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Santra HK, Banerjee D. Bioactivity study and metabolic profiling of Colletotrichum alatae LCS1, an endophyte of club moss Lycopodium clavatum L. PLoS One 2022; 17:e0267302. [PMID: 35482744 PMCID: PMC9049576 DOI: 10.1371/journal.pone.0267302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/06/2022] [Indexed: 01/23/2023] Open
Abstract
Endophytes are silent microbial partners of green plants that ensure hosts' survival in odd conditions. They are known as the factories of multipotent metabolites with diverse bioactivities beneficial to modern pharmaceuticals industry. Endophytic fungi have been screened from a variety of plants and it is the first-time endophytes of club moss is being studied for production of antibacterial and antioxidative compounds. The present study reveals that Lycopodium clavatum L. harbors a potent niche of bioactive endophytic fungi and Colletotrichum alatae LCS1 was the prime producer of antibacterial and antioxidative compounds among them. The minimum inhibitory and bactericidal concentrations of ethyl- acetate culture extract ranged from 15.62 to 250 μg/mL against four Gram negative and three Gram positive microorganisms including methicillin resistant Staphylococcus aureus (ATCC-33591). Bio-autogram based screening followed by Gas chromatographic analysis confirmed the occurrence of 17 bioactive compounds and α-bisabolol is known to be the prime one. Alfa bisabolol is a unique and versatile bioactive essential oil and facilitates variety of functions. Killing kinetics data along with leakage of macromolecules into extracellular environment supports the cidal activity of the antibacterial principles at MBC values. Isolate C. alatae LCS1 was optimized by one variable at a time system coupled with response surface methodology for broad spectrum antibacterial production. The organism yielded maximum response (22.66±0.894 mm of zone of inhibition against MRSA) in 250 mL Erlenmeyer flask containing 50 mL potato dextrose broth supplemented with (g/L) glucose, 7.53; yeast extract concentration, 0.47; NaCl, 0.10 with medium pH 6.46; after 134 hours of incubation at 26°C. Optimized fermentation parameters enhanced antibacterial activity up-to more than 50% than the pre-optimized one (10.33±0.57 mm). Endophytic LCS1 was also efficient in free radical scavenging tested by DPPH, ABTS, H2O2 and FRAP assay with an IC50 values of 23.38±5.32 to 82.873±6.479 μg/mL.
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Affiliation(s)
- Hiran Kanti Santra
- Microbiology and Microbial Biotechnology Laboratory, Department of Botany and Forestry, Vidyasagar University, Midnapore, West Bengal, India
| | - Debdulal Banerjee
- Microbiology and Microbial Biotechnology Laboratory, Department of Botany and Forestry, Vidyasagar University, Midnapore, West Bengal, India
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Romero-Jiménez MJ, Rudgers JA, Jumpponen A, Herrera J, Hutchinson M, Kuske C, Dunbar J, Knapp DG, Kovács GM, Porras-Alfaro A. Darksidea phi, sp. nov., a dark septate root-associated fungus in foundation grasses in North American Great Plains. Mycologia 2022; 114:254-269. [PMID: 35394886 DOI: 10.1080/00275514.2022.2031780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Darksidea is a common genus of dark septate fungi-a group of ascomycetes in semiarid regions. A survey reported D. alpha and a distinct Darksidea lineage as abundant root-associated fungi of foundational grasses in North America. Fungi were isolated, and metabarcode data were obtained from sequencing of fungal communities of grass roots in the United States. During a comprehensive investigation of the Darksidea lineage, we carried out polyphasic taxonomy, genomic characterization, and identification of host associations, geographic distribution, and environmental factors that correlate with its abundance. For molecular phylogenetic studies, seven loci were sequenced. Isolates of the distinct Darksidea had variable colony morphology. No sexual reproductive structures were detected, but chlamydospores were frequently observed. The complete genome of an isolate of the lineage was sequenced with a size of 52.3 Mb including 14 707 gene models. Based on morphology and phylogenetic analysis, we propose the novel species Darksidea phi, sp. nov. Metabarcoding data showed that D. phi distribution and relative abundance were not limited to semiarid regions or a specific grass species, suggesting low host specificity among graminoids. This new species, D. phi, expands the distribution of the genus in the United States beyond prior reports from arid regions.
