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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. Sci Total Environ 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Wang N, Ren J, Wang L, Wang Y, Wang Z, Guo D. A preliminary study to explain how Streptomyces pactum (Act12) works on phytoextraction: soil heavy metal extraction, seed germination, and plant growth. Environ Monit Assess 2023; 195:757. [PMID: 37247015 DOI: 10.1007/s10661-023-11340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
Streptomyces pactum (Act12) can both promote plant growth and strengthen heavy metal mobilization. Nevertheless, the mechanisms of how Act12 works during the phytoextraction process are still unknown. The present work investigated whether the metabolites produced by Act12 could influence the seed germination and the growth of potherb mustard and explored its mobilizing effect on soil cadmium (Cd) and zinc (Zn). The results showed that the germination potential and rate of potherb mustard seed treated with Act12 fermentation broth were 1.0- and 0.32-folds higher than those of control, probably due to the interruption of seed dormant stage. We also found that Act12 inoculation not only promoted the dry biomass (6.82%) of potherb mustard, but also increased the leaf chlorophyll (11.8%) and soluble protein (0.35%) production. The boosted seed germination rate under Act12 treatment (up to 63.3%) indicated that Act12 enhanced the resistance of potherb mustard seeds to Cd and Zn and alleviated their physiological toxicity. The generated metabolites during the Act12 fermentation posed positive impact on the availability of soil Cd and Zn. These findings bring new insight into the Act12-assisted phytoextraction of Cd and Zn from contaminated soils.
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Affiliation(s)
- Nina Wang
- School of Petroleum and Environment Engineering, Yan'an University, Yan'an, 716000, Shaanxi, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, Shaanxi, China
| | - Jie Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, Shaanxi, China
| | - Linlin Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, Shaanxi, China
| | - Yuheng Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, Shaanxi, China
| | - Ze Wang
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Di Guo
- School of Petroleum and Environment Engineering, Yan'an University, Yan'an, 716000, Shaanxi, China.
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Singh S, Aghdam SA, Lahowetz RM, Brown AMV. Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions. Environ Microbiome 2023; 18:36. [PMID: 37085932 PMCID: PMC10120106 DOI: 10.1186/s40793-023-00493-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microbiomes are critical to plants, promoting growth, elevating stress tolerance, and expanding the plant's metabolic repertoire with novel defense pathways. However, generally microbiomes within plant tissues, which intimately interact with their hosts, remain poorly characterized. These endospheres have become a focus in banana (Musa spp.)-an important plant for study of microbiome-based disease protection. Banana is important to global food security, while also being critically threatened by pandemic diseases. Domestication and clonal propagation are thought to have depleted protective microbiomes, whereas wild relatives may hold promise for new microbiome-based biological controls. The goal was to compare metapangenomes enriched from 7 Musa genotypes, including wild and cultivated varieties grown in sympatry, to assess the host associations with root and leaf endosphere functional profiles. RESULTS Density gradients successfully generated culture-free microbial enrichment, dominated by bacteria, with all together 24,325 species or strains distinguished, and 1.7 million metagenomic scaffolds harboring 559,108 predicted gene clusters. About 20% of sequence reads did not match any taxon databases and ~ 62% of gene clusters could not be annotated to function. Most taxa and gene clusters were unshared between Musa genotypes. Root and corm tissues had significantly richer endosphere communities that were significantly different from leaf communities. Agrobacterium and Rhizobium were the most abundant in all samples while Chitinophagia and Actinomycetia were more abundant in roots and Flavobacteria in leaves. At the bacterial strain level, there were > 2000 taxa unique to each of M. acuminata (AAA genotype) and M. balbisiana (B-genotype), with the latter 'wild' relatives having richer taxa and functions. Gene ontology functional enrichment showed core beneficial functions aligned with those of other plants but also many specialized prospective beneficial functions not reported previously. Some gene clusters with plant-protective functions showed signatures of phylosymbiosis, suggesting long-standing associations or heritable microbiomes in Musa. CONCLUSIONS Metapangenomics revealed key taxa and protective functions that appeared to be driven by genotype, perhaps contributing to host resistance differences. The recovery of rich novel taxa and gene clusters provides a baseline dataset for future experiments in planta or in vivo bacterization or engineering of wild host endophytes.
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Affiliation(s)
- Simrandeep Singh
- Department of Microbiology, University of Illinois, Urbana, IL USA
| | - Shiva A. Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
| | - Rachel M. Lahowetz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Amanda M. V. Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
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Chesters D, Liu X, Bell KL, Orr MC, Xie T, Zhou Q, Zhu C. An integrative bioinformatics pipeline shows that honeybee-associated microbiomes are driven primarily by pollen composition. Insect Sci 2023; 30:555-568. [PMID: 36001735 DOI: 10.1111/1744-7917.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/11/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
The microbiomes associated with bee nests influence colony health through various mechanisms, although it is not yet clear how honeybee congeners differ in microbiome assembly processes, in particular the degrees to which floral visitations and the environment contribute to different aspects of diversity. We used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species (Apis cerana, A. dorsata, A. florea, and A. laboriosa) sampled throughout Yunnan, China, a global biodiversity hotspot. We developed a computational pipeline integrating multiple databases for quantifying key facets of diversity, including compositional, taxonomic, phylogenetic, and functional ones. Further, we assessed candidate drivers of observed microbiome dissimilarity, particularly differences in floral visitations, habitat disturbance, and other key environmental variables. Analyses revealed that microbiome alpha diversity was broadly equivalent across the study sites and between bee species, apart from functional diversity which was very low in nests of the reclusive A. laboriosa. Turnover in microbiome composition across Yunnan was driven predominantly by pollen composition. Human disturbance negatively impacted both compositional and phylogenetic alpha diversity of nest microbiomes, but did not correlate with microbial turnover. We herein make progress in understanding microbiome diversity associated with key pollinators in a biodiversity hotspot, and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of diversity, which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Xiuwei Liu
- Institute of Agro-Products Processing, Yunnan Province Academy of Agricultural Science, Kunming, China
| | - Karen L Bell
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- CSIRO Health & Biosecurity, Floreat, WA, Australia
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Xie
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui Province, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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Becker R, Ulrich K, Behrendt U, Schneck V, Ulrich A. Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback. Plants (Basel) 2022; 11:3487. [PMID: 36559599 PMCID: PMC9781493 DOI: 10.3390/plants11243487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.
