herschberger
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
| | - Bijay Subedi
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Chemical Ecology, Ecology Institute, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Victoria M Pocius
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Wesley J Neely
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Sasha E Greenspan
- Department of Biology, The University of Alabama, Tuscaloosa, Alabama, USA
| | - C Guilherme Becker
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, Center for Infectious Disease Dynamics, Ecology Institute, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Gustavo Q Romero
- Laboratório de Interações Multitróficas e Biodiversidade, Departamento de Biologia Animal, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Mônica F Kersch-Becker
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Chemical Ecology, Ecology Institute, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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6
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Alam M, Pandit B, Moin A, Iqbal UN. Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture. Indian J Microbiol 2024; 64:343-366. [PMID: 39011025 PMCID: PMC11246410 DOI: 10.1007/s12088-024-01225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/07/2024] [Indexed: 07/17/2024] Open
Abstract
Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.
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Affiliation(s)
- Masrure Alam
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Baishali Pandit
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
- Department of Botany, Surendranath College, 24/2 MG Road, Kolkata, West Bengal 700009 India
| | - Abdul Moin
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Umaimah Nuzhat Iqbal
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
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7
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Bai Y, Yang M, Mei Y, Chen X, Wu X, Zhang J. The Populations of Two Differently Medicine-Used Plants of Hedyotis diffusa and Hedyotis corymbosa Shoot-Assembling Rich Bacterial and Fungal Communities with Varied Compositions but Conserved Structures. Curr Microbiol 2024; 81:192. [PMID: 38801460 DOI: 10.1007/s00284-024-03726-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
The plant-colonized microbial communities have closely micro-ecological effects on host plant growth and health. There are many medicinal plants in the genus Hedyotis, but it is yet unclear about the shoot-assembled bacterial and fungal communities (SBFC) of Hedyotis plants. Hence, eight plant populations of Hedyotis diffusa (HD) and H. corymbosa (HC) were evaluated with 16S rRNA gene and ITS sequences, for comparing the types, abundance, or/and potential functions of SBFC at plant species- and population levels. In tested HD- and HC-SBFC, 682 fungal operational taxonomic units and 1,329 bacterial zero-radius operational taxonomic units were identified, with rich species compositions and varied alpha diversities. Notably, the SBFC compositions of HD and HC plant populations were exhibited with partly different types and abundances at phylum and genus levels but without significantly different beta diversities at plant species and population levels. Typically, the SBFC of HD and HC plant populations were presented with abundance-different biomarkers, such as Frankiaceae and Bryobacteraceae, and with similar micro-ecological functions of microbial metabolisms of lipids, terpenoids,and xenobiotics. Taken together, HD- and HC-SBFC possessed with varied rich compositions, conservative taxonomic structures, and similar metabolic functions, but with small-scale type and abundance differences at plant species- and population- levels.
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Affiliation(s)
- Yachao Bai
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Mingting Yang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yunfei Mei
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xuhan Chen
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaoqing Wu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jun Zhang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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8
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Liu Y, Lu W, Li Y, Zhai B, Zhang B, Qin H, Xu P, Yang Y, Fan S, Wang Y, Li C, Zhao J, Ai J. Diversity of Endophytes of Actinidia arguta in Different Seasons. Life (Basel) 2024; 14:149. [PMID: 38276278 PMCID: PMC10819999 DOI: 10.3390/life14010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.
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Affiliation(s)
- Yingxue Liu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Wenpeng Lu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Yang Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (Y.L.); (B.Z.); (J.Z.)
| | - Boyu Zhai
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (Y.L.); (B.Z.); (J.Z.)
| | - Baoxiang Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Hongyan Qin
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Peilei Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Yiming Yang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Yue Wang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Changyu Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Jianjun Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (Y.L.); (B.Z.); (J.Z.)
| | - Jun Ai
- College of Horticulture, Jilin Agricultural University, Changchun 130112, China
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Xu P, Stirling E, Xie H, Li W, Lv X, Matsumoto H, Cheng H, Xu A, Lai W, Wang Y, Zheng Z, Wang M, Liu X, Ma B, Xu J. Continental scale deciphering of microbiome networks untangles the phyllosphere homeostasis in tea plant. J Adv Res 2023; 44:13-22. [PMID: 36725184 PMCID: PMC9936419 DOI: 10.1016/j.jare.2022.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/21/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Assembly and co-occurrence of the host co-evolved microbiota are essential ecological and evolutionary processes, which is not only crucial for managing individual plant fitness but also ecological function. However, understanding of the microbiome assembly and co-occurrence in higher plants is not well understood. The tea plant was shown to contribute the forest fitness due to the microbiome assembled in the phyllosphere; the landscape of microbiome assembly in the tea plants and its potential implication on phyllosphere homestasis still remains untangled. OBJECTIVES This study aimed to deciphering of the microbiome networks of the tea plants at a continental scale. It would provide fundamental insights into the factors driving the microbiome assembly, with an extended focus on the resilience towards the potential pathogen in the phyllosphere. METHODS We collected 225 samples from 45 locations spanning approximately 2000-km tea growing regions across China. By integration of high-throughput sequencing data, physicochemical properties profiling and bioinformatics analyses, we investigated continental scale microbiome assembly and co-occurrence in the tea plants. Synthetic assemblages, interaction assay and RT-qPCR were further implemented to analyze the microbial interaction indexed in phyllosphere. RESULTS A trade-off between stochastic and deterministic processes in microbiomes community assembly was highlighted. Assembly processes were dominated by deterministic processes in bulk and rhizosphere soils, and followed by stochastic processes in roots and leaves with amino acids as critical drivers for environmental selection. Sphingobacteria and Proteobacteria ascended from soils to leaves to sustain a core leaf taxa. The core taxa formed a close association with a prevalent foliar pathogen in the co-occurrence network and significantly attenuated the expression of a set of essential virulence genes in pathogen. CONCLUSION Our study unveils the mechanism underpinning microbiome assembly in the tea plants, and a potential implication of the microbiome-mediated resilience framework on the phyllosphere homeostasis.