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Affiliation(s)
- María-José Romero-Jiménez
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455
| | - Jennifer A Rudgers
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - José Herrera
- Office of the Provost and Executive Vice President for Academic Affairs, Cedar Falls, Iowa 50614
| | | | - Cheryl Kuske
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - John Dunbar
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Dániel G Knapp
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor M Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Andrea Porras-Alfaro
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Division of Environmental Biology, National Science Foundation, Alexandria, Virginia 22314
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Abdoulaye AH, Jia J, Abbas A, Hai D, Cheng J, Fu Y, Lin Y, Jiang D, Xie J. Fusarivirus accessory helicases present an evolutionary link for viruses infecting plants and fungi. Virol Sin 2022; 37:427-436. [PMID: 35314402 PMCID: PMC9243621 DOI: 10.1016/j.virs.2022.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Abstract
A significant number of mycoviruses have been identified that are related to plant viruses, but their evolutionary relationships are largely unexplored. A fusarivirus, Rhizoctonia solani fusarivirus 4 (RsFV4), was identified in phytopathogenic fungus Rhizoctonia solani (R. solani) strain XY74 co-infected by an alphaendornavirus. RsFV4 had a genome of 10,833 nt (excluding the poly-A tail), and consisted of four non-overlapping open reading frames (ORFs). ORF1 encodes an 825 aa protein containing a conserved helicase domain (Hel1). ORF3 encodes 1550 aa protein with two conserved domains, namely an RNA-dependent RNA polymerase (RdRp) and another helicase (Hel2). The ORF2 and ORF4 likely encode two hypothetical proteins (520 and 542 aa) with unknown functions. The phylogenetic analysis based on Hel2 and RdRp suggest that RsFV4 was positioned within the fusarivirus group, but formed an independent branch with three previously reported fusariviruses of R. solani. Notably, the Hel1 and its relatives were phylogenetically closer to helicases of potyviruses and hypoviruses than fusariviruses, suggesting fusarivirus Hel1 formed an evolutionary link between these three virus groups. This finding provides evidence of the occurrence of a horizontal gene transfer or recombination event between mycoviruses and plant viruses or between mycoviruses. Our findings are likely to enhance the understanding of virus evolution and diversity. Rhizoctonia solani strain XY74 hosts two mycoviruses, fusarivirus (RsFV4) and endornavirus (RsAEV1). RsFV4 consists of four ORFs and is evolutionarily associated to fusariviruses. Two ORFs of RsFV4 encode two helicases belonging to superfamly II. The accessory helicase of RsFV4 and its relatives are phylogenetically related to mycoviruses and plant viruses.
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Santra HK, Maity S, Banerjee D. Production of Bioactive Compounds with Broad Spectrum Bactericidal Action, Bio-Film Inhibition and Antilarval Potential by the Secondary Metabolites of the Endophytic Fungus Cochliobolus sp. APS1 Isolated from the Indian Medicinal Herb Andrographis paniculata. Molecules 2022; 27:1459. [PMID: 35268559 PMCID: PMC8912084 DOI: 10.3390/molecules27051459] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Endophytes, being the co-evolution partners of green host plants, are factories of pharmaceutically valuable novel natural products. Cochliobolus sp. APS1, an endophyte of Andrographis paniculata (Green Chiretta), produces a plethora of natural bioactive compounds and the multipotent alkaloid Aziridine, 1-(2-aminoethyl)-, is the prime one among them. The isolate exhibited antibacterial, anti-biofilm, and antilarval potency. The MIC and MBC values of the ethyl-acetate culture extract ranged from 15.62 to 250 µg/mL against ten pathogenic microorganisms (including MRSA and VRSA). Killing kinetics data along with the leakage of macromolecules into the extracellular environment supports the cidal activity of the antibacterial principles. The broad spectrum antibacterial activity of Aziridine, 1-(2-aminoethyl)-, was optimized by a one-variable-at-a-time system coupled with response surface methodology, which led to a 45% enhancement of the antibacterial activity. The maximum response (22.81 ± 0.16 mm of zone of inhibition against MRSA) was marked in 250 mL Erlenmeyer flask containing 90 mL potato dextrose broth supplemented with (g%/L) glucose, 9.7; urea concentration, 0.74; with medium pH 6.48; after 8.76 days of incubation at 26 °C. APS1 strongly inhibited biofilm formation in the tested pathogenic microorganisms and acts as a larvicidal agent against the Dengue-vector Aedes aegypti. This is probably the first report of Aziridine, 1-(2-aminoethyl)-, from any endophytic source. Cochliobolus sp. APS1 possesses industrial importance for the production of bioactive alkaloids.