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Affiliation(s)
- Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Volker Schneck
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
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Lalzar M, Zeevi A, Frenkel O, Gamliel A, Abbo S, Iasur Kruh L. Seed-Derived Microbial Community of Wild Cicer Seedlings: Composition and Augmentation to Domesticated Cicer. Microbiol Spectr 2022; 10:e0278521. [PMID: 35638782 DOI: 10.1128/spectrum.02785-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Seed-borne bacteria are a unique group of microorganisms capable of maintaining stable populations within plant tissues and seeds. These bacteria may benefit their host from germination to maturation and are of great interest for basic and applied plant-microbe interaction studies. Furthermore, many such beneficial bacteria present in wild plant species are missing in their respective congeneric domesticated forms. The objectives of this study were to explore the bacterial communities within the seeds of wild Cicer species and to select beneficial bacteria which could be used to improve production of domesticated chickpea (C. arietinum). We analyzed the composition of seed-borne bacteria of chickpea (Cicer spp.), comparing wild and domesticated species from different geographic locations. Subsequently, we isolated the dominant and prevalent seed-borne bacteria from wild Cicer judaicum and assessed their ability to colonize and affect the growth of domesticated chickpea and other legume crops. The composition and structure of seed-borne bacteria, determined by amplicon sequencing of the 16S rRNA gene, differed between wild and domesticated chickpea and varied among geographic locations. The genus Burkholderia dominated samples from domesticated chickpea at all examined sites, while Bacillus or Sphingomonas dominated cultures isolated from wild C. judaicum, dependent on geographic location. A particular Bacillus strain, Bacillus sp. CJ, representing the most prevalent bacterium in wild C. judaicum, was further isolated. Bacillus sp. CJ, applied by seed coating, successfully inhabited domesticated chickpea plants and improved plant growth parameters. These results demonstrate the potential for reconstructing the microbiota of crop plants using the wild microbiota reservoir. IMPORTANCE Chickpea (garbanzo bean, hummus, Cicer arietinum) representing the third legume crop produced globally. As is the case for many other domesticated crops, the adaptation and resistance of chickpea to biotic and abiotic stresses is inferior compared to that of their wild progenitors and relatives. Re-establishing desirable characteristics from wild to domesticated species may be achieved by reconstructing beneficial microbiota. In this study, we examined the seed-associated microbiota of both wild and domesticated chickpea and applied isolated beneficial bacteria originating from wild Cicer judaicum to domesticated chickpea by seed coating. This isolate, Bacillus sp. CJ, was successfully established in the crop and enhanced its growth, demonstrating effective and efficient manipulation of the chickpea microbiota as a potential model for future application in other crop plants.
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Lu M, Schneider D, Daniel R. Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. Front Microbiol 2022; 13:851969. [PMID: 35756004 PMCID: PMC9226776 DOI: 10.3389/fmicb.2022.851969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
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Affiliation(s)
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
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Fan Y, Zhang M, Cheng J, Yong D, Ji J, Wu Q, He C. Elucidating nitrifying performance, nitrite accumulation and microbial community in a three-stage plug flow moving bed biofilm reactor (PF - MBBR). Chemosphere 2022; 297:134087. [PMID: 35216986 DOI: 10.1016/j.chemosphere.2022.134087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/13/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
A three-stage plug flow moving bed biofilm reactor (PF - MBBR, consisting of three identical chambers of N1, N2 and N3) was proposed for nitrifier enrichment using synthetic wastewater. During the stable operation, the average NH4+-N effluent was 0.67 mg/L and NH4+-N removal was as high as 97.19% with the nitrite accumulation ratio (NAR) of 54.23%, although the biofilm thickness and biomass both presented downward trends from N1 (296 μm, 2280 mg/L), N2 (248 μm, 1850 mg/L) to N3 (198 μm, 1545 mg/L). Particularly, the comparative results of three stages revealed that N2 showed the optimum NH4+-N removal (77.27%) and NAR (75.21%) in the continuous-flow, while NAR of N3 unexpectedly maintained a high level of 65.83% in the batch test, suggesting that ammonia oxidizing bacteria (AOB) accounted for absolute advantage over nitrite oxidizing bacteria (NOB). High-throughput sequencing initially verified different distribution of bacterial community structure, where N2 was far away from N1 and N3 with the lowest community richness and community diversity (operational taxonomic units (OTUs): 454(N2)<527(N3)<621(N1)). Proteobacteria (77.60%-83.09%), Bacteroidetes (1.66%-3.66%), Acidobacteria (2.28%-4.67%), and Planctomycetes (1.19%-6.63%) were the major phyla. At the genus level, AOB (mainly Nitrosomonas) accounted for 5.08% (N1), 20.74% (N2) and 14.24% (N3) while NOB (mainly Nitrospira) increased from 0.14% (N1), 7.06% (N2) to 4.91% (N3) with the total percentages of 5.22%, 27.80% and 19.15%. Finally, the application feasibility of MBBR optimization linked with nitrite (NO2--N) accumulation for deep-level nutrient removal was discussed.
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Affiliation(s)
- Yajun Fan
- College of Hydraulic Science and Engineering, Yangzhou University, Yangzhou, 225100, PR China
| | - Miao Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China.
| | - Jilin Cheng
- College of Hydraulic Science and Engineering, Yangzhou University, Yangzhou, 225100, PR China
| | - Daming Yong
- Yangzhou Polytechnic Institute, Yangzhou, 225127, PR China
| | - Junjie Ji
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China
| | - Qichao Wu
- Yangzhou Polytechnic Institute, Yangzhou, 225127, PR China
| | - Chengda He
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China
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Ulrich K, Becker R, Behrendt U, Kube M, Schneck V, Ulrich A. Physiological and genomic characterisation of Luteimonas fraxinea sp. nov., a bacterial species associated with trees tolerant to ash dieback. Syst Appl Microbiol 2022; 45:126333. [DOI: 10.1016/j.syapm.2022.126333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022]
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Mutungi PM, Wekesa VW, Onguso J, Kanga E, Baleba SBS, Boga HI. Culturable Bacterial Endophytes Associated With Shrubs Growing Along the Draw-Down Zone of Lake Bogoria, Kenya: Assessment of Antifungal Potential Against Fusarium solani and Induction of Bean Root Rot Protection. Front Plant Sci 2022; 12:796847. [PMID: 35222451 PMCID: PMC8864308 DOI: 10.3389/fpls.2021.796847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Vascular shrubs growing along the draw-down zones of saline lakes must develop adaptive mechanisms to cope with high salinity, erratic environmental conditions, and other biotic and abiotic stresses. Microbial endophytes from plants growing in these unique environments harbor diverse metabolic and genetic profiles that play an important role in plant growth, health, and survival under stressful conditions. A variety of bacterial endophytes have been isolated from salt tolerant plants but their potential applications in agriculture have not been fully explored. To further address this gap, the present study sought to isolate culturable bacterial endophytes from shrubs growing along the draw-down zone of Lake Bogoria, a saline alkaline lake, and examined their functional characteristics and potential in the biocontrol of the bean root rot pathogen, Fusarium solani. We collected shrubs growing within 5 m distance from the shoreline of Lake Bogoria and isolated 69 bacterial endophytes. The endophytic bacteria were affiliated to three different phyla (Firmicutes, Proteobacteria, and Actinobacteria) with a bias in the genera, Bacillus, and they showed no tissue or plant specificity. All selected isolates were positive for catalase enzyme grown in 1.5 M NaCl; three isolates (B23, B19, and B53) produced indole acetic acid (IAA) and only one isolate, B23 did not solubilize phosphate on Pikovskaya agar. Isolates, B19 and B53 exhibited more than 50% of mycelial inhibition in the dual culture assay and completely inhibited the germination of F. solani spores in co-culture assays while two isolates, B07 and B39 had delayed fungal spore germination after an overnight incubation. All isolates were able to establish endophytic association in the roots, stems, and leaves of been seedlings in both seed soaking and drenching methods. Colonization of bean seedlings by the bacterial endophytes, B19 and B53 resulted in the biocontrol of F. solani in planta, reduced disease severity and incidence, and significantly increased both root and shoot biomass compared to the control. Taxonomic identification using 16S rRNA revealed that the two isolates belong to Enterobacter hormaechei subsp., Xiangfangensis and Bacillus megaterium. Our results demonstrate the potential use of these two isolates in the biocontrol of the bean root rot pathogen, F. solani and plant growth promotion.