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Affiliation(s)
- Ping Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Erinne Stirling
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Hengtong Xie
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Wenbing Li
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou 310018, China
| | - Haruna Matsumoto
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Haiyan Cheng
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Anan Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Wanyi Lai
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yuefei Wang
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Zuntao Zheng
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China.
| | - Xingmei Liu
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China.
| | - Jianming Xu
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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10
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Adhikary R, Mandal S, Mandal V. Seasonal Variation Imparts the Shift in Endophytic Bacterial Community Between Mango and its Hemiparasites. Curr Microbiol 2022; 79:287. [PMID: 35962289 DOI: 10.1007/s00284-022-02987-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
Abstract
The study of community composition and community structure is important to know the ecological behaviour and community dynamics of the participating species and to understand the molecular interplay that lies between them. The community diversity greatly lies in the physiological status of the host and the environmental factors. The present study aims to explore the endophytic bacterial communities and their dynamics in the pre-flowering and post-flowering seasons in the horticulturally important Mango (Mangifera indica L.) and its hemiparasites: Loranthus parasiticus (L.) Marr. and Macrosolen colchinchinensis (Lour.) Tiegh. through a metagenomic approach using the sequence of V3 region of 16S rRNA gene. The genera Bacillus, Acinetobacter and Corynebacterium, under the phyla Firmicutes, Proteobacteria and Actinobacteria, respectively, were found to be the most abundant genera present in mango and its hemiparasites. It was found that during the post-flowering season, the twigs and leaves of mango had lesser endophytes than in other seasons while the alpha-diversity indices of the representative genera were the highest in L. parasiticus during the same seasons. However, in M. colchinchinensis, the alpha diversity was also higher in the post-flowering season similar to another hemiparasite plant L. parasiticus. The ecological, taxonomic and complex correlation studies unravelled that the hemiparasites act as the potent reservoirs of endophytic communities throughout the year and during favourable conditions, these bacterial communities disseminate to the mango plant.
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Affiliation(s)
- Rajsekhar Adhikary
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour, Banga, P.O. - Mokdumpur, Malda, WB, 732103, India.,Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
| | - Vivekananda Mandal
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour, Banga, P.O. - Mokdumpur, Malda, WB, 732103, India.
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11
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Dai YF, Wu XM, Wang HC, Li WH, Cai LT, Li JX, Wang F, Sehar S, Shamsi IH. Spatio-Temporal Variation in the Phyllospheric Microbial Biodiversity of Alternaria Alternata-Infected Tobacco Foliage. Front Microbiol 2022; 13:920109. [PMID: 35966692 PMCID: PMC9370072 DOI: 10.3389/fmicb.2022.920109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Phyllospheric microbial composition of tobacco (Nicotiana tabacum L.) is contingent upon certain factors, such as the growth stage of the plant, leaf position, and cultivar and its geographical location, which influence, either directly or indirectly, the growth, overall health, and production of the tobacco plant. To better understand the spatiotemporal variation of the community and the divergence of phyllospheric microflora, procured from healthy and diseased tobacco leaves infected by Alternaria alternata, the current study employed microbe culturing, high-throughput technique, and BIOLOG ECO. Microbe culturing resulted in the isolation of 153 culturable fungal isolates belonging to 33 genera and 99 bacterial isolates belonging to 15 genera. High-throughput sequencing revealed that the phyllosphere of tobacco was dominantly colonized by Ascomycota and Proteobacteria, whereas, the most abundant fungal and bacterial genera were Alternaria and Pseudomonas. The relative abundance of Alternaria increased in the upper and middle healthy groups from the first collection time to the third, whereas, the relative abundance of Pseudomonas, Sphingomonas, and Methylobacterium from the same positions increased during gradual leaf aging. Non-metric multi-dimensional scaling (NMDs) showed clustering of fungal communities in healthy samples, while bacterial communities of all diseased and healthy groups were found scattered. FUNGuild analysis, from the first collection stage to the third one in both groups, indicated an increase in the relative abundance of Pathotroph-Saprotroph, Pathotroph-Saprotroph-Symbiotroph, and Pathotroph-Symbiotroph. Inclusive of all samples, as per the PICRUSt analysis, the predominant pathway was metabolism function accounting for 50.03%. The average values of omnilog units (OUs) showed relatively higher utilization rates of carbon sources by the microbial flora of healthy leaves. According to the analysis of genus abundances, leaf growth and leaf position were the important drivers of change in structuring the microbial communities. The current findings revealed the complex ecological dynamics that occur in the phyllospheric microbial communities over the course of a spatiotemporal varying environment with the development of tobacco brown spots, highlighting the importance of community succession.
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Affiliation(s)
- Yuan-feng Dai
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Bijie Tobacco Company, Bijie, China
| | - Xiao-mao Wu
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Xiao-mao Wu
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Han-cheng Wang
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Ji-xin Li
- Guizhou Tobacco Company of CNTC, China National Tobacco Corporation, Guiyang, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Feng Wang
| | - Shafaque Sehar
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Haider Shamsi
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Imran Haider Shamsi
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12
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Maela MP, van der Walt H, Serepa-Dlamini MH. The Antibacterial, Antitumor Activities, and Bioactive Constituents’ Identification of Alectra sessiliflora Bacterial Endophytes. Front Microbiol 2022; 13:870821. [PMID: 35865925 PMCID: PMC9294510 DOI: 10.3389/fmicb.2022.870821] [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: 02/07/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Due to increased antimicrobial resistance against current drugs, new alternatives are sought. Endophytic bacteria associated with medicinal plants are recognized as valuable sources of novel secondary metabolites possessing antimicrobial, antitumor, insecticidal, and antiviral activities. In this study, five bacterial endophytes were isolated and identified from the medicinal plant, Alectra sessiliflora, and their antibacterial and antitumor activities were investigated. In addition, the crude extracts of the endophytes were analyzed using gas chromatography (GC) coupled with time-of-flight mass spectrometry (TOF-MS). The identified bacterial endophytes belong to three genera viz Lysinibacillus, Peribacillus, and Bacillus, with the latter as the dominant genus with three species. Ethyl acetate extracts from the endophytes were used for antimicrobial activity against eleven pathogenic strains through minimum inhibitory concentration (MIC). The antitumor activity against the Hela cervical, Hek 293 kidney, and A549 lung carcinoma cells was determined by the MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay. Lysinibacillus sp. strain AS_1 exhibited broad antibacterial activity against the pathogenic strains with MIC values ranging from 4 to 8 mg/ml, while Bacillus sp. strain AS_3 displayed MIC of 0.25 mg/ml. Crude extracts of Lysinibacillus sp. strain AS_1, Peribacillus sp. strain AS_2, and Bacillus sp. strain AS_3 showed growth inhibition of more than 90% against all the cancer cell lines at a concentration of 1,000 μg/ml. Untargeted secondary metabolite profiling of the crude extracts revealed the presence of compounds with reported biological activity, such as antimicrobial, antioxidant, anti-inflammatory, antitumor, and antidiabetic properties. This study reported for the first time, bacterial endophytes associated with A. sessiliflora with antibacterial and antitumor activities.