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Affiliation(s)
| | | | - Debdulal Banerjee
- Microbiology and Microbial Biotechnology Laboratory, Department of Botany and Forestry, Vidyasagar University, Midnapore 721102, West Bengal, India; (H.K.S.); (S.M.)
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55
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Galindo-Solís JM, Fernández FJ. Endophytic Fungal Terpenoids: Natural Role and Bioactivities. Microorganisms 2022; 10:microorganisms10020339. [PMID: 35208794 PMCID: PMC8875210 DOI: 10.3390/microorganisms10020339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
Endophytic fungi are a highly diverse group of fungi that intermittently colonize all plants without causing symptoms of the disease. They sense and respond to physiological and environmental changes of their host plant and microbiome. The inter-organism interactions are largely driven by chemical networks mediated by specialized metabolites. The balance of these complex interactions leads to healthy and strong host plants. Endophytic strains have particular machinery to produce a plethora of secondary metabolites with a variety of bioactivities and unknown functions in an ecological niche. Terpenoids play a key role in endophytism and represent an important source of bioactive molecules for human health and agriculture. In this review, we describe the role of endophytic fungi in plant health, fungal terpenoids in multiple interactions, and bioactive fungal terpenoids recently reported from endophytes, mainly from plants used in traditional medicine, as well as from algae and mangroves. Additionally, we highlight endophytic fungi as producers of important chemotherapeutic terpenoids, initially discovered in plants. Despite advances in understanding endophytism, we still have much to learn in this field. The study of the role, the evolution of interactions of endophytic fungi and their terpenoids provide an opportunity for better applications in human health and agriculture.
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Affiliation(s)
- Juan M. Galindo-Solís
- Posgrado en Biotecnología, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Mexico City CP 09340, Mexico;
| | - Francisco J. Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, San Rafael Atlixco No. 186, Col. Vicentina, Mexico City CP 09340, Mexico
- Correspondence: ; Tel.: +52-(55)-5804-6453
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Native Rhizospheric and Endophytic Fungi as Sustainable Sources of Plant Growth Promoting Traits to Improve Wheat Growth under Low Nitrogen Input. J Fungi (Basel) 2022; 8:jof8020094. [PMID: 35205849 PMCID: PMC8875171 DOI: 10.3390/jof8020094] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/15/2022] [Indexed: 02/06/2023] Open
Abstract
Wheat crops require effective nitrogen fertilization to produce high yields. Only half of chemical N2 fertilizers are absorbed into plants while the rest remains in the soil, causing environmental problems. Fungi could maximize nitrogen absorption, and from an environmental and biodiversity point of view, there is an urgent necessity for bioprospecting native fungi associated with wild plants growing in harsh environments, e.g., St. Katherine Protectorate (SKP) in the arid Sinai. Recovered taxa, either endophytic and/or rhizospheric, were screened for their plant growth-promoting (PGP) traits. Eighteen fungal isolates (15 rhizospheric and 