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Affiliation(s)
- Priscillar Mumo Mutungi
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Ecological Monitoring Department, Kenya Wildlife Service, Nairobi, Kenya
| | | | - Justus Onguso
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Erustus Kanga
- State Department for Wildlife, Ministry of Tourism and Wildlife, Nairobi, Kenya
| | - Steve B. S. Baleba
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Hamadi Iddi Boga
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
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Michalska-Smith M, Song Z, Spawn-Lee SA, Hansen ZA, Johnson M, May G, Borer ET, Seabloom EW, Kinkel LL. Network structure of resource use and niche overlap within the endophytic microbiome. ISME J 2022; 16:435-446. [PMID: 34413476 PMCID: PMC8776778 DOI: 10.1038/s41396-021-01080-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function.
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Affiliation(s)
- Matthew Michalska-Smith
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA.
- Department of Plant Pathology, University of Minnesota, St Paul, MN, USA.
| | - Zewei Song
- Department of Plant Pathology, University of Minnesota, St Paul, MN, USA
| | - Seth A Spawn-Lee
- Department of Geography, University of Wisconsin, Madison, WI, USA
- Center for Sustainability and the Global Environment (SAGE), University of Wisconsin, Madison, WI, USA
| | - Zoe A Hansen
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Mitch Johnson
- Department of Horticultural Science, University of Minnesota, St Paul, MN, USA
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, USA
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, St Paul, MN, USA
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Ji C, Wang X, Song X, Zhou Q, Li C, Chen Z, Gao Q, Li H, Li J, Zhang P, Cao H. Effect of Bacillus velezensis JC-K3 on Endophytic Bacterial and Fungal Diversity in Wheat Under Salt Stress. Front Microbiol 2021; 12:802054. [PMID: 34987493 PMCID: PMC8722765 DOI: 10.3389/fmicb.2021.802054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023] Open
Abstract
Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant's above-ground and underground parts, which may be the cause of the plant's "Induced Systemic Tolerance." The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat's biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.
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Affiliation(s)
- Chao Ji
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, China
- College of Biological and Agricultural Engineering, Weifang University, Weifang, China
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Xiaohui Wang
- College of Forestry, Shandong Agriculture University, Taian, China
- Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
- Ministry of Agriculture Key Laboratory of Seaweed Fertilizers, Qingdao, China
| | - Xin Song
- College of Forestry, Shandong Agriculture University, Taian, China
- Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Qisheng Zhou
- Animal Husbandry and Veterinary Service Center of Xintai City, Taian, China
| | - Chaohui Li
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Zhizhang Chen
- College of Foreign Languages, Weifang University, Weifang, China
| | - Qixiong Gao
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Huying Li
- College of Forestry, Shandong Agriculture University, Taian, China
- Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Jintai Li
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Pengcheng Zhang
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Hui Cao
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, China
- College of Biological and Agricultural Engineering, Weifang University, Weifang, China
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Kunda P, Mukherjee A, Dhal PK. Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India. World J Microbiol Biotechnol 2021; 37:184. [PMID: 34580777 DOI: 10.1007/s11274-021-03153-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.
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Lin G, Chen B, Hu C, Lin W. The Impacts of Field Management on Soil and Tea Root Microbiomes. Appl Microbiol 2021; 1:361-76. [DOI: 10.3390/applmicrobiol1020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures.
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Beltran-Garcia MJ, Martínez-Rodríguez A, Olmos-Arriaga I, Valdes-Salas B, Di Mascio P, White JF. Nitrogen fertilization and stress factors drive shifts in microbial diversity in soils and plants. Symbiosis 2021. [DOI: 10.1007/s13199-021-00787-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Xu T, Jiang W, Qin D, Liu T, Zhang J, Chen W, Gao L. Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat. Sci Rep 2021; 11:5773. [PMID: 33707584 PMCID: PMC7952392 DOI: 10.1038/s41598-021-85281-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/26/2021] [Indexed: 11/11/2022] Open
Abstract
Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.
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Affiliation(s)
- Tongshuo Xu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenli Jiang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,School of Agriculture, Yangtze University, Jingzhou, China
| | - Dandan Qin
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianmin Zhang
- School of Agriculture, Yangtze University, Jingzhou, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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Hamid B, Zaman M, Farooq S, Fatima S, Sayyed RZ, Baba ZA, Sheikh TA, Reddy MS, El Enshasy H, Gafur A, Suriani NL. Bacterial Plant Biostimulants: A Sustainable Way towards Improving Growth, Productivity, and Health of Crops. Sustainability 2021; 13:2856. [DOI: 10.3390/su13052856] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review presents a comprehensive and systematic study of the field of bacterial plant biostimulants and considers the fundamental and innovative principles underlying this technology. Plant biostimulants are an important tool for modern agriculture as part of an integrated crop management (ICM) system, helping make agriculture more sustainable and resilient. Plant biostimulants contain substance(s) and/or microorganisms whose function when applied to plants or the rhizosphere is to stimulate natural processes to enhance plant nutrient uptake, nutrient use efficiency, tolerance to abiotic stress, biocontrol, and crop quality. The use of plant biostimulants has gained substantial and significant heed worldwide as an environmentally friendly alternative to sustainable agricultural production. At present, there is an increasing curiosity in industry and researchers about microbial biostimulants, especially bacterial plant biostimulants (BPBs), to improve crop growth and productivity. The BPBs that are based on PGPR (plant growth-promoting rhizobacteria) play plausible roles to promote/stimulate crop plant growth through several mechanisms that include (i) nutrient acquisition by nitrogen (N2) fixation and solubilization of insoluble minerals (P, K, Zn), organic acids and siderophores; (ii) antimicrobial metabolites and various lytic enzymes; (iii) the action of growth regulators and stress-responsive/induced phytohormones; (iv) ameliorating abiotic stress such as drought, high soil salinity, extreme temperatures, oxidative stress, and heavy metals by using different modes of action; and (v) plant defense induction modes. Presented here is a brief review emphasizing the applicability of BPBs as an innovative exertion to fulfill the current food crisis.