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Affiliation(s)
- Mehabo Penistacia Maela
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg, South Africa
| | | | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg, South Africa
- *Correspondence: Mahloro Hope Serepa-Dlamini,
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13
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Pandey SS, Jain R, Bhardwaj P, Thakur A, Kumari M, Bhushan S, Kumar S. Plant Probiotics – Endophytes pivotal to plant health. Microbiol Res 2022; 263:127148. [DOI: 10.1016/j.micres.2022.127148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/22/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022]
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14
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [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: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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15
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The Microbiome of the ‘Williams’ Pear Variety Grown in the Organic Orchard and Antifungal Activity by the Autochthonous Bacterial and Yeast Isolates. Microorganisms 2022; 10:microorganisms10071282. [PMID: 35889000 PMCID: PMC9321879 DOI: 10.3390/microorganisms10071282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 01/04/2023] Open
Abstract
The total diversity of bacterial and fungal communities associated with the phyllosphere (fruits and leaves) of the ‘Williams’ pear variety was analyzed in two phenological stages during fruit development and maturation. The antagonistic potential of autochthonous bacterial and yeast isolates against phytopathogenic fungi was also evaluated. A metabarcoding approach revealed Pantoea, Sphingomonas, Hymenobacter, Massilia, and Pseudomonas as dominant bacterial constituents of the pear phyllosphere, whilst most abundant among the fungal representatives identified were Metschnikowia, Filobasidium, Aureobasidiumpullulans, Botrytis cinerea, and Taphrina. The traditional culturable approach revealed that the Pseudomonas genus with P. graminis, P. putida, and P. congelans was most prevalent. The most frequently cultivated fungal representatives belonged to the genus Fusarium with six identified species. A broad range of the antagonistic activity was detected for the Hannaella luteola and Metschnikowia pulcherrima yeasts, significantly affecting the growth of many fungal isolates in the range of 53–70%. Fusarium sporotrichioides was the most susceptible fungal isolate. The autochthonous antagonistic yeasts H. luteola and M. pulcherrima might be powerful biological control agents of postharvest diseases caused by Fusarium spp. and common pathogens like Monilinia laxa, Botrytis cinerea, Alternaria tenuissima, and Cladosporium cladosporioides.
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16
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Gardner CM, Gerhard WA, Redfern LK, Gunsch CK. Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35319433 DOI: 10.1099/mic.0.001155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (r S≥0.70 or r S≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.
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Affiliation(s)
- Courtney M Gardner
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Washington State University, Civil and Environmental Engineering, 405 Spokane St., PO Box 642910, Pullman, WA 99164, USA
| | - William A Gerhard
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA
| | - Lauren K Redfern
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Florida Gulf Coast University, Environmental and Civil Engineering, 10501 FGCU Blvd. South, Ft. Myers, FL 33965, USA
| | - Claudia K Gunsch
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Duke University, Durham, NC 27708, USA
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17
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Riva V, Mapelli F, Bagnasco A, Mengoni A, Borin S. A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities. Appl Environ Microbiol 2022; 88:e0253721. [PMID: 35138928 PMCID: PMC8939329 DOI: 10.1128/aem.02537-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large data set of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.
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Affiliation(s)
- Valentina Riva
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Agnese Bagnasco
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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18
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Michalko J, Medo J, Ferus P, Konôpková J, Košútová D, Hoťka P, Barta M. Changes of Endophytic Bacterial Community in Mature Leaves of Prunus laurocerasus L. during the Seasonal Transition from Winter Dormancy to Vegetative Growth. PLANTS 2022; 11:plants11030417. [PMID: 35161398 PMCID: PMC8839770 DOI: 10.3390/plants11030417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023]
Abstract
Diverse communities of bacterial endophytes inhabit plant tissues, and these bacteria play important roles for plant growth and health. Cherry laurel (Prunus laurocerasus L.) is a broadleaf evergreen shrub that is widely grown in temperate zones for its ornamental and medicinal properties, however virtually nothing is known about its associated bacterial community. In this study, we analysed the matured one-year-old leaves of this plant using Illumina-based 16S rRNA gene metabarcoding to reveal the community structure of endophytic bacteria and understand its shifts during the seasonal transition from winter dormancy to a spring vegetative state. The overall community was composed of four dominant phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes). Corynebacterium, Acinetobacter, and Chryseobacterium genera were the most prevalent bacteria, comprising 13.3%, 6.9%, and 6.8% of the amplicon sequence variants (ASVs), respectively. The ASV richness and diversity increased significantly in May as compared to other sampling months (February, March, and April). We observed high variation in the overall community structure of endophytic bacteria among collection dates. The variation was only reflected by a few core community members, suggesting that the changes of the endophytic community during winter/spring seasonal transition are mostly associated with the less abundant community members. We identified biomarker taxa for late winter, mid spring, and late spring collection dates. This study is the first one to report on the diversity and composition of bacterial endophytes in the leaves of cherry laurel and its shifts across the dormancy-to-vegetative seasonal transition.
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Affiliation(s)
- Jaroslav Michalko
- Mlynany Arboretum, Institute of Forest Ecology, Slovak Academy of Sciences, 951-52 Slepcany, Slovakia; (P.F.); (J.K.); (D.K.); (P.H.)
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, 949-76 Nitra, Slovakia;
- Correspondence:
| | - Juraj Medo
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, 949-76 Nitra, Slovakia;
| | - Peter Ferus
- Mlynany Arboretum, Institute of Forest Ecology, Slovak Academy of Sciences, 951-52 Slepcany, Slovakia; (P.F.); (J.K.); (D.K.); (P.H.)
| | - Jana Konôpková
- Mlynany Arboretum, Institute of Forest Ecology, Slovak Academy of Sciences, 951-52 Slepcany, Slovakia; (P.F.); (J.K.); (D.K.); (P.H.)
| | - Dominika Košútová
- Mlynany Arboretum, Institute of Forest Ecology, Slovak Academy of Sciences, 951-52 Slepcany, Slovakia; (P.F.); (J.K.); (D.K.); (P.H.)
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, 949-74 Nitra, Slovakia
| | - Peter Hoťka
- Mlynany Arboretum, Institute of Forest Ecology, Slovak Academy of Sciences, 951-52 Slepcany, Slovakia; (P.F.); (J.K.); (D.K.); (P.H.)
| | - Marek Barta
- Department of Plant Pathology and Mycology, Institute of Forest Ecology, Slovak Academy of Sciences, 949-01 Nitra, Slovakia;
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19
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Wang P, Dai J, Luo L, Liu Y, Jin D, Zhang Z, Li X, Fu W, Tang T, Xiao Y, Hu Y, Liu E. Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field. FRONTIERS IN PLANT SCIENCE 2022; 12:766128. [PMID: 35095946 PMCID: PMC8794795 DOI: 10.3389/fpls.2021.766128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.
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Affiliation(s)
- Pei Wang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Jianping Dai
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Luyun Luo
- Yangtze Normal University, Chongqing, China
| | - Yong Liu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Decai Jin
- Chinese Academy of Sciences Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhuo Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiaojuan Li
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Wei Fu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Tao Tang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Youlun Xiao
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yang Hu
- Zhejiang Academy of Forestry, Hangzhou, China
| | - Erming Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
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20
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Zhu J, Sun X, Tang QY, Zhang ZD. Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress. Front Microbiol 2021; 12:778327. [PMID: 34975801 PMCID: PMC8716815 DOI: 10.3389/fmicb.2021.778327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/29/2021] [Indexed: 01/16/2023] Open
Abstract
Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.