3 endophytic) belonging to anamorphic ascomycetes were recovered from 9 different wild plants, and their PGP traits (indole-3-acetic acid [IAA] production, phosphate solubilization, siderophore production, and hydrolytic enzyme production) were measured. Rhizospheric isolate NGB-WS14 (Chaetosphaeronema achilleae) produced high levels of IAA (119.1 μg mL−1) in the presence of tryptophan, while NGB-WS 8 (Acrophialophora levis) produced high IAA levels (42.4 μg mL−1) in the absence of tryptophan. The highest phosphate-solubilizing activity (181.9 μg mL−1) was recorded by NGB-WFS2 (Penicillium chrysogenum). Endophytic isolate NGB-WFE16 (Fusarium petersiae) exhibited a high percentage level of Siderophore Unit (96.5% SU). All isolates showed variability in the secretion of extracellular hydrolytic enzymes. Remarkably, all isolates had antagonistic activity (55.6% to 87.3% suppression of pathogen growth) against the pathogenic taxon Alternaria alternata (SCUF00001378) in the dual-assay results. Out of the 18 isolates, 4 rhizospheric and 1 endophytic isolate showed significant increases in shoot dry weight and shoot nitrogen and chlorophyll content of wheat plants subjected to low inputs of chemical nitrogen (N) fertilizers (50% reduction) compared with the non-inoculated control in a pot experiment. Potent taxa were subjected to sequencing for molecular confirmation of phenotypic identification. The retrieved ITS sequences in this study have been deposited in GenBank under accession numbers from LC642736 to LC642740. This study considered the first report of endophytic fungi of Cheilanthes vellea, a wild plant with PGPF which improves wheat growth. These results recommend using PGPF as inoculants to alleviate low nitrogen fertilization.
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57
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Maitra S, Brestic M, Bhadra P, Shankar T, Praharaj S, Palai JB, Shah MMR, Barek V, Ondrisik P, Skalický M, Hossain A. Bioinoculants-Natural Biological Resources for Sustainable Plant Production. Microorganisms 2021; 10:51. [PMID: 35056500 PMCID: PMC8780112 DOI: 10.3390/microorganisms10010051] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.
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Affiliation(s)
- Sagar Maitra
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Preetha Bhadra
- Department of Biotechnology, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India;
| | - Tanmoy Shankar
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Subhashisa Praharaj
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Jnana Bharati Palai
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | | | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Peter Ondrisik
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Milan Skalický
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Akbar Hossain
- Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh;
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Yuan Z, Druzhinina IS, Gibbons JG, Zhong Z, Van de Peer Y, Rodriguez RJ, Liu Z, Wang X, Wei H, Wu Q, Wang J, Shi G, Cai F, Peng L, Martin FM. Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus. THE ISME JOURNAL 2021; 15:3468-3479. [PMID: 34108667 PMCID: PMC8629976 DOI: 10.1038/s41396-021-01023-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/09/2021] [Accepted: 05/24/2021] [Indexed: 02/05/2023]
Abstract
Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.