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18
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Wang P, Kong X, Chen H, Xiao Y, Liu H, Li X, Zhang Z, Tan X, Wang D, Jin D, Deng Y, Cernava T. Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars. Front Microbiol 2021; 12:629852. [PMID: 33664718 PMCID: PMC7920960 DOI: 10.3389/fmicb.2021.629852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022] Open
Abstract
Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.
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Affiliation(s)
- Pei Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiao Kong
- School of Public Health, Qingdao University, Qingdao, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hongsong Chen
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Youlun Xiao
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Huijun Liu
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, China
| | - Xiaojuan Li
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhuo Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xinqiu Tan
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Diandong Wang
- College of Life Science and Technology, Yangtze Normal University, Chongqing, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Szymańska S, Sikora M, Hrynkiewicz K, Tyburski J, Tretyn A, Gołębiewski M. Choosing source of microorganisms and processing technology for next generation beet bioinoculant. Sci Rep 2021; 11:2829. [PMID: 33531601 PMCID: PMC7854725 DOI: 10.1038/s41598-021-82436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022] Open
Abstract
The increase of human population and associated increasing demand for agricultural products lead to soil over-exploitation. Biofertilizers based on lyophilized plant material containing living plant growth-promoting microorganisms (PGPM) could be an alternative to conventional fertilizers that fits into sustainable agricultural technologies ideas. We aimed to: (1) assess the diversity of endophytic bacteria in sugar and sea beet roots and (2) determine the influence of osmoprotectants (trehalose and ectoine) addition during lyophilization on bacterial density, viability and salt tolerance. Microbiome diversity was assessed based on 16S rRNA amplicons sequencing, bacterial density and salt tolerance was evaluated in cultures, while bacterial viability was calculated by using fluorescence microscopy and flow cytometry. Here we show that plant genotype shapes its endophytic microbiome diversity and determines rhizosphere soil properties. Sea beet endophytic microbiome, consisting of genera characteristic for extreme environments, is more diverse and salt resistant than its crop relative. Supplementing osmoprotectants during root tissue lyophilization exerts a positive effect on bacterial community salt stress tolerance, viability and density. Trehalose improves the above-mentioned parameters more effectively than ectoine, moreover its use is economically advantageous, thus it may be used to formulate improved biofertilizers.
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Affiliation(s)
- Sonia Szymańska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University (NCU), Lwowska 1, 87-100, Toruń, Poland
| | - Marcin Sikora
- Center for Modern Interdisciplinary Technologies, Nicolaus Copernicus University (NCU), Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University (NCU), Lwowska 1, 87-100, Toruń, Poland.
| | - Jarosław Tyburski
- Center for Modern Interdisciplinary Technologies, Nicolaus Copernicus University (NCU), Toruń, Poland.,Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University (NCU), Lwowska 1, 87-100, Toruń, Poland
| | - Andrzej Tretyn
- Center for Modern Interdisciplinary Technologies, Nicolaus Copernicus University (NCU), Toruń, Poland.,Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University (NCU), Lwowska 1, 87-100, Toruń, Poland
| | - Marcin Gołębiewski
- Center for Modern Interdisciplinary Technologies, Nicolaus Copernicus University (NCU), Toruń, Poland. .,Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University (NCU), Lwowska 1, 87-100, Toruń, Poland.
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20
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Gaube P, Junker RR, Keller A. Changes amid constancy: Flower and leaf microbiomes along land use gradients and between bioregions. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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21
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Lin H, Liu C, Li B, Dong Y. Trifolium repens L. regulated phytoremediation of heavy metal contaminated soil by promoting soil enzyme activities and beneficial rhizosphere associated microorganisms. J Hazard Mater 2021; 402:123829. [PMID: 33254810 DOI: 10.1016/j.jhazmat.2020.123829] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/28/2023]
Abstract
Rhizosphere soil physiochemical properties, enzyme activities and rhizosphere associated microbial communities are of the central importance for modulating phytoremediation in heavy metal contaminated soil. In this study, the rhizosphere micro-ecological characteristics of phytoremediation in seven groups of contaminated soil with different heavy metal species and concentrations were examined. The results showed that heavy metal-enrichment inhibited plant growth, but enhanced both anions (Cr2O72-) and cations (Cd2+ and Pb2+) uptake with corresponding mean values ranging from 19.37 to 168.74 mg/kg in roots and 10.89-86.53 mg/kg in shoots. Trifolium repens L. planting was able to compensate the lost caused by the heavy metal on the soil organic matter, available N, available P, available K and enzyme activities as well. According to the cluster, some species like Lysobacter, Kaistobacter and Pontibacter, was significantly related to heavy metal accumulation while others such as Flavisolibacter, Adhaeribacter and Bacillus promoted plant growth. The importance of root-associated microbial community could relatively regulate plant growth and heavy metal uptake. Our study not only illustrated the correlation among rhizosphere micro-ecological parameters, and the possible mechanisms of phytoremediation regulation, but also provide clear strategy for improving the phytoremediation efficiency.
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Affiliation(s)
- Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing 100083, China.
| | - Chenjing Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing 100083, China.
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22
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Kracmarova M, Karpiskova J, Uhlik O, Strejcek M, Szakova J, Balik J, Demnerova K, Stiborova H. Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization. Microorganisms 2020; 8:E1377. [PMID: 32911685 PMCID: PMC7566005 DOI: 10.3390/microorganisms8091377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 11/16/2022] Open
Abstract
An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers.
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Affiliation(s)
- Martina Kracmarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic; (J.K.); (O.U.); (M.S.); (K.D.)
| | - Jana Karpiskova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic; (J.K.); (O.U.); (M.S.); (K.D.)
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic; (J.K.); (O.U.); (M.S.); (K.D.)
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic; (J.K.); (O.U.); (M.S.); (K.D.)
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague – Suchdol, 165 21, Czech Republic; (J.S.); (J.B.)
| | - Jiri Balik
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague – Suchdol, 165 21, Czech Republic; (J.S.); (J.B.)
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic; (J.K.); (O.U.); (M.S.); (K.D.)
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic; (J.K.); (O.U.); (M.S.); (K.D.)
