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Dangar BV, Chavada P, Bhatt PJ, Raviya R. Reviewing bryophyte-microorganism association: insights into environmental optimization. Front Microbiol 2024; 15:1407391. [PMID: 38946907 PMCID: PMC11211263 DOI: 10.3389/fmicb.2024.1407391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024] Open
Abstract
Bryophytes, the second-largest group of plants, play a crucial role as early colonizers of land and are a prolific source of naturally occurring substances with significant economic potential. Microorganisms, particularly bacteria, cyanobacteria, fungi form intricate associations with plants, notably bryophytes, contributing to the ecological functioning of terrestrial ecosystems and sometimes it gives negative impact also. This review elucidates the pivotal role of endophytic bacteria in promoting plant growth, facilitating nutrient cycling, and enhancing environmental health. It comprehensively explores the diversity and ecological significance of fungal and bacterial endophytes across various ecosystems. Furthermore, it highlights the moss nitrogen dynamics observed in select moss species. Throughout the review, emphasis is placed on the symbiotic interdependence between bryophytes and microorganisms, offering foundational insights for future research endeavors. By shedding light on the intricate bryophyte-microorganism associations, this study advances our understanding of the complex interplay between plants, microbes, and their environment, paving the way for further research and applications in environmental and biotechnological realms.
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Affiliation(s)
| | | | | | - Rajesh Raviya
- Department of Life Sciences, Bhakta Kavi Narsinh Mehta University, Junagadh, Gujarat, India
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2
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Baev V, Gecheva G, Apostolova E, Gozmanova M, Yahubyan G. Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic. PLANTS (BASEL, SWITZERLAND) 2024; 13:1210. [PMID: 38732425 PMCID: PMC11085137 DOI: 10.3390/plants13091210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Gana Gecheva
- Department of Ecology and Environmental Conservation, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria;
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
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Stelmasiewicz M, Świątek Ł, Gibbons S, Ludwiczuk A. Bioactive Compounds Produced by Endophytic Microorganisms Associated with Bryophytes—The “Bryendophytes”. Molecules 2023; 28:molecules28073246. [PMID: 37050009 PMCID: PMC10096483 DOI: 10.3390/molecules28073246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
The mutualistic coexistence between the host and endophyte is diverse and complex, including host growth regulation, the exchange of substances like nutrients or biostimulants, and protection from microbial or herbivore attack. The latter is commonly associated with the production by endophytes of bioactive natural products, which also possess multiple activities, including antibacterial, insecticidal, antioxidant, antitumor, and antidiabetic properties, making them interesting and valuable model substances for future development into drugs. The endophytes of higher plants have been extensively studied, but there is a dearth of information on the biodiversity of endophytic microorganisms associated with bryophytes and, more importantly, their bioactive metabolites. For the first time, we name bryophyte endophytes “bryendophytes” to elaborate on this important and productive source of biota. In this review, we summarize the current knowledge on the diversity of compounds produced by endophytes, emphasizing bioactive molecules from bryendophytes. Moreover, the isolation methods and biodiversity of bryendophytes from mosses, liverworts, and hornworts are described.