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Affiliation(s)
- Zhilin Yuan
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China ,grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Irina S. Druzhinina
- grid.27871.3b0000 0000 9750 7019Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - John G. Gibbons
- grid.266683.f0000 0001 2166 5835Department of Food Science, University of Massachusetts, Amherst, MA USA
| | - Zhenhui Zhong
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China ,grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA USA
| | - Yves Van de Peer
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Ghent, Belgium ,grid.49697.350000 0001 2107 2298Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Russell J. Rodriguez
- grid.34477.330000000122986657Adaptive Symbiotic Technologies, University of Washington, Seattle, WA USA
| | - Zhongjian Liu
- grid.256111.00000 0004 1760 2876Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyu Wang
- grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Huanshen Wei
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China ,grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Qi Wu
- grid.9227.e0000000119573309State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jieyu Wang
- grid.9227.e0000000119573309Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guohui Shi
- grid.9227.e0000000119573309State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng Cai
- grid.27871.3b0000 0000 9750 7019Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Long Peng
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China ,grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Francis M. Martin
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.29172.3f0000 0001 2194 6418Université de Lorraine, INRAE, UMR Interactions Arbres/Micro-Organismes, Centre INRAE Grand Est Nancy, Champenoux, France
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59
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Ahmed MM, Hagagy N, AbdElgawad H. Establishment of actinobacteria-Satureja hortensis interactions under future climate CO 2-enhanced crop productivity in drought environments of Saudi Arabia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:62853-62867. [PMID: 34218379 DOI: 10.1007/s11356-021-14777-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Drought is a significant global constraint on agricultural production and food security. As a promising approach to improve plant growth and yield under challenging conditions, plant growth-promoting actinobacteria has attracted much interest. Further, elevated levels of atmospheric CO2 (eCO2) may promote the plant-actinobacteria interactions which could be effective to improve the plant growth for food production. Herein, we have investigated the impact of actinobacteria and/or CO2 on biomass production, photosynthesis, macronutrients, levels of organic acids, amino acids, and essential oils as well as antioxidant activities of Satureja hortensis under water-deficit conditions. Among different actinobacterial isolates evaluated for development of secondary metabolites and biological activities, Ac9 was highly capable of producing flavonoids, and it also showed high antioxidant and microbial activities. It markedly induced the plant growth, photosynthesis, and global metabolic improvement, under water-deficit conditions. Interestingly, treatment with Ac9 in combination with eCO2 substantially minimized drought stress-induced biomass and photosynthesis reductions in Satureja hortensis. Improved photosynthesis by Ac9 and/or eCO2 induced the primary and secondary metabolisms in drought-stressed plants. The levels of the majority of the detected organic acids, essential oil, and amino acids were further improved as a result of the synergistic action of Ac9 and eCO2, as compared to the individual treatments. Furthermore, Ac9 or eCO2 significantly improved the antioxidant activities in stressed plants; however, much more positive impact was obtained by their synchronous application. Thus, the current study suggests that actinobacterial treatment induces global metabolic changes in water-stressed Satureja hortensis, the effects that have been much more strengthened under eCO2.
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Affiliation(s)
- Marwa M Ahmed
- Electrical Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Nashwa Hagagy
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, 21921, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Hamada AbdElgawad
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62521, Egypt.
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60
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Ndinga-Muniania C, Mueller RC, Kuske CR, Porras-Alfaro A. Seasonal variation and potential roles of dark septate fungi in an arid grassland. Mycologia 2021; 113:1181-1198. [PMID: 34686124 DOI: 10.1080/00275514.2021.1965852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High temperatures and extended drought in temperate and tropical arid ecosystems promote the colonization of diverse microenvironments by dark septate fungi (DSF). These fungi contribute to soil nutrient cycling, soil stabilization, and plant survival, but the roles of individual DSF species, their distributions, and their community diversity are poorly understood. The objective of this study was to evaluate the distribution, seasonal variation, and potential roles of DSF on plant growth. We collected biocrust (lichen-, moss-, and cyanobacterium-dominated biocrusts) soils at different depths and rhizosphere soils from two grasses, Bromus tectorum and Pleuraphis jamesii, in an arid grassland near Moab, Utah, USA. Seasonal variation of DSF was evaluated using culture-based approaches and compared with fungal community profiles from next-generation sequencing (NGS). Culturing showed that DSF were 30% more abundant in biocrusts compared with the focal rhizospheres. The abundance of DSF varied seasonally in belowground samples (rhizosphere and below-biocrust), with a significant increase during the summer months. Pleosporales was the dominant order (35%) in both biocrust and rhizosphere soils out of 817 isolated fungi. Dominant DSF genera in culture included Alternaria, Preussia, Cladosporium, Phoma, and an unknown Pleosporales. Similar results were observed in biocrust and rhizosphere soils NGS. Further, seed germination experiments using dominant taxa were conducted to determine their potential roles on germination and seedling growth using maize as a model plant. Cladosporium and unknown Pleosporales isolates showed plant growth-promoting ability. The variation in abundance of DSF, their differential occurrence in different microenvironments, and their ability to grow in a xerotolerant medium reflect adaptations to summer environmental conditions and to changes in the abundance of organic matter, as well as a potential increase in plant investment in these fungi when heat and drought stresses are more severe.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, 55108, Minnesota
| | - Rebecca C Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Andrea Porras-Alfaro
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Division of Environmental Biology, National Science Foundation, Alexandria, Virginia 22314
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61
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Błaszczyk L, Salamon S, Mikołajczak K. Fungi Inhabiting the Wheat Endosphere. Pathogens 2021; 10:1288. [PMID: 34684238 PMCID: PMC8539314 DOI: 10.3390/pathogens10101288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 01/22/2023] Open
Abstract
Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat-fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.