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Tosi M, Gaiero J, Linton N, Mafa-Attoye T, Castillo A, Dunfield K. Bacterial Endophytes: Diversity, Functional Importance, and Potential for Manipulation. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-981-15-6125-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Tosi M, Mitter EK, Gaiero J, Dunfield K. It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome. Can J Microbiol 2020; 66:413-433. [DOI: 10.1139/cjm-2020-0085] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.
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Affiliation(s)
- Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Jonathan Gaiero
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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Borowik A, Wyszkowska J, Kucharski M, Kucharski J. The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity. Sensors (Basel) 2020; 20:s20123362. [PMID: 32545819 PMCID: PMC7349710 DOI: 10.3390/s20123362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C6–C12) degradation was higher by 17%; mineral oil (C12–C35), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.
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Ulrich K, Becker R, Behrendt U, Kube M, Ulrich A. A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus. Front Microbiol 2020; 11:966. [PMID: 32547506 PMCID: PMC7273808 DOI: 10.3389/fmicb.2020.00966] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.
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Affiliation(s)
- Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | - Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Michael Kube
- Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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Wemheuer F, Taylor JA, Daniel R, Johnston E, Meinicke P, Thomas T, Wemheuer B. Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environ Microbiome 2020; 15:11. [PMID: 33902725 PMCID: PMC8067651 DOI: 10.1186/s40793-020-00358-7] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/09/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. In addition, there is also a lack of tools to predict functional gene redundancy in microbial communities. RESULTS To address these challenges, we developed Tax4Fun2, an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences. We demonstrate that functional profiles predicted by Tax4Fun2 are highly correlated to functional profiles derived from metagenomes of the same samples. We further show that Tax4Fun2 has higher accuracies than PICRUSt and Tax4Fun. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles is substantially enhanced. In addition, functional gene redundancies predicted with Tax4Fun2 are highly correlated to functional gene redundancies determined for simulated microbial communities. CONCLUSIONS Tax4Fun2 provides researchers with a unique tool to predict and investigate functional profiles of prokaryotic communities based on 16S rRNA gene sequencing data. It is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles. Another unique feature of Tax4Fun2 is that it allows researchers to calculate the redundancy of specific functions, which is a potentially important measure of how resilient a community will be to environmental perturbation. Tax4Fun2 is implemented in R and freely available at https://github.com/bwemheu/Tax4Fun2.
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Affiliation(s)
- Franziska Wemheuer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
| | - Jessica A Taylor
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Emma Johnston
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
| | - Peter Meinicke
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
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Araujo R, Dunlap C, Franco CM. Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14. Mol Plant Pathol 2020; 21:622-635. [PMID: 32056349 PMCID: PMC7170773 DOI: 10.1111/mpp.12918] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/26/2019] [Accepted: 01/21/2020] [Indexed: 05/05/2023]
Abstract
Two Pythium-infested soils were used to compare the wheat root and rhizosphere soil microbial communities from plants grown in the field or in greenhouse trials and their stability in the presence of biocontrol agents. Bacteria showed the highest diversity at early stages of wheat growth in both field and greenhouse trials, while fungal diversity increased later on, at 12 weeks of the crop cycle. The microbial communities were stable in roots and rhizosphere samples across both soil types used in this study. Such stability was also observed irrespective of the cultivation system (field or greenhouse) or addition of biocontrol coatings to wheat seeds to control Pythium disease (in this study soil infected with Pythium sp. clade F was tested). In greenhouse plant roots, Archaeorhizomyces, Debaryomyces, Delftia, and unclassified Pseudeurotiaceae were significantly reduced when compared to plant roots obtained from the field trials. Some operational taxonomic units (OTUs) represented genetic determinants clearly transmitted vertically by seed endophytes (specific OTUs were found in plant roots) and the plant microbiota was enriched over time by OTUs from the rhizosphere soil. This study provided key information regarding the microbial communities associated with wheat roots and rhizosphere soils at different stages of plant growth and the role that Paenibacillus and Streptomyces strains play as biocontrol agents in supporting plant growth in infested soils.
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Affiliation(s)
- Ricardo Araujo
- Department Medical BiotechnologyFlinders UniversitySouth Australia
- i3S, Institute of Research and Innovation in HealthUniversity of PortoPortugal
| | - Christopher Dunlap
- Crop Bioprotection ResearchThe United States Department of AgriculturePeoriaILUSA
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Abstract
High-quality draft genome sequences were determined for 6 Massilia sp. type strains. The genomes of these strains show considerable biosynthetic potential for producing secondary metabolites. High-quality draft genome sequences were determined for 6 Massilia sp. type strains. The genomes of these strains show considerable biosynthetic potential for producing secondary metabolites.
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Alok D, Annapragada H, Singh S, Murugesan S, Singh NP. Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L). Sci Rep 2020; 10:5453. [PMID: 32214159 PMCID: PMC7096491 DOI: 10.1038/s41598-020-62199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/10/2020] [Indexed: 01/11/2023] Open
Abstract
Symbiotic nitrogen fixation (SNF) of transgenic grain legumes might be influenced either by the site of transgene integration into the host genome or due to constitutive expression of transgenes and antibiotic-resistant marker genes. The present investigation confirmed proper nodulation of five tested Bt-chickpea events (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) by native Mesorhizobium under field environment. Quantitative variations for nodulation traits among Bt-chickpea were determined and IPCT3 was found superior for nodule number and nodule biomass. Diversity, as well as richness indices, confirmed the changes in bacterial community structure of root and root-nodules from Bt-chickpea events IPCa2 and IPCT10. Especially, Gram-positive bacteria belonging to Firmicutes and Actinobacteria were selectively eliminated from root colonization of IPCa2. Richness indices (CHAO1 and ACE) of the root-associated bacterial community of IPCa2 was 13-14 times lesser than that of parent cv DCP92-3. Root nodule associated bacterial community of IPCT10 was unique with high diversity and richness, similar to the roots of non-Bt and Bt-chickpea. It indicated that the root nodules of IPCT10 might have lost their peculiar characteristics and recorded poor colonization of Mesorhizobium with a low relative abundance of 0.27. The impact of Bt-transgene on bacterial community structure and nodulation traits should be analyzed across the years and locations to understand and stabilize symbiotic efficiency for ecosystem sustainability.