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Affiliation(s)
- Mateusz Stelmasiewicz
- Department of Pharmacognosy with the Medicinal Plant Garden, Medical University of Lublin, 20-093 Lublin, Poland
| | - Łukasz Świątek
- Department of Virology with Viral Diagnostics Laboratory, Medical University of Lublin, 20-093 Lublin, Poland
| | - Simon Gibbons
- Centre for Natural Products Discovery (CNPD), Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Agnieszka Ludwiczuk
- Department of Pharmacognosy with the Medicinal Plant Garden, Medical University of Lublin, 20-093 Lublin, Poland
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Insuk C, Pongpamorn P, Forsythe A, Matsumoto A, Ōmura S, Pathom-aree W, Cheeptham N, Xu J. Taxonomic and Metabolite Diversities of Moss-Associated Actinobacteria from Thailand. Metabolites 2021; 12:metabo12010022. [PMID: 35050144 PMCID: PMC8777641 DOI: 10.3390/metabo12010022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/22/2021] [Accepted: 12/25/2021] [Indexed: 01/08/2023] Open
Abstract
Actinobacteria are a group of ecologically important bacteria capable of producing diverse bioactive compounds. However, much remains unknown about the taxonomic and metabolic diversities of actinobacteria from many geographic regions and ecological niches. In this study, we report the isolation of actinobacteria from moss and moss-associated rhizosphere soils in Thailand. Among the 89 isolates analyzed for their bioactivities, 86 strains produced indole-3-acetic acid (IAA, ranging from 0.04 to 59.12 mg/L); 42 strains produced hydroxamate type of siderophore; 35 strains produced catecholate type of siderophore; 21 strains solubilized tricalcium phosphate; and many strains exhibited antagonistic activities against one to several of the seven selected plant, animal, and human pathogens. Overall, actinobacteria from the rhizosphere soil of mosses showed greater abilities to produce IAA and siderophores and to solubilize tricalcium phosphate than those from mosses. Among these 89 isolates, 37 were analyzed for their 16S rRNA gene sequences, which revealed their diverse phylogenetic distributions among seven genera, Streptomyces, Micromonospora, Nocardia, Actinoplanes, Saccharothrix, Streptosporangium, and Cryptosporangium. Furthermore, gas chromatography-mass spectrometry analyses of ethyl acetate crude extracts of three selected isolates with inhibitory effects against a methicillin-resistant Staphylococcus aureus strain revealed diverse metabolites with known antimicrobial activities. Together, our results demonstrate that actinobacteria from mosses in Thailand are taxonomically diverse and capable of producing a range of metabolites with plant-growth-promoting and microbial pathogen-inhibiting potentials.
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Affiliation(s)
- Chadabhorn Insuk
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.I.); (A.F.)
| | - Pornkanok Pongpamorn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
| | - Adrian Forsythe
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.I.); (A.F.)
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan; (A.M.); (S.Ō.)
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan; (A.M.); (S.Ō.)
| | - Wasu Pathom-aree
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (W.P.-a.); (N.C.); (J.X.)
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
- Correspondence: (W.P.-a.); (N.C.); (J.X.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.I.); (A.F.)
- Correspondence: (W.P.-a.); (N.C.); (J.X.)
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5
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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de França Bettencourt GM, Degenhardt J, Dos Santos GD, Vicente VA, Soccol CR. Metagenomic analyses, isolation and characterization of endophytic bacteria associated with Eucalyptus urophylla BRS07-01 in vitro plants. World J Microbiol Biotechnol 2021; 37:164. [PMID: 34458956 DOI: 10.1007/s11274-021-03127-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/12/2021] [Indexed: 11/28/2022]
Abstract
Eucalyptus is the main species for the forestry industry in Brazil. Biotechnology and, more recently, gene editing offer significant opportunities for rapid improvements in Eucalyptus breeding programs. However, the recalcitrance of Eucalyptus species to in vitro culture is also a major limitation for commercial deployment of biotechnology techniques in Eucalyptus improvement. We evaluated various clones of Eucalyptus urophylla for their in vitro regeneration potential identified a clone, BRS07-01, with considerably higher regeneration rate (85%) in organogenesis, and significantly higher than most works described in literature. Endophytic bacteria are widely reported to improve in vitro plant growth and development. Hence, we believe that inclusion of endophytic plant growth promoting bacteria enhanced was responsible for the improved plantlets growth and development of this clone under in vitro culture. Metagenomic analysis was performed to isolate and characterize the prominent endophytic bacteria on BRS07-01 leaf tissue in vitro micro-cultures, and evaluate their impact on plant growth promotion. The analysis revealed the presence of the phyla Firmicutes (35%), Proteobacteria (30%) and much smaller quantities of Actinobacteria, Bacteroidetes, Gemmatimonadetes, Crenarchaeota, Euryarchaeota and Acidobacteria. Of the thirty endophytic bacterial strains isolated, eleven produced indole-3-acetic acid. Two of the isolates were identified as Enterobacter sp. and Paenibacillus polymyxa, which are nitrogen-fixing and capable of phosphate and produce ammonium. These isolates also showed similar positive effects on the germination of common beans (Phaseolus spp.). The isolates will now be tested as a growth promoter in Eucalyptus in vitro cultures. Graphical abstract for the methodology using cultivation independent and dependent methodologies to investigate the endophytic bacteria community from in vitro Eucalyptus urophylla BRS07-01.