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Affiliation(s)
- Lidia Błaszczyk
- Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszyńska Street, 60-479 Poznań, Poland; (S.S.); (K.M.)
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62
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Gonçalves DR, Pena R, Zotz G, Albach DC. Effects of fungal inoculation on the growth of Salicornia (Amaranthaceae) under different salinity conditions. Symbiosis 2021. [DOI: 10.1007/s13199-021-00783-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AbstractEndophytic fungi are known to be present in roots of salt marsh plants, but their ecological role in this symbiosis is still largely unknown. Generally considered parasitic or saprophytic, they may still be mutualistic, at least under certain circumstances. Among salt marsh plants, Salicornia spp. are recognized as particularly salt-tolerant and their frequent colonization by root endophytes has also been reported. This study aimed to investigate whether the inoculation of Salicornia with different root endophytes isolated from field-collected Salicornia affects biomass production, nutrient uptake and photosynthesis (assessed via chlorophyll fluorescence). In addition, we investigated whether fungal inoculation confers tolerance to salt stress given that endophytes are suggested to increase salt tolerance and improve plant fitness in other less salt-tolerant plants. The inoculation of Salicornia with an isolate of the genus Stemphylium positively influenced total biomass production and nitrogen concentration in roots at optimum salinity condition (150 mM NaCl). However, under salt stress (650 mM NaCl), no significant effects of fungal inoculation on biomass production and photosynthesis were observed. Further, positive and negative effects of fungal inoculation on nutrient concentrations were observed in roots and shoots, respectively. Our results indicate that different endophytic fungi and their interaction result in distinct fungal species-specific plant growth responses of Salicornia under different growth conditions.
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63
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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64
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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65
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Ye S, Bhattacharjee M, Siemann E. Stress tolerance alteration in the freshwater cnidarian green hydra (Hydra viridissima) via symbiotic algae mutagenesis. Symbiosis 2020. [DOI: 10.1007/s13199-020-00712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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66
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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67
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Ghadge V, Kumar P, Singh S, Mathew DE, Bhattacharya S, Nimse SB, Shinde PB. Natural Melanin Produced by the Endophytic Bacillus subtilis 4NP-BL Associated with the Halophyte Salicornia brachiata. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6854-6863. [PMID: 32496055 DOI: 10.1021/acs.jafc.0c01997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Natural melanin with many interesting properties has potential applications in cosmetics, drug delivery, semiconductors, etc. However, conventional production methods are not efficient, resulting in its high cost (350-650 USD g-1), which has been a bottleneck for its efficient commercial utilization. To explore a faster extraction method with a higher yield, a melanin-producing endophytic bacterium was isolated from the halophyte Salicornia brachiata and further identified as Bacillus subtilis 4NP-BL by phylogenetic analysis of 16S rRNA gene sequences. The maximum melanin yield of up to 1.5 g dry wt L-1 of production media was obtained through central composite design (CCD). The isolated melanin belonged to the eumelanin class with an irregular structure on the basis of elemental analysis, UV-vis, Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), electron paramagnetic resonance (EPR), and NMR studies. Furthermore, purified melanin displayed antioxidant activity and antimicrobial activity against pathogens Xanthomonas campestris and Alteromonas macleodii. Thus, this study further suggests a probable role of endophytes that produce melanin in aiding host plant protection from environmental stress and other pathogens.