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Affiliation(s)
- Das Alok
- Division of Plant Biotechnology, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Harika Annapragada
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Shilpa Singh
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Senthilkumar Murugesan
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India.
| | - Narendra Pratap Singh
- Division of Plant Biotechnology, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
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Wemheuer F, Berkelmann D, Wemheuer B, Daniel R, Vidal S, Bisseleua Daghela HB. Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves. Microorganisms 2020; 8:E405. [PMID: 32183118 PMCID: PMC7143032 DOI: 10.3390/microorganisms8030405] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/04/2020] [Accepted: 03/11/2020] [Indexed: 12/22/2022] Open
Abstract
Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T. cacao. To close this knowledge gap, we investigated the diversity, community composition, and function of bacterial and fungal endophytes in the leaves of T. cacao trees growing in five major cacao-growing regions in the central region of Cameroon using DNA metabarcoding. Fungal but not bacterial alpha diversity measures differed significantly between the agroforestry management systems. Interestingly, less managed home-garden cacao forests harbored the lowest fungal richness and diversity. Our results suggest that the composition of bacterial and fungal endophyte communities is predominantly affected by agroforestry management systems and, to a lesser extent, by environmental properties. The core microbiome detected comprised important fungal phytopathogens, such as Lasiodiplodia species. Several predicted pathways of bacterial endophytes and functional guilds of fungal endophytes differed between the agroforest systems which might be attributed to bacteria and fungi specifically associated with a single agroforest. Our results provide the basis for future studies on foliar fungal and bacterial endophytes of T. cacao and their responsiveness towards agroforestry management systems.
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Affiliation(s)
- Franziska Wemheuer
- Section of Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany; (F.W.); (H.B.B.D.)
| | - Dirk Berkelmann
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany; (D.B.); (B.W.); (R.D.)
| | - Bernd Wemheuer
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany; (D.B.); (B.W.); (R.D.)
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany; (D.B.); (B.W.); (R.D.)
| | - Stefan Vidal
- Section of Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany; (F.W.); (H.B.B.D.)
| | - Hervé Bertin Bisseleua Daghela
- Section of Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany; (F.W.); (H.B.B.D.)
- Laboratory of Entomology, Institute of Agricultural Research for Development (IRAD), BP 2067, Yaoundé, Cameroon
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Oberhofer M, Hess J, Leutgeb M, Gössnitzer F, Rattei T, Wawrosch C, Zotchev SB. Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum. Front Microbiol 2019; 10:2531. [PMID: 31781058 PMCID: PMC6857621 DOI: 10.3389/fmicb.2019.02531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/21/2019] [Indexed: 11/24/2022] Open
Abstract
The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.
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Affiliation(s)
- Martina Oberhofer
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Jaqueline Hess
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Marlene Leutgeb
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Florian Gössnitzer
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Wawrosch
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Sergey B. Zotchev
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
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Gupta VVSR, Zhang B, Penton CR, Yu J, Tiedje JM. Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil. Front Mol Biosci 2019; 6:115. [PMID: 31750314 PMCID: PMC6848460 DOI: 10.3389/fmolb.2019.00115] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022] Open
Abstract
Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity (15N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg-1 day-1 and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.
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Affiliation(s)
| | - Bangzhou Zhang
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Christopher Ryan Penton
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Julian Yu
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
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Dominguez JJA, Bacosa HP, Chien MF, Inoue C. Enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) in the rhizosphere of sudangrass (Sorghum × drummondii). Chemosphere 2019; 234:789-795. [PMID: 31247488 DOI: 10.1016/j.chemosphere.2019.05.290] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
Grasses are advantageous in the removal of polycyclic aromatic hydrocarbons (PAHs) in soil because of their fibrous root, high tolerance to environmental stress, and low nutritional requirements. In this study, a pot experiment was conducted to test the ability of four grasses to remove PAHs in the soil, and to investigate the corresponding bacterial community shift in the rhizosphere of each. Sudangrass achieved the maximum removal of PAHs at 98% dissipation rate after 20 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that sudangrass specially enriched the growth of a known PAHs degrader, Sphingomonadales, regardless of the presence or absence of PAHs in the soil. Moreover, the gene copy numbers of PAHs catabolic genes, PAH-RHDα and nidA, as measured by real time-PCR (RT-PCR) were highest in the soil planted with sudangrass. Overall, this study suggested that sudangrass further enhanced the dissipation of PAHs by enriching Sphingomonadales in its rhizosphere.
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Affiliation(s)
- John Jewish A Dominguez
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
| | - Hernando P Bacosa
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai, 980-8579, Japan; Department of Marine Sciences, Texas A&M University at Galveston, Galveston, TX, United States
| | - Mei-Fang Chien
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
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Wemheuer F, Wemheuer B, Daniel R, Vidal S. Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands. Sci Rep 2019; 9:14183. [PMID: 31578453 PMCID: PMC6775154 DOI: 10.1038/s41598-019-50540-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/10/2019] [Indexed: 01/04/2023] Open
Abstract
Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of Acer campestre and A. platanoides. GLA samples of A. campestre and A. platanoides were dominated by Sawadaea polyfida and S. bicornis, respectively, suggesting that these fungi might be responsible for the green islands. We detected a higher fungal richness and diversity in CL compared to GLA samples of A. campestre. Leaf status (CL, GLA, YLA) significantly altered the composition of fungal communities of A. campestre. This was related to differences in fungal community composition between YLA and GLA samples. Site was the main driver of bacterial communities, suggesting that bacterial and fungal endophytes are shaped by different factors. Overall, we observed Acer species-specific responses of endophyte communities towards the presence of green islands and/or leaf type, which might be attributed to several fungi and bacteria specifically associated with one Acer species.
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Affiliation(s)
- Franziska Wemheuer
- Department of Crop Sciences, University of Göttingen, Grisebachstr.6, D-37077, Göttingen, Germany
- Applied Marine and Estuarine Ecology, Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Stefan Vidal
- Department of Crop Sciences, University of Göttingen, Grisebachstr.6, D-37077, Göttingen, Germany.
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Ávila MP, Oliveira-Junior ES, Reis MP, Hester ER, Diamantino C, Veraart AJ, Lamers LPM, Kosten S, Nascimento AMA. The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling. Microb Ecol 2019; 78:575-588. [PMID: 30706113 DOI: 10.1007/s00248-019-01331-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.
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Affiliation(s)
- Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Ernandes S Oliveira-Junior
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Eric R Hester
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Cristiane Diamantino
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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Saleh D, Jarry J, Rani M, Aliferis K, Seguin P, Jabaji S. Diversity, distribution and multi‐functional attributes of bacterial communities associated with the rhizosphere and endosphere of timothy (Phleum pratenseL.). J Appl Microbiol 2019; 127:794-811. [DOI: 10.1111/jam.14334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 05/09/2019] [Accepted: 05/15/2019] [Indexed: 11/29/2022]
Affiliation(s)
- D. Saleh
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - J. Jarry
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - M. Rani
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - K.A. Aliferis
- Laboratory of Pesticide Science Agricultural University of Athens Athens Greece
| | - P. Seguin
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - S.H. Jabaji
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
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Manjunatha BS, Paul S, Aggarwal C, Bandeppa S, Govindasamy V, Dukare AS, Rathi MS, Satyavathi CT, Annapurna K. Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities. Microb Ecol 2019; 77:676-688. [PMID: 30209586 DOI: 10.1007/s00248-018-1257-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/30/2018] [Indexed: 05/02/2023]
Abstract
Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.