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Affiliation(s)
- Jing Zhu
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, China
| | - Xiang Sun
- School of Life Sciences, Hebei University, Baoding, China
| | - Qi-Yong Tang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, China
| | - Zhi-Dong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, China
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21
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Alves-Júnior M, de Sousa FO, Silva TF, Albino UB, Garcia MG, Moreira SMCDO, Vieira MRDS. Functional and morphological analysis of isolates of phylloplane and rhizoplane endophytic bacteria interacting in different cocoa production systems in the Amazon. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100039. [PMID: 34841330 PMCID: PMC8610332 DOI: 10.1016/j.crmicr.2021.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 11/25/2022] Open
Abstract
Endophytic bacteria colonize different internal tissues of plants without damaging their cells. They can establish themselves in the same niche as other microorganisms and develop antagonistic activities against phytopathogens. There is little research on the functional and morphological characterization of these bacteria in production systems in the Amazon. Thus, the objective of this work was to functionally and morphologically characterize endophytic bacteria isolated from cocoa trees (Theobroma cacao L.) and evaluate their antagonistic potential against phytopathogens. A total of 197 endophytic bacteria isolates were obtained from leaves and roots of cocoa plants with different production systems and at different times of the year. The characterization of functional groups consisted of proteolytic, amylolytic and cellulolytic activity and ability to fix nitrogen and solubilize phosphate. Morphological diversity was evaluated mainly according to the following parameters: shape, color, size and elevation of the colony. Thirteen isolates of endophytic bacteria, selected by cluster analysis, were used to evaluate the antagonistic potential in paired trials against four species of phytopathogenic fungi. The largest amount of endophytic bacteria was isolated from the root (95.9%), in the dry season. The most expressive activities with regards to the enzyme index were amylolytic (71.9%), proteolytic (70.2%) and nitrogen fixing (38.6%), respectively. The similarity analysis formed two clusters with isolates CS R 2.4 and CS R 2.25 exhibiting 100% similarity. Five isolates displayed inhibitory activity against phytopathogenic fungi, most notably isolate TS R 2.19, which exhibited antagonistic activity against all fungi and mycelial growth inhibition rates between 25.7% and 50.7%. Understanding the interaction between endophytes in cocoa plants is important as a possible additional tool in biological control. Our studies are incipient and the first to be carried out in different cocoa production systems in the state of Pará, Brazil.
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Affiliation(s)
- Miguel Alves-Júnior
- Faculty of Agronomic Engineering, Laboratory of Agricultural and Forestry Phytopathology, Federal University of Pará, Altamira, PA, 68372-040, Brazil
| | - Fabiana Oliveira de Sousa
- Faculty of Agronomic Engineering, Laboratory of Agricultural and Forestry Phytopathology, Federal University of Pará, Altamira, PA, 68372-040, Brazil
| | - Thays Ferreira Silva
- Faculty of Agronomic Engineering, Laboratory of Agricultural and Forestry Phytopathology, Federal University of Pará, Altamira, PA, 68372-040, Brazil
| | - Ulisses Brigatto Albino
- Faculty of Chemistry, Institute of Exact Sciences, Federal University of the South and Southeast of Pará, Marabá, PA 68507-590, Brazil
| | - Magali Gonçalves Garcia
- Faculty of Biological Sciences, Laboratory of Microbiology, Federal University of Pará, Altamira, PA 68372-040, Brazil
| | | | - Marcos Ribeiro da Silva Vieira
- Faculty of Agronomic Engineering, Laboratory of Physiology and Post-Harvest, Technology, Federal University of Pará, Altamira, PA 68372-040, Brazil
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22
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Gorai PS, Ghosh R, Mandal S, Ghosh S, Chatterjee S, Gond SK, Mandal NC. Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res 2021; 252:126859. [PMID: 34536676 DOI: 10.1016/j.micres.2021.126859] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/21/2021] [Accepted: 08/29/2021] [Indexed: 11/29/2022]
Abstract
Exploration of endophytic bacteria with multiple plant growth promoting (PGP) attributes is considered as an eco-friendly and cost-effective alternative to agricultural chemicals for increasing crop productivity. In the present endeavor, healthy chickpea plants (Cicer arietinum L.) collected from district Birbhum, West Bengal, India were subjected for the isolation of endophytic bacteria having multifarious PGP properties. One potent endophytic Gram positive bacterial strain CNE6 was isolated from the nodule of chickpea and was identified as Bacillus siamensis based on 16S rDNA sequence homologies. The isolate showed a number of PGP properties like phosphate solubilization, IAA production, nitrogen fixation, hydroxamate type of siderophore production and ACC deaminase activities. The isolate CNE6 produced 33.27 ± 2.16 μg/mL of IAA in the presence of tryptophan. Production of IAA was also confirmed by HPLC analysis and it was found effective for inducing lateral root branching in chickpea. In addition, the isolate displayed significant antagonistic activity against a number of plant pathogenic fungi when tested by dual culture overlay and agar well diffusion assay. 50 % cell free supernatant of CNE6 was found effective for 60-80 % inhibition of radial growth of pathogenic fungi tested. Scanning electron microscopic observation revealed massive degradation of pathogenic fungal mycelia by the antifungal metabolites of CNE6. LC-MS analysis of bacterial lipopeptides suggested the production of antifungal antibiotics like surfactin, fengycin and iturin by the isolate. The presence of genes encoding antifungal lipopeptides was also confirmed by PCR amplification using specific primers. Green fluorescent protein (GFP) tagging of CNE6 using broad host range plasmid vector (pDSK-GFPuv) followed by colonization study indicated very good host colonization potential of the isolate and its probable movement through xylem vessels. Enhanced shoot and root length and chlorophyll content upon treatment with CNE6 as observed in in vivo pot experiments also supported the positive role of the endophytic isolate on overall development and growth of the chickpea plants. This is the first report of Bacillus siamensis as an endophyte of Cicer arietinum L. which can be successfully applied for improving the productivity of this crop plant.
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Affiliation(s)
- Pralay Shankar Gorai
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva-Bharati, Santiniketan, 731235, India
| | - Ranjan Ghosh
- Department of Botany, Bankura Sammilani College, Kenduadihi, Bankura, 722102, India
| | - Subhrangshu Mandal
- Department of Botany, Siksha Bhavana, Visva-Bharati, Santiniketan, 731235, India
| | - Suvranil Ghosh
- Division of Molecular Medicine, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Sumit Chatterjee
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Surendra Kumar Gond
- Department of Botany, MMV, Banaras Hindu University, Varanasi, 221005, India
| | - Narayan Chandra Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva-Bharati, Santiniketan, 731235, India.