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Affiliation(s)
- Gisela Manuela de França Bettencourt
- Department of Bioprocess and Biotechnology Engineering, Federal University of Paraná, Avenida Cel. Francisco Heráclito dos Santos, 210, Curitiba, Paraná, Brazil.
| | | | - Germana Davila Dos Santos
- Department of Patology, Federal University of Paraná, Avenida Cel. Francisco Heráclito dos Santos, 210, Curitiba, Paraná, Brazil
| | - Vânia Aparecida Vicente
- Department of Patology, Federal University of Paraná, Avenida Cel. Francisco Heráclito dos Santos, 210, Curitiba, Paraná, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess and Biotechnology Engineering, Federal University of Paraná, Avenida Cel. Francisco Heráclito dos Santos, 210, Curitiba, Paraná, Brazil
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The Pioneering Role of Bryophytes in Ecological Restoration of Manganese Waste Residue Areas, Southwestern China. J CHEM-NY 2021. [DOI: 10.1155/2021/9969253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mining of manganese brings excellent wealth to humankind. However, it destroys the ecological environment, mainly manifested as heavy metal pollution and vegetation destruction. The restoration of ecological vegetation in manganese mining areas has become an important work after mineral exploitation. The effect of bryophytes on ecological restoration in mining areas is irreplaceable. The bryophytes diversity and its pioneering role in two types of manganese waste residue areas were investigated in Guizhou province, China. The results showed that there were 24 species of mosses in mine waste slag areas, and all of them belonged to 6 families and 15 genera; the species Gymnostomum subrigidulum, Pohlia gedeana, and Bryum atrovirens were the dominant mosses. There were 6 species of mosses in electrolytic manganese slag areas, and all of them belonged to 5 families and 5 genera. The dominant moss was B. atrovirens. The bryophytes diversity in the electrolytic manganese slag areas with lower pH was poorer than that in mine slag areas. The accumulation of heavy metals in mosses showed that B. atrovirens collected from two types of areas had a strong ability to accumulate Mn with the cumulants 5588.00 μg/g and 4283.41 μg/g, respectively. All mosses had a strong enrichment ability to Cd. It indicated that mosses had strong tolerance to heavy metals. Bryophytes increased the available nutrients and bacterial community diversity of mosses growth substrates in two types of areas. Besides, we studied the relationships between bacterial community structure and soil factors. The main soil factor affecting the bacterial community structure was available nitrogen (AN) in mine waste slag areas, while it was pH in the electrolytic manganese residue areas. The systematic study suggested that bryophytes increased the available nutrients and the microbial community diversity of the growth substrates in manganese waste residue areas, which provided the basic conditions for the growth of vascular plants.
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Community structure and function of cultivable Endophytic Bacteria isolated from four Moss species in Qilian Mountain. Symbiosis 2020. [DOI: 10.1007/s13199-020-00669-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Cao W, Xiong Y, Zhao D, Tan H, Qu J. Bryophytes and the symbiotic microorganisms, the pioneers of vegetation restoration in karst rocky desertification areas in southwestern China. Appl Microbiol Biotechnol 2020; 104:873-891. [PMID: 31822979 PMCID: PMC6943408 DOI: 10.1007/s00253-019-10235-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 01/03/2023]
Abstract
In karst rocky desertification areas, bryophytes coexist with algae, bacteria, and fungi on exposed calcareous rocks to form a bryophyte crust, which plays an irreplaceable role in the restoration of karst degraded ecosystems. We investigated the biodiversity of crust bryophytes in karst rocky desertification areas from Guizhou Province, China. A total of 145 species in 22 families and 56 genera were identified. According to frequency and coverage, seven candidate dominant mosses were screened out, and five drought-resistant indexes of them were measured. Hypnum leptothallum, Racopilum cuspidigerum, and Hyophila involuta have high drought adaptability. We explored the interactions between two dominant mosses (H. leptothallum, H. involuta) and the structure of microbial communities in three karst rocky desertification types. Microbial diversity and function analysis showed that both moss species and karst rocky desertification types affect microbial communities. Moss species much more strongly affected the diversity and changed the community composition of these microbial groups. Bacteria were more sensitive in the microbiome as their communities changed strongly between mosses and drought resistance factors. Moreover, several species of fungi and bacteria could be significantly associated with three drought-resistant indexes: Pro (free proline content), SOD (superoxide dismutase activity), and POD (peroxidase activity), which were closely related to the drought adaptability of mosses. Our results enforced the potential role of moss-associated microbes that are important components involved in the related biological processes when bryophytes adapted to arid habitats, or as one kind of promoters in the distribution pattern of early mosses succession in karst rocky desertification areas.