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Affiliation(s)
- B S Manjunatha
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Sangeeta Paul
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India.
| | - Chetana Aggarwal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110 012, India
| | - S Bandeppa
- Division of Soil Science, ICAR-Indian Institute of Rice Research, Hyderabad, 500 030, India
| | - V Govindasamy
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Ajinath S Dukare
- Division of Horticultural Crop Processing, ICAR-Central Institute of Post Harvest Engineering and Technology, Abohar, Punjab, 152 116, India
| | - Maheshwar S Rathi
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - C T Satyavathi
- ICAR-All India Coordinated Research Project on Pearl Millet, Jodhpur, Rajasthan, 342 304, India
| | - K Annapurna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
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Wemheuer B, Thomas T, Wemheuer F. Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes. Microorganisms 2019; 7:E37. [PMID: 30691243 PMCID: PMC6407066 DOI: 10.3390/microorganisms7020037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/26/2022] Open
Abstract
Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.
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Affiliation(s)
- Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Franziska Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
- Division of Agricultural Entomology, Department of Crop Sciences, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
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Araujo R, Dunlap C, Barnett S, Franco CM. Decoding Wheat Endosphere-Rhizosphere Microbiomes in Rhizoctonia solani-Infested Soils Challenged by Streptomyces Biocontrol Agents. Front Plant Sci 2019; 10:1038. [PMID: 31507625 PMCID: PMC6718142 DOI: 10.3389/fpls.2019.01038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/24/2019] [Indexed: 05/21/2023]
Abstract
The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study, we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants were grown in a glasshouse standardized system, and the bacterial and fungal microbiomes of 233 samples of wheat roots (endosphere) and rhizosphere soils were monitored for 20 weeks, from seed to mature plant stage. The results showed highly dynamic and diverse microbial communities that changed over time, with Sphingomonas bacteria and Aspergillus, Dipodascus, and Trichoderma fungi increasing over time. Application of biocontrol Streptomyces strains promoted plant growth and maturation of wheat heads and modulated the root microbiome, decreasing Paenibacillus and increasing other bacterial and fungal OTUs. The soils with the highest levels of R. solani had increased reads of Thanatephorus (Rhizoctonia anamorph) and increased root disease levels and increased Balneimonas, Massilia, Pseudomonas, and unclassified Micrococcaceae. As we enter the era of biologically sustainable agriculture, it may be possible to reduce and limit the effects of serious fungal infestations by promoting a beneficial microbiome through the application of biocontrol agents during different periods of plant development.
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Affiliation(s)
- Ricardo Araujo
- Department of Medical Biotechnology, Flinders University, Adelaide, SA, Australia
- i3S, University of Porto, Porto, Portugal
- *Correspondence: Ricardo Araujo,
| | - Christopher Dunlap
- Crop Bioprotection Research, The United States Department of Agriculture, Peoria, IL, United States
| | - Steve Barnett
- Department of Medical Biotechnology, Flinders University, Adelaide, SA, Australia
- South Australian Research & Development Institute (SARDI), Adelaide, SA, Australia
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Kunda P, Dhal PK, Mukherjee A. Endophytic bacterial community of rice (Oryza sativa L.) from coastal saline zone of West Bengal: 16S rRNA gene based metagenomics approach. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Kiani T, Khan SA, Noureen N, Yasmin T, Zakria M, Ahmed H, Mehboob F, Farrakh S. Isolation and characterization of culturable endophytic bacterial community of stripe rust-resistant and stripe rust-susceptible Pakistani wheat cultivars. Int Microbiol 2018; 22:191-201. [PMID: 30810983 DOI: 10.1007/s10123-018-00039-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 10/27/2022]
Abstract
In this study, endophytic bacteria isolated from root, stem, and leaf tissues of stripe rust-susceptible (Inqilab 91, Galaxy 2013, and 15BT023) and stripe rust-resistant (NARC 2011, Ujala 2015, TW1410) cultivars were identified and characterized. Abundance of endophytes was found in roots as compared with stems and leaves. Resistant and susceptible cultivars significantly differed in abundance of endophytic bacteria. Restriction analysis of 16S rRNA genes amplified from 100 bacterial isolates produced 17 unique patterns. Representatives of each of the 17 unique patterns were sequenced and identified. Among the sequenced bacteria, 8 belonged to Firmicutes, 7 were Proteobacteria, and 2 were Actinobacteria. Most of the isolates have plant growth-promoting properties and a few have the potential of producing hydrolytic enzymes. Two isolates showed significant inhibition of rust spore germination. These endophytic bacteria not only can be helpful in growth-promoting activities but also can assist in biocontrol of stripe rust disease.
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Affiliation(s)
- Tehmina Kiani
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Shahzad Abid Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Nighat Noureen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Haroon Ahmed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
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Fan D, Schwinghamer T, Smith DL. Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada. Syst Appl Microbiol 2018; 41:629-40. [DOI: 10.1016/j.syapm.2018.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 11/19/2022]
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Ikeda-Ohtsubo W, Brugman S, Warden CH, Rebel JMJ, Folkerts G, Pieterse CMJ. How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture. Front Nutr 2018; 5:90. [PMID: 30333981 PMCID: PMC6176000 DOI: 10.3389/fnut.2018.00090] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022] Open
Abstract
All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.
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Affiliation(s)
- Wakako Ikeda-Ohtsubo
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Craig H Warden
- Departments of Pediatrics, Neurobiology Physiology and Behavior, University of California, Davis, Davis, CA, United States
| | - Johanna M J Rebel
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
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Mareque C, da Silva TF, Vollú RE, Beracochea M, Seldin L, Battistoni F. The Endophytic Bacterial Microbiota Associated with Sweet Sorghum ( Sorghum bicolor) Is Modulated by the Application of Chemical N Fertilizer to the Field. Int J Genomics 2018; 2018:7403670. [PMID: 30363992 DOI: 10.1155/2018/7403670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/16/2018] [Indexed: 11/17/2022] Open
Abstract
Sweet sorghum (Sorghum bicolor) is a multipurpose crop used as a feedstock to produce bioethanol, sugar, energy, and animal feed. However, it requires high levels of N fertilizer application to achieve the optimal growth, which causes environmental degradation. Bacterial endophytes, which live inside plant tissues, play a key role in the health and productivity of their host. This particular community may be influenced by different agronomical practices. The aim of the work was to evaluate the effects of N fertilization on the structure, diversity, abundance, and composition of endophytic and diazotrophic bacterial community associated with field-grown sweet sorghum. PCR-DGGE, quantitative PCR, and high-throughput sequencing were performed based on the amplification of rrs and nifH genes. The level of N fertilization affected the structure and abundance but not the diversity of the endophytic bacterial communities associated with sweet sorghum plants. This effect was pronounced in the roots of both bacterial communities analyzed and may depend on the physiological state of the plants. Specific bacterial classes and genera increased or decreased when the fertilizer was applied. The data obtained here contribute to a better understanding on the effects of agronomical practices on the microbiota associated with this important crop, with the aim to improve its sustainability.