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23
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Faticov M, Abdelfattah A, Roslin T, Vacher C, Hambäck P, Blanchet FG, Lindahl BD, Tack AJM. Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak. THE NEW PHYTOLOGIST 2021; 231:1770-1783. [PMID: 33960441 DOI: 10.1111/nph.17434] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/15/2021] [Indexed: 05/13/2023]
Abstract
Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multifactorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak Quercus robur across one growing season. Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially at the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming × genotype interactions on species richness and community composition. Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.
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Affiliation(s)
- Maria Faticov
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, A-8010, Austria
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, PO Box 7044, Uppsala, SE-756 51, Sweden
| | | | - Peter Hambäck
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - F Guillaume Blanchet
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département de Mathématique, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC, J1H 5N4, Canada
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, PO Box 7014, Uppsala, SE-750 07, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
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24
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Processing of leafy vegetables matters: Damage and microbial community structure from field to bag. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors. mSphere 2021; 6:e0131620. [PMID: 34106767 PMCID: PMC8265678 DOI: 10.1128/msphere.01316-20] [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] [Indexed: 01/04/2023] Open
Abstract
Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors. IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.
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26
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Bacterial Endophytes: The Hidden Actor in Plant Immune Responses against Biotic Stress. PLANTS 2021; 10:plants10051012. [PMID: 34069509 PMCID: PMC8161118 DOI: 10.3390/plants10051012] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Bacterial endophytes constitute an essential part of the plant microbiome and are described to promote plant health by different mechanisms. The close interaction with the host leads to important changes in the physiology of the plant. Although beneficial bacteria use the same entrance strategies as bacterial pathogens to colonize and enter the inner plant tissues, the host develops strategies to select and allow the entrance to specific genera of bacteria. In addition, endophytes may modify their own genome to adapt or avoid the defense machinery of the host. The present review gives an overview about bacterial endophytes inhabiting the phytosphere, their diversity, and the interaction with the host. Direct and indirect defenses promoted by the plant-endophyte symbiont exert an important role in controlling plant defenses against different stresses, and here, more specifically, is discussed the role against biotic stress. Defenses that should be considered are the emission of volatiles or antibiotic compounds, but also the induction of basal defenses and boosting plant immunity by priming defenses. The primed defenses may encompass pathogenesis-related protein genes (PR family), antioxidant enzymes, or changes in the secondary metabolism.
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27
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Lefèvre E, Gardner CM, Gunsch CK. A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization. FEMS Microbiol Ecol 2020; 96:5850752. [PMID: 32490528 DOI: 10.1093/femsec/fiaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.
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Affiliation(s)
- Emilie Lefèvre
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane street, Sloan 101, Box 642910, Pullman, WA 99164, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
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28
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Yao H, Sun X, He C, Li XC, Guo LD. Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest. FEMS Microbiol Ecol 2020; 96:5800982. [PMID: 32149339 DOI: 10.1093/femsec/fiaa038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 03/05/2020] [Indexed: 01/24/2023] Open
Abstract
Interactions between plants and microbes are involved in biodiversity maintenance, community stability and ecosystem functioning. However, differences in the community and network structures between phyllosphere epiphytic and endophytic bacteria have rarely been investigated. Here, we examined phyllosphere epiphytic and endophytic bacterial communities of six mangrove species using Illumina MiSeq sequencing of the 16S rRNA gene. The results revealed that the community structure of epiphytic and endophytic bacteria was different. Plant identity significantly affected the diversity and community structure of both epiphytic and endophytic bacteria, with a greater effect on the community structure of the former than the latter. Network analysis showed that both plant-epiphytic and plant-endophytic bacterial network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the epiphytic bacterial network was more highly specialized and modular but less connected and more strongly anti-nested than the endophytic bacterial network. This study reveals that the phyllosphere epiphytic and endophytic bacterial community structures differ and plant identity has a greater effect on the epiphytic than on the endophytic bacteria, which may provide a comprehensive insight into the role of plant identity in driving the phyllosphere epiphytic and endophytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Hui Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Dasgupta MG, Burragoni S, Amrutha S, Muthupandi M, Parveen ABM, Sivakumar V, Ulaganathan K. Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance. Microbiol Res 2020; 241:126579. [PMID: 32861101 DOI: 10.1016/j.micres.2020.126579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022]
Abstract
The genus Eucalyptus with over 747 species occurs in wide ecological range and is preferred for bioenergy plantations due to their short rotation, rapid growth and superior wood properties. They are planted in 22 million ha area and India is third largest planter of Eucalyptus. In the present study, the bacterial endophyte community in leaves of six Eucalyptus clones belonging to E. tereticornis and E. camaldulensis was assessed by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The clones were selected based on their response to progressive water stress. A total of 4947 operational taxonomic units (OTUs) were obtained and the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes. Escherichia coli was enriched in all samples at species level. Comparison of endophyte diversity was conducted between the two species and across the water stress tolerant and susceptible clones. The alpha-diversity analysis revealed that species richness and diversity was high in E. camaldulensis and water stress susceptible clones. LefSe analysis predicted 69 and 54 significantly enriched taxonomic biomarkers between species and stress response groups respectively. A maximum of 49 taxonomic biomarkers were recorded in susceptible group and the significantly enriched species were Bacteroides thetaiotaomicron and Turicibacter sanguinis, while the tolerant group documented 5 biomarkers including oscillibacter sp. The presence of functional biomarkers was also assessed in both the groups. The findings of the present study provides an insight into the diversity of bacterial endophyte in Eucalyptus leaves and to our knowledge this is the first report on documenting the endophyte abundance in water stress responsive Eucalyptus clones.
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Affiliation(s)
| | - Sravanthi Burragoni
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Sivanantham Amrutha
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Muthusamy Muthupandi
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | | | - Veerasamy Sivakumar
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
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30
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Fadiji AE, Babalola OO. Exploring the potentialities of beneficial endophytes for improved plant growth. Saudi J Biol Sci 2020; 27:3622-3633. [PMID: 33304173 PMCID: PMC7714962 DOI: 10.1016/j.sjbs.2020.08.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 11/23/2022] Open
Abstract
Pathogen affects plant growth, host health and productivity. Endophytes, presumed to live inside the plant tissues, might be helpful in sustaining the future of agriculture. Although recent studies have proven that endophytes can be pathogenic, commensal, non-pathogenic, and/or beneficial, this review will focus on the beneficial category only. Beneficial endophytes produce a number of compounds which are useful for protecting plants from environmental conditions, enhancing plant growth and sustainability, while living conveniently inside the hosts. The population of endophytes is majorly controlled by location, and climatic conditions where the host plant grows. Often the most frequently isolated endophytes from the tissues of the plant are fungi, but sometimes greater numbers of bacteria are isolated. Beneficial endophytes stand a chance to replace the synthetic chemicals currently being used for plant growth promotion if carefully explored by researchers and embraced by policymakers. However, the roles of endophytes in plant growth improvement and their behavior in the host plant have not been fully understood. This review presents the current development of research into beneficial endophytes and their effect in improving plant growth.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, South Africa
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31
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The endosphere bacteriome of diseased and healthy tomato plants. Arch Microbiol 2020; 202:2629-2642. [PMID: 32710156 DOI: 10.1007/s00203-020-01987-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/29/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022]
Abstract
Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.