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Affiliation(s)
- Wei Cao
- College of Life Sciences, Guizhou University, Guiyang, 550025, China
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yuanxin Xiong
- College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Degang Zhao
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Hongying Tan
- Guiyang A'ha Lake National Wetland Park Management Division, Guiyang, 550002, China
| | - Jiaojiao Qu
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China.
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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: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [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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11
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Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.
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12
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Chen KH, Liao HL, Bellenger JP, Lutzoni F. Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium. Environ Microbiol 2019; 21:2273-2289. [PMID: 30900793 DOI: 10.1111/1462-2920.14605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/05/2023]
Abstract
Bryophytes harbour microbiomes, including diverse communities of fungi. The molecular mechanisms by which perennial mosses interact with these fungal partners along their senescence gradients are unknown, yet this is an ideal system to study variation in gene expression associated with trophic state transitions. We investigated differentially expressed genes of fungal communities and their host Dicranum scoparium across its naturally occurring senescence gradient using a metatranscriptomic approach. Higher activity of fungal nutrient-related (carbon, nitrogen, phosphorus and sulfur) transporters and Carbohydrate-Active enZyme (CAZy) genes was detected toward the bottom, partially decomposed, layer of the moss. The most prominent variation in the expression levels of fungal nutrient transporters was from inorganic nitrogen-related transporters, whereas the breakdown of organonitrogens was detected as the most enriched gene ontology term for the host D. scoparium, for those transcripts having higher expression in the partially decomposed layer. The abundance of bacterial rRNA transcripts suggested that more living members of Cyanobacteria are associated with the photosynthetic layer of D. scoparium, while members of Rhizobiales are detected throughout the gametophytes. Plant genes for specific fungal-plant communication, including defense responses, were differentially expressed, suggesting that different genetic pathways are involved in plant-microbe crosstalk in photosynthetic tissues compared to partially decomposed tissues.
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Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
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Moss habitats distinctly affect their associated bacterial community structures as revealed by the high-throughput sequencing method. World J Microbiol Biotechnol 2018; 34:58. [PMID: 29605884 DOI: 10.1007/s11274-018-2436-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 03/17/2018] [Indexed: 10/17/2022]
Abstract
To better understand the factors that influence the distribution of bacteria associated with mosses, the communities inhabiting in five moss species from two different habitats in Beijing Songshan National Nature Reserve were investigated using the high-throughput sequencing method. The sequencing was performed based on the bacterial 16S rRNA and 16S rDNA libraries. Results showed that there are abundant bacteria inhabiting in all the mosses sampled. The taxonomic analysis of these bacteria showed that they mainly consisted of those in the phyla Proteobacteria and Actinobacteria, and seldom were from phylum Armatimonadetes, Bacteroidetes and Firmicutes. The hierarchical cluster tree, based on the OTU level, divided the bacteria associated with all samples into two branches according to the habitat types of the host (terrestrial and aquatic). The PCoA diagram further divided the bacterial compositions into four groups according to both types of habitats and the data sources (DNA and RNA). There were larger differences in the bacterial community composition in the mosses collected from aquatic habitat than those of terrestrial one, whether at the DNA or RNA level. Thus, this survey supposed that the habitat where the host was growing was a relevant factor influencing bacterial community composition. In addition, the bacterial community detected at the RNA level was more sensitive to the habitat of the growing host, which could also be proved by the significantly differences in the predicted function by PICRUSt and the metabolically active dominant genera between different groups. This study expands the knowledge about the interactions between mosses and microbes.
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Illumina sequencing of bacterial 16S rDNA and 16S rRNA reveals seasonal and species-specific variation in bacterial communities in four moss species. Appl Microbiol Biotechnol 2017; 101:6739-6753. [DOI: 10.1007/s00253-017-8391-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 11/27/2022]
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15
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Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep 2017; 7:40914. [PMID: 28102323 PMCID: PMC5244420 DOI: 10.1038/srep40914] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/13/2016] [Indexed: 11/09/2022] Open
Abstract
Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.
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Affiliation(s)
- Franziska Wemheuer
- Section of Agricultural Entomology, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Kristin Kaiser
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Stefan Vidal
- Section of Agricultural Entomology, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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Shen F, Li Y, Zhang M, Awasthi MK, Ali A, Li R, Wang Q, Zhang Z. Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA. Sci Rep 2016; 6:39148. [PMID: 27958371 PMCID: PMC5153631 DOI: 10.1038/srep39148] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/18/2016] [Indexed: 02/01/2023] Open
Abstract
In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils.