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Trovero MF, Scavone P, Platero R, de Souza EM, Fabiano E, Rosconi F. Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability. Front Microbiol 2018; 9:1430. [PMID: 30018605 PMCID: PMC6037834 DOI: 10.3389/fmicb.2018.01430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/11/2018] [Indexed: 01/20/2023] Open
Abstract
Herbaspirillum seropedicae Z67 is a nitrogen-fixing endophyte that colonizes many important crops. Like in almost all organisms, vital cellular processes of this endophyte are iron dependent. In order to efficiently acquire iron to fulfill its requirements, this bacterium produces the siderophores serobactins. However, the presence in its genome of many others iron acquisition genes suggests that serobactins are not the only strategy used by H. seropedicae to overcome metal deficiency. The aim of this work was to identify genes and proteins differentially expressed by cells growing in low iron conditions in order to describe H. seropedicae response to iron limitation stress. For this purpose, and by using a transcriptomic approach, we searched and identified a set of genes up-regulated when iron was scarce. One of them, Hsero_2337, codes for a TonB-dependent transporter/transducer present in the serobactins biosynthesis genomic locus, with an unknown function. Another TonB-dependent receptor, the one encoded by Hsero_1277, and an inner membrane ferrous iron permease, coded by Hsero_2720, were also detected. By using a proteomic approach focused in membrane proteins, we identified the specific receptor for iron-serobactin internalization SbtR and two non-characterized TonB-dependent receptors (coded by genes Hsero_1277 and Hsero_3255). We constructed mutants on some of the identified genes and characterized them by in vitro growth, biofilm formation, and interaction with rice plants. Characterization of mutants in gene Hsero_2337 showed that the TonB-dependent receptor coded by this gene has a regulatory role in the biosynthesis of serobactins, probably by interacting with the alternative sigma factor PfrI, coded by gene Hsero_2338. Plant colonization of the mutant strains was not affected, since the mutant strain normally colonize the root and aerial part of rice plants. These results suggest that the strategies used by H. seropedicae to acquire iron inside plants are far more diverse than the ones characterized in this work. In vivo expression studies or colonization competition experiments between the different mutant strains could help us in future works to determine the relative importance of the different iron acquisition systems in the interaction of H. seropedicae with rice plants.
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Affiliation(s)
- María F Trovero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Paola Scavone
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Raúl Platero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Emanuel M de Souza
- Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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Li L, Mohamad OAA, Ma J, Friel AD, Su Y, Wang Y, Musa Z, Liu Y, Hedlund BP, Li W. Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F. Antonie Van Leeuwenhoek 2018. [PMID: 29516314 DOI: 10.1007/s10482-018-1062-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Little is known about the composition, diversity, and geographical distribution of bacterial communities associated with medicinal plants in arid lands. To address this, a collection of 116 endophytic bacteria were isolated from wild populations of the herb Glycyrrhiza uralensis Fisch (licorice) in Xinyuan, Gongliu, and Tekesi of Xinjiang Province, China, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 20 genera and 35 species. The number of distinct bacterial genera obtained from root tissues was higher (n = 14) compared to stem (n = 9) and leaf (n = 6) tissue. Geographically, the diversity of culturable endophytic genera was higher at the Tekesi (n = 14) and Xinyuan (n = 12) sites than the Gongliu site (n = 4), reflecting the extremely low organic carbon content, high salinity, and low nutrient status of Gongliu soils. The endophytic bacteria exhibited a number of plant growth-promoting activities ex situ, including diazotrophy, phosphate and potassium solubilization, siderophore production, auxin synthesis, and production of hydrolytic enzymes. Twelve endophytes were selected based on their ex situ plant growth-promoting activities for growth chamber assays to test for their ability to promote growth of G. uralensis F. and Triticum aestivum (wheat) plants. Several strains belonging to the genera Bacillus (n = 6) and Achromobacter (n = 1) stimulated total biomass production in both G. uralensis and T. aestivum under low-nutrient conditions. This work is the first report on the isolation and characterization of endophytes associated with G. uralensis F. in arid lands. The results demonstrate the broad diversity of endophytes associated with wild licorice and suggest that some Bacillus strains may be promising candidates for biofertilizers to promote enhanced survival and growth of licorice and other valuable crops in arid environments.
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Affiliation(s)
- Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Osama Abdalla Abdelshafy Mohamad
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
- Institute for Post Graduate Environmental Studies, Environmental Science Department, Arish University, North-Sinai, 45516, Egypt
| | - Jinbiao Ma
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Yangui Su
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Yun Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Zulpiya Musa
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yonghong Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA.
| | - Wenjun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China.
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat Sen University, Guangzhou, 510275, China.
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Wemheuer F, Hollensteiner J, Poehlein A, Liesegang H, Daniel R, Wemheuer B. Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM6LP Isolated from Lolium perenne. Genome Announc 2018; 6:e00011-18. [PMID: 29437086 DOI: 10.1128/genomeA.00011-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bacillus mycoides GM6LP is an endophyte isolated from plant tissues of Lolium perenne L. Here, we report its draft genome sequence (6.2 Mb), which contains 96 contigs and 6,129 protein-coding genes. Knowledge about its genome will enable us to evaluate the potential use of GM6LP as a plant growth-promoting bacterium.
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Liu J, Abdelfattah A, Norelli J, Burchard E, Schena L, Droby S, Wisniewski M. Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence. Microbiome 2018; 6:18. [PMID: 29374490 PMCID: PMC5787276 DOI: 10.1186/s40168-018-0403-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/18/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component. RESULTS Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9). CONCLUSIONS The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the "holobiont" concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.
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Affiliation(s)
- Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants/College of Forestry and Life Science, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160 China
| | - Ahmed Abdelfattah
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - John Norelli
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
| | - Erik Burchard
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Samir Droby
- Agricultural Research Organization (ARO), the Volcani Center, 50250 Bet Dagan, Israel
| | - Michael Wisniewski
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
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Hollensteiner J, Poehlein A, Granzow S, Liesegang H, Daniel R, Vidal S, Wemheuer F. Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM5LP Isolated from Lolium perenne. Genome Announc 2018; 6:e01517-17. [PMID: 29371354 DOI: 10.1128/genomeA.01517-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus mycoides GM5LP is a Gram-positive endophytic bacterium isolated from aerial plant tissues of Lolium perenne L. The 6.0-Mb draft genome harbors 6,132 protein-coding sequences, some of which might be involved in the biosynthesis of antimicrobial substances.
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