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32
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Drivers of Foliar Fungal Endophytic Communities of Kudzu (Pueraria montana var. lobata) in the Southeast United States. DIVERSITY 2020. [DOI: 10.3390/d12050185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fungal endophytes play important roles in plant fitness and plant–microbe interactions. Kudzu (Pueraria montana var. lobata) is a dominant, abundant, and highly aggressive invasive plant in the Southeast United States. Kudzu serves as a pathogen reservoir that impacts economically important leguminous crops. We conducted the first investigations on kudzu fungal endophytes (Illumina MiSeq—ITS2) to elucidate drivers of endophytic communities across the heart of the invasive range in the Southeast United States (TN, MS, AL, GA). We tested the impacts of multiple environmental parameters (Chlorophyll, NO3−, K+, soil pH, leaf area, host genotype, traffic intensity, and geographic location) on foliar endophyte communities. Endophytic communities were diverse and structured by many factors in our PerMANOVA analyses, but location, genotype, and traffic (proxy for pollution) were the strongest drivers of community composition (R2 = 0.152, p < 0.001, R2 = 0.129, p < 0.001, and R2 = 0.126, p < 0.001, respectively). Further, we examined the putative ecological interactions between endophytic fungi and plant pathogens. We identify numerous OTUs that are positively and strongly associated with pathogen occurrence, largely within the families Montagnulaceae and Tremellales incertae sedis. Taken together, these data suggest location, host genetics and local pollution play instrumental roles in structuring communities, and integrative plant management must consider these factors when developing management strategies.
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33
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Cardoso V, Campos F, Santos A, Ottoni M, Rosa C, Almeida V, Grael C. Biotechnological applications of the medicinal plant
Pseudobrickellia brasiliensis
and its isolated endophytic bacteria. J Appl Microbiol 2020; 129:926-934. [DOI: 10.1111/jam.14666] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/19/2020] [Accepted: 04/10/2020] [Indexed: 11/29/2022]
Affiliation(s)
- V.M. Cardoso
- Departamento de Farmácia Universidade Federal dos Vales do Jequitinhonha e Mucuri Diamantina MG Brazil
| | - F.F. Campos
- Faculdade de Medicina Universidade Federal dos Vales do Jequitinhonha e Mucuri Diamantina MG Brazil
| | - A.R.O. Santos
- Departamento de Microbiologia ICB, C. P. 486 Universidade Federal de Minas Gerais Belo Horizonte MG Brazil
| | - M.H.F. Ottoni
- Departamento de Farmácia Universidade Federal dos Vales do Jequitinhonha e Mucuri Diamantina MG Brazil
| | - C.A. Rosa
- Departamento de Microbiologia ICB, C. P. 486 Universidade Federal de Minas Gerais Belo Horizonte MG Brazil
| | - V.G. Almeida
- Departamento de Farmácia Universidade Federal dos Vales do Jequitinhonha e Mucuri Diamantina MG Brazil
| | - C.F.F. Grael
- Departamento de Farmácia Universidade Federal dos Vales do Jequitinhonha e Mucuri Diamantina MG Brazil
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Seasonal Variation Influence Endophytic Actinobacterial Communities of Medicinal Plants from Tropical Deciduous Forest of Meghalaya and Characterization of Their Plant Growth-Promoting Potentials. Curr Microbiol 2020; 77:1689-1698. [PMID: 32300926 DOI: 10.1007/s00284-020-01988-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
The endophytic actinobacteria constitute a diverse community which has vast potential importance that may be exploited in pharmaceutical, agricultural, and biotechnological industries. However, the effects of seasonal changes on distribution of endophytic actinobacteria in medicinal plants of Meghalaya are largely uncharacterized. Here, we investigated host and seasonal influence on diversity of endophytic actinobacteria residing in roots of six medicinal plant species of Meghalaya. A total of 493 cultivable endophytic actinobacterial isolates representing 41 species were obtained from root segments of six plant species which had been collected during four different seasons of 2011-2012 and 2012-2013. Among the host plant species, maximum actinobacterial colonization was observed in Costus speciosus and minimum in Potentilla fulgens. In regard to seasons, the highest actinobacterial colonization and relative abundance were observed during summer season and least was recorded during the winter season. It was ascertained that though endophytic actinobacteria have varying capacity to colonize in different plant species during the seasons, colonization is not found to be species-specific. Culture-independent attempt also inferred that actinobacterial community varied amongst the six medicinal plants during the different seasons. Hence, seasons are influential factors in the colonization capacity of endophytic actinobacterial community. Furthermore, plant growth-promoting activities were recorded in 34.15% of the isolates. Hence, these results indicate that endophytic actinobacteria from the selected medicinal plants also represent an important source of plant growth-promoting bioactive metabolites.
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Anguita-Maeso M, Olivares-García C, Haro C, Imperial J, Navas-Cortés JA, Landa BB. Culture-Dependent and Culture-Independent Characterization of the Olive Xylem Microbiota: Effect of Sap Extraction Methods. FRONTIERS IN PLANT SCIENCE 2020; 10:1708. [PMID: 32038682 PMCID: PMC6988092 DOI: 10.3389/fpls.2019.01708] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/04/2019] [Indexed: 05/03/2023]
Abstract
Microbial endophytes are well known to protect host plants against pathogens, thus representing a promising strategy for the control of xylem-colonizing pathogens. To date, the vast majority of microbial communities inhabiting the olive xylem are unknown; therefore, this work pursues the characterization of the xylem-limited microbiome and determines whether the culture isolation medium, olive genotype, and the plant material used to analyze it can have an effect on the bacterial populations retrieved. Macerated xylem tissue and xylem sap extracted with the Scholander chamber from olive branches obtained from two cultivated and a wild olive genotypes were analyzed using culture-dependent and -independent approaches. In the culture-dependent approach using four solid culture media, a total of 261 bacterial isolates were identified after performing Sanger sequencing of 16S rRNA. Culturable bacteria clustered into 34 genera, with some effect of culture media for bacterial isolation. The cultivated bacteria belonged to four phyla and the most abundant genera included Frigoribacterium (18.8%), Methylobacterium (16.4%), and Sphingomonas (14.6%). On the other hand, in the culture-independent approach conducted using Illumina MiSeq 16S rRNA amplicon sequencing [next-generation sequencing (NGS)] of the xylem extracts, we identified a total of 48 operational taxonomic units (OTUs) belonging to five phyla, being Sphingomonas (30.1%), Hymenobacter (24.1%) and Methylobacterium (22.4%) the most representative genera (>76% of reads). In addition, the results indicated significant differences in the bacterial communities detected in the xylem sap depending on the genotype of the olive tree studied and, to a minor extent, on the type of sap extraction method used. Among the total genera identified using NGS, 14 (41.2%) were recovered in the culture collection, whereas 20 (58.8%) in the culture collection were not captured by the NGS approach. Some of the xylem-inhabiting bacteria isolated are known biocontrol agents of plant pathogens, whereas for others little information is known and are first reported for olive. Consequently, the potential role of these bacteria in conferring olive tree protection against xylem pathogens should be explored in future research.