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Affiliation(s)
- Vishal Ghadge
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), Bhavnagar364002, Gujarat, India
| | - Pankaj Kumar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), Bhavnagar364002, Gujarat, India
| | - Sanju Singh
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), Bhavnagar364002, Gujarat, India
| | - Doniya Elze Mathew
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India
| | - Sourish Bhattacharya
- Process Design & Engineering Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India
| | - Satish Balasaheb Nimse
- Institute of Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200702, Republic of Korea
| | - Pramod B Shinde
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), Bhavnagar364002, Gujarat, India
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68
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69
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Abstract
Endosymbiosis is found in all types of ecosystems and it can be sensitive to environmental changes due to the intimate interaction between the endosymbiont and the host. Indeed, global climate change disturbs the local ambient environment and threatens endosymbiotic species, and in some cases leads to local ecosystem collapse. Recent studies have revealed that the endosymbiont can affect holobiont (endosymbiont and host together) stress tolerance as much as the host does, and manipulation of the microbial partners in holobionts may mitigate the impacts of the environmental stress. Here, we first show how the endosymbiont presence affects holobiont stress tolerance by discussing three well-studied endosymbiotic systems, which include plant-fungi, aquatic organism-algae, and insect-bacteria systems. We then review how holobionts are able to alter their stress tolerance via associated endosymbionts by changing their endosymbiont composition, by adaptation of their endosymbionts, or by acclimation of their endosymbionts. Finally, we discuss how different transmission modes (vertical or horizontal transmission) might affect the adaptability of holobionts. We propose that the endosymbiont is a good target for modifying holobiont stress tolerance, which makes it critical to more fully investigate the role of endosymbionts in the adaptive responses of holobionts to stress.
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70
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Větrovský T, Kohout P, Kopecký M, Machac A, Man M, Bahnmann BD, Brabcová V, Choi J, Meszárošová L, Human ZR, Lepinay C, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Morais D, Navrátilová D, Odriozola I, Štursová M, Švec K, Tláskal V, Urbanová M, Wan J, Žifčáková L, Howe A, Ladau J, Peay KG, Storch D, Wild J, Baldrian P. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat Commun 2019; 10:5142. [PMID: 31723140 PMCID: PMC6853883 DOI: 10.1038/s41467-019-13164-8] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa. The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.,Faculty of Science, Charles University, Albertov 6, 12844, Praha 2, Czech Republic
| | - Martin Kopecký
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521, Praha 6, Czech Republic
| | - Antonin Machac
- Faculty of Science, Charles University, Albertov 6, 12844, Praha 2, Czech Republic.,Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, 11000, Praha 1, Czech Republic.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen, Denmark.,Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Matěj Man
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA, 50011, USA
| | - Lenka Meszárošová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Zander Rainier Human
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Diana Navrátilová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Joe Wan
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lucia Žifčáková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA, 50011, USA
| | - Joshua Ladau
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | | | - David Storch
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, 11000, Praha 1, Czech Republic.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Jan Wild
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Biotechnological application of endophytic filamentous bipolaris and curvularia: a review on bioeconomy impact. World J Microbiol Biotechnol 2019; 35:69. [PMID: 31011888 DOI: 10.1007/s11274-019-2644-7] [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: 01/12/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
The filamentous Bipolaris and Curvularia genera consist of species known to cause severe diseases in plants and animals amounting to an estimated annual loss of USD $10 billion worldwide. Despite the harmful effect of Bipolaris and Curvularia species, scarce attention is paid on beneficial areas where the fungi are used in industrial processes to generate biotechnological products. Catalytic potential of Bipolaris and Curvularia species in the production of biodiesel, bioflucculant, biosorbent, and mycoherbicide are promising for the bioeconomy. It is herein demonstrated that knowledge-based application of some endophytic Bipolaris and Curvularia species are indispensable vectors of sustainable economic development. In the twenty-first century, India, China, and the USA have taken progress in the biotechnological application of these fungi to generate wealth. As such, some Bipolaris and Curvularia species significantly impact on global crop improvement, act as catalyst in batch-reactors for biosynthesis