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MESH Headings
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/growth & development
- Benzopyrans/toxicity
- Biodiversity
- Cadmium/toxicity
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Humic Substances/toxicity
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
- Soil Microbiology
- Soil Pollutants/chemistry
- Soil Pollutants/toxicity
- Zinc/toxicity
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Affiliation(s)
- Feng Shen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanxia Li
- School of Environment, Beijing Normal University, Beijing, China
| | - Min Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Amjad Ali
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
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17
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Tang JY, Ma J, Li XD, Li YH. Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China. BMC Microbiol 2016; 16:276. [PMID: 27852238 PMCID: PMC5112639 DOI: 10.1186/s12866-016-0892-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022] Open
Abstract
Background Previous studies on the bacteria associated with the bryophytes showed that there were abundant bacteria inhabited in/on these hosts. However, the type of bacteria and whether these discriminate between different bryophytes based on a particular factor remains largely unknown. Results This study was designed to analyze the biodiversity and community of the bacteria associated with ten liverworts and ten mosses using Illumina-sequencing techniques based on bacterial 16S rRNA gene. A total of 125,762 high quality sequences and 437 OTUs were obtained from twenty bryophytes. Generally, there were no obvious differences between the richness of bacteria associated with liverworts and mosses; however, the diversity was significantly higher in liverworts than in mosses. The taxonomic analyses showed that there were abundant bacteria inhabited with each bryophyte and those primarily detected in all samples were within the phyla Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Armatimonadetes and Planctomycetes. In addition, bacteria assigned to Chloroflexi, Fibrobacteres, Gemmatimonadetes, Chlamydiae, group of TM6 and WCHB1-60 also appeared in part of the bryophytes. The assigned bacteria included those adapted to aquatic, anaerobic and even extreme drought environments, which is consistent with the bryophyte transition from aquatic to terrestrial conditions. Of them, approximately 10 recognized genera were shared by all the samples in a higher proportion, such as Burkholderia, Novosphingobium, Mucilaginibacter, Sorangium, Frankia, Frondihatitans, Haliangium, Rhizobacter, Granulicella and Hafnia, and 11 unclassified genera were also detected in all samples, which exhibited that large amounts of unclassified bacteria could interact with the bryophytes. The Heatmap and Principle Coordinate Analyses showed that bacteria associated with six mosses displayed a higher community similarity. Notably, the bacteria associated with another four mosses exhibited higher similarity with the ten liverworts. Conclusions The result of further analysis of the bacterial community in different bryophytes revealed that the phylogeny of hosts might portray a strong influence on the associated bacterial community and that niche also played important roles when the hosts were phylogenetically more similar. Further studies are needed to confirm the role of phylogeny on bacterial communities and determine the level of influence on predicting which bacteria is associated with the host.
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Affiliation(s)
- Jing Yan Tang
- College of Life Science, Capital Normal University, Xisanhuan North Road 105#, Haidian District, Beijing, 100048, China
| | - Jing Ma
- College of Life Science, Capital Normal University, Xisanhuan North Road 105#, Haidian District, Beijing, 100048, China
| | - Xue Dong Li
- College of Life Science, Capital Normal University, Xisanhuan North Road 105#, Haidian District, Beijing, 100048, China
| | - Yan Hong Li
- College of Life Science, Capital Normal University, Xisanhuan North Road 105#, Haidian District, Beijing, 100048, China.
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18
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Goryluk-Salmonowicz A, Piórek M, Rekosz-Burlaga H, Studnicki M, Błaszczyk M. Endophytic Detection in Selected European Herbal Plants. Pol J Microbiol 2016; 65:369-375. [PMID: 29334055 DOI: 10.5604/17331331.1215617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A total of 181 cultivable endophytic bacterial isolates were collected from stems of 13 species of herbs inhabiting Europe (Poland): Chelidonium majus L., Elymus repens L., Erigeron annuus L., Euphrasia rostkoviana Hayne, Foeniculum vulgare L., Geranium pratense L., Humulus lupulus L., Matricaria chamomilla L., Mentha arvensis L., Papaver rhoeas L., Rosmarinus officinalis L., Solidago gigantea L. and Vinca minor L. The isolates were screened for their antifungal activity and fifty three were found to inhibit fungal growth. Of these, five had strong antifungal properties. These selected isolates were identified as: Pseudomonas azotoformans, P. cedrina, Bacillus subtilis group and Erwinia persicina.