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Affiliation(s)
- Manuel Anguita-Maeso
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | | | - Carmen Haro
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Juan Imperial
- Institute of Agricultural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Juan A. Navas-Cortés
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Blanca B. Landa
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
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36
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Janakiev T, Dimkić I, Bojić S, Fira D, Stanković S, Berić T. Bacterial communities of plum phyllosphere and characterization of indigenous antagonistic Bacillus thuringiensis R3/3 isolate. J Appl Microbiol 2019; 128:528-543. [PMID: 31606926 DOI: 10.1111/jam.14488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
AIMS The characterization of bacterial communities diversity on four local plum cultivars in two phenological stages using culture-dependent and culture-independent methods and screening among culturable plum community for indigenous bacteria active against phytopathogens. METHODS AND RESULTS The bacterial communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Metagenomic approach revealed Methylobacterium, Sphingomonas and Hymenobacter as dominant genera. The most frequently isolated representatives with cultivable approach were pseudomonads with Pseudomonas syringae and Pseudomonas graminis, the most likely resident species of plum community. Antagonistic Bacillus thuringiensis R3/3 isolate from plum phyllosphere had ability to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture environment and show quorum quenching activity. CONCLUSIONS Plum cultivar and growth season contribute to the structure of the bacterial community associated with plum. Plum phyllosphere is good source of antagonists effective against phytopathogens. SIGNIFICANCE AND IMPACT OF STUDY Knowledge of bacterial communities on plum will have an impact on studies related to phyllosphere ecology and biocontrol. The indigenous antagonistic isolate, B. thuringiensis R3/3, from plum could be further investigated for its potential use in biological control of plum diseases.
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Affiliation(s)
- T Janakiev
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - I Dimkić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Bojić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - D Fira
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Stanković
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - T Berić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
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Grady KL, Sorensen JW, Stopnisek N, Guittar J, Shade A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat Commun 2019; 10:4135. [PMID: 31515535 PMCID: PMC6742659 DOI: 10.1038/s41467-019-11974-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Perennial grasses are promising feedstocks for biofuel production, with potential for leveraging their native microbiomes to increase their productivity and resilience to environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We sample leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identify core leaf taxa based on occupancy. Virtually all leaf taxa are also detected in soil; source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is an important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support crop production. Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.
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Affiliation(s)
- Keara L Grady
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA.,The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA
| | - Jackson W Sorensen
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA.,The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA
| | - Nejc Stopnisek
- The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - John Guittar
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA.,Kellogg Biological Station, Michigan State University, 3700 E. Gull Lake Dr, Hickory Corners, MI, 49060, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA. .,The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA. .,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA. .,The Plant Resilience Institute, Michigan State University, East Lansing, MI, 48840, USA. .,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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38
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Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status. mBio 2019; 10:mBio.01296-19. [PMID: 31266874 PMCID: PMC6606809 DOI: 10.1128/mbio.01296-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications. Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia.
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Luo L, Zhang Z, Wang P, Han Y, Jin D, Su P, Tan X, Zhang D, Muhammad-Rizwan H, Lu X, Liu Y. Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber. AMB Express 2019; 9:76. [PMID: 31134393 PMCID: PMC6536563 DOI: 10.1186/s13568-019-0800-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/16/2019] [Indexed: 01/07/2023] Open
Abstract
The phyllosphere is colonized by a wide variety of microorganisms including epiphytes, plant-pathogenic fungus, bacteria, as well as human or animal pathogens. However, little is known about how microbial community composition changes with the development of angular leaf-spot of cucumber. Here, 18 mixed samples were collected based on the lesion coverage rate (LCR) of angular leaf-spot of cucumber from three disease severity groups (DM1: symptomatic-mild, DM2: symptomatic-moderate, DM3: symptomatic-severe). In our study, the microbial community structure and diversity were examined by Illumina MiSeq sequencing. A significant differences was observed in α diversity and community structure among three disease severity groups. The phyllosphere microbiota was observed to be dominated by bacterial populations from Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal species from Ascomycota and Basidiomycota. In addition, some plant-specific microbe such as Sphingomonas, Methylobacterium, Pseudomonas, and Alternaria showed significant changes in their relative abundance of population. The LCR was correlated negatively with Sphingomonas, Methylobacterium, Quadrisphaera, and Lactobacillus, whereas correlated positively with Pseudomonas and Kineococcus (p < 0.05). The LCR was negatively correlated with Alternaria and Arthrinium of the fungal communities (p < 0.05). Molecular ecological networks of the microbial communities were constructed to show the interactions among the OTUs. Our current results indicated that the competitive relationships among species were broken with the development of angular leaf-spot of cucumber. The microbial community composition changed over the development of angular leaf-spot of cucumber. The result of molecular ecological networks indicated that the overall bacterial community tends toward mutualism from the competition. The development of angular leaf-spot of cucumber affected the ecosystem functioning by disrupting the stability of the microbial community network. This work will help us to understand the host plant-specific microbial community structures and shows how these communities change throughout the development of angular leaf-spot of cucumber.
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40
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Eichmeier A, Kiss T, Necas T, Penazova E, Tekielska D, Bohunicka M, Valentova L, Cmejla R, Morais D, Baldrian P. High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum". MICROBIAL ECOLOGY 2019; 77:664-675. [PMID: 30194483 DOI: 10.1007/s00248-018-1250-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
"Candidatus Phytoplasma prunorum" (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.
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Affiliation(s)
- Ales Eichmeier
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valtická 334, 691 44, Lednice, Czech Republic.
| | - Tomas Kiss
- Department of Fruit Growing, Mendel University in Brno, Valtická 337, 691 44, Lednice, Czech Republic
| | - Tomas Necas
- Department of Fruit Growing, Mendel University in Brno, Valtická 337, 691 44, Lednice, Czech Republic
| | - Eliska Penazova
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valtická 334, 691 44, Lednice, Czech Republic
| | - Dorota Tekielska
- Department of Plant Protection, University of Agriculture in Krakow, 29 Listopada 54, 31-425, Krakow, Poland
| | - Marketa Bohunicka
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, 500 03, Hradec Králové, Czech Republic
| | - Lucie Valentova
- Research and Breeding Institute of Pomology Holovousy Ltd, Holovousy 129, 508 01, Hořice, Czech Republic
| | - Radek Cmejla
- Research and Breeding Institute of Pomology Holovousy Ltd, Holovousy 129, 508 01, Hořice, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
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Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants. Microbiol Res 2019; 221:36-49. [DOI: 10.1016/j.micres.2019.02.001] [Citation(s) in RCA: 258] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/11/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022]
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Toju H, Kurokawa H, Kenta T. Factors Influencing Leaf- and Root-Associated Communities of Bacteria and Fungi Across 33 Plant Orders in a Grassland. Front Microbiol 2019; 10:241. [PMID: 30837969 PMCID: PMC6390183 DOI: 10.3389/fmicb.2019.00241] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
In terrestrial ecosystems, plants interact with diverse taxonomic groups of bacteria and fungi in the phyllosphere and rhizosphere. Although recent studies based on high-throughput DNA sequencing have drastically increased our understanding of plant-associated microbiomes, we still have limited knowledge of how plant species in a species-rich community differ in their leaf and root microbiome compositions. In a cool-temperate semi-natural grassland in Japan, we compared leaf- and root-associated microbiomes across 137 plant species belonging to 33 plant orders. Based on the whole-microbiome inventory data, we analyzed how sampling season as well as the taxonomy, nativeness (native or alien), lifeform (herbaceous or woody), and mycorrhizal type of host plants could contribute to variation in microbiome compositions among co-occurring plant species. The data also allowed us to explore prokaryote and fungal lineages showing preferences for specific host characteristics. The list of microbial taxa showing significant host preferences involved those potentially having some impacts on survival, growth, or environmental resistance of host plants. Overall, this study provides a platform for understanding how plant and microbial communities are linked with each other at the ecosystem level.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Kyoto, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Hiroko Kurokawa
- Forestry and Forest Products Research Institute, Tsukuba, Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
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Khare E, Mishra J, Arora NK. Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects. Front Microbiol 2018; 9:2732. [PMID: 30498482 PMCID: PMC6249440 DOI: 10.3389/fmicb.2018.02732] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/25/2018] [Indexed: 11/13/2022] Open
Abstract
Microbial endophytes are present in all known plant species. The ability to enter and thrive in the plant tissues makes endophytes unique, showing multidimensional interactions within the host plant. Several vital activities of the host plant are known to be influenced by the presence of endophytes. They can promote plant growth, elicit defense response against pathogen attack, and can act as remediators of abiotic stresses. To date, most of the research has been done assuming that the interaction of endophytes with the host plant is similar to the plant growth-promoting (PGP) microbes present in the rhizosphere. However, a new appreciation of the difference of the rhizosphere environment from that of internal plant tissues is gaining attention. It would be interesting to explore the impact of endosymbionts on the host’s gene expression, metabolism, and other physiological aspects essential in conferring resistance against biotic and abiotic stresses. A more intriguing and inexplicable issue with many endophytes that has to be critically evaluated is their ability to produce host metabolites, which can be harnessed on a large scale for potential use in diverse areas. In this review, we discuss the concept of endophytism, looking into the latest insights related to the multifarious interactions beneficial for the host plant and exploring the importance of these associations in agriculture and the environment and in other vital aspects such as human health.
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Affiliation(s)
- Ekta Khare
- Department of Microbiology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Jitendra Mishra
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Naveen Kumar Arora
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition. Antonie van Leeuwenhoek 2018; 112:283-295. [DOI: 10.1007/s10482-018-1157-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
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45
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Phalnikar K, Kunte K, Agashe D. Dietary and developmental shifts in butterfly-associated bacterial communities. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171559. [PMID: 29892359 PMCID: PMC5990769 DOI: 10.1098/rsos.171559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts.
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Affiliation(s)
| | | | - Deepa Agashe
- Authors for correspondence: Deepa Agashe e-mail:
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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Hamonts K, Trivedi P, Garg A, Janitz C, Grinyer J, Holford P, Botha FC, Anderson IC, Singh BK. Field study reveals core plant microbiota and relative importance of their drivers. Environ Microbiol 2018; 20:124-140. [PMID: 29266641 DOI: 10.1111/1462-2920.14031] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022]
Abstract
Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane-associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time-associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity.
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Affiliation(s)
- Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Anshu Garg
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Caroline Janitz
- Next-generation Sequencing Facility, Western Sydney University, Penrith, NSW, Australia
| | - Jasmine Grinyer
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Paul Holford
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | | | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-based Innovation, Western Sydney University, Penrith, NSW, Australia
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Liu H, Carvalhais LC, Crawford M, Singh E, Dennis PG, Pieterse CMJ, Schenk PM. Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria. Front Microbiol 2017; 8:2552. [PMID: 29312235 PMCID: PMC5742157 DOI: 10.3389/fmicb.2017.02552] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/08/2017] [Indexed: 02/05/2023] Open
Abstract
One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.
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Affiliation(s)
- Hongwei Liu
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lilia C. Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Mark Crawford
- Department of Natural Resources and Mines, Toowoomba, QLD, Australia
| | - Eugenie Singh
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Paul G. Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Peer M. Schenk
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Zhang L, Wang S. Bacterial community diversity on in-shell walnut surfaces from six representative provinces in China. Sci Rep 2017; 7:10054. [PMID: 28855583 PMCID: PMC5577159 DOI: 10.1038/s41598-017-10138-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/04/2017] [Indexed: 11/09/2022] Open
Abstract
Walnuts (Juglans regia) have been associated with foodborne illness outbreaks in recent years. Thus, the purpose of this study was to investigate the distribution of bacteria on in-shell walnut surfaces from six representative provinces in China. The bacterial populations on walnut surfaces were investigated by high-throughput sequencing based on the bacterial 16 S rRNA hypervariable region V4. Twenty-eight samples were collected from fourteen regions in six provinces and harvested in different periods (the fresh in 2016 and the old in 2015). Proteobacteria was the most dominant phylum in all samples except for XJ1. In XJ1, and the most abundant phylum was Cyanobacteria, which also accounted for a large proportion of the abundance in YN1, YN11, XJ2 and SC11. In addition, Firmicutes and Actinobacteria were also the abundant phyla in the given samples. Some genera belonging to the opportunistic pathogens were detected, such as Pseudomonas, Acinetobacter, Burkholderia and Bacillus. The results revealed that the composition and abundance of bacterial consortiums on walnut surfaces varied among the geographical sites where they were harvested. Moreover, the storage time of samples also had impact on the abundance of bacteria. This study may provide a better understanding of the bacterial communities' diversity on in-shell walnut surfaces.
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Affiliation(s)
- Lihui Zhang
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shaojin Wang
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China. .,Department of Biological Systems Engineering, Washington State University, Pullman, WA, 99164-6120, USA.
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Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep 2017; 7:40914. [PMID: 28102323 PMCID: PMC5244420 DOI: 10.1038/srep40914] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/13/2016] [Indexed: 11/09/2022] Open
Abstract
Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.
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Affiliation(s)
- Franziska Wemheuer
- Section of Agricultural Entomology, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Kristin Kaiser
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Stefan Vidal
- Section of Agricultural Entomology, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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