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Affiliation(s)
- Agata Goryluk-Salmonowicz
- Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Poland
| | - Monika Piórek
- Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Poland
| | - Hanna Rekosz-Burlaga
- Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Poland
| | - Marcin Studnicki
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology Warsaw University of Life Sciences, Poland
| | - Mieczysław Błaszczyk
- Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Poland
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Tian Y, Li YH. Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing. J Basic Microbiol 2016; 57:57-67. [PMID: 27515736 DOI: 10.1002/jobm.201600358] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/06/2016] [Indexed: 11/07/2022]
Abstract
To understand the differences of the bacteria associated with different mosses, a phylogenetic study of bacterial communities in three mosses was carried out based on 16S rDNA and 16S rRNA sequencing. The mosses used were Hygroamblystegium noterophilum, Entodon compressus and Grimmia montana, representing hygrophyte, shady plant and xerophyte, respectively. In total, the operational taxonomic units (OTUs), richness and diversity were different regardless of the moss species and the library level. All the examined 1183 clones were assigned to 248 OTUs, 56 genera were assigned in rDNA libraries and 23 genera were determined at the rRNA level. Proteobacteria and Bacteroidetes were considered as the most dominant phyla in all the libraries, whereas abundant Actinobacteria and Acidobacteria were detected in the rDNA library of Entodon compressus and approximately 24.7% clones were assigned to Candidate division TM7 in Grimmia montana at rRNA level. The heatmap showed the bacterial profiles derived from rRNA and rDNA were partly overlapping. However, the principle component analysis of all the profiles derived from rDNA showed sharper differences between the different mosses than that of rRNA-based profiles. This suggests that the metabolically active bacterial compositions in different mosses were more phylogenetically similar and the differences of the bacteria associated with different mosses were mainly detected at the rDNA level. Obtained results clearly demonstrate that combination of 16S rDNA and 16S rRNA sequencing is preferred approach to have a good understanding on the constitution of the microbial communities in mosses.
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Affiliation(s)
- Yang Tian
- College of Life Science, Capital Normal University, Haidian District, Beijing, China
| | - Yan Hong Li
- College of Life Science, Capital Normal University, Haidian District, Beijing, China
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20
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Fidalgo C, Henriques I, Rocha J, Tacão M, Alves A. Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:10200-14. [PMID: 26875822 DOI: 10.1007/s11356-016-6208-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/29/2016] [Indexed: 05/27/2023]
Abstract
Halimione portulacoides is abundant in salt marshes, accumulates mercury (Hg), and was proposed as useful for phytoremediation and pollution biomonitoring. Endophytic bacteria promote plant growth and provide compounds with industrial applications. Nevertheless, information about endophytic bacteria from H. portulacoides is scarce. Endophytic isolates (n = 665) were obtained from aboveground and belowground plant tissues, from two Hg-contaminated sites (sites E and B) and a noncontaminated site (site C), in the estuary Ria de Aveiro. Representative isolates (n = 467) were identified by 16S rRNA gene sequencing and subjected to functional assays. Isolates affiliated with Proteobacteria (64 %), Actinobacteria (23 %), Firmicutes (10 %), and Bacteroidetes (3 %). Altererythrobacter (7.4 %), Marinilactibacillus (6.4 %), Microbacterium (10.2 %), Salinicola (8.8 %), and Vibrio (7.8 %) were the most abundant genera. Notably, Salinicola (n = 58) were only isolated from site C; Hoeflea (17), Labrenzia (22), and Microbacterium (67) only from belowground tissues. This is the first report of Marinilactibacillus in the endosphere. Principal coordinate analysis showed that community composition changes with the contamination gradient and tissue. Our results suggest that the endosphere of H. portulacoides represents a diverse bacterial hotspot including putative novel species. Many isolates, particularly those affiliated to Altererythrobacter, Marinilactibacillus, Microbacterium, and Vibrio, tested positive for enzymatic activities and plant growth promoters, exposing H. portulacoides as a source of bacteria and compounds with biotechnological applications.
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Affiliation(s)
- Cátia Fidalgo
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- iBiMED and CESAM, Departamento de Biologia, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Isabel Henriques
- iBiMED and CESAM, Departamento de Biologia, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
| | - Jaqueline Rocha
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Marta Tacão
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Artur Alves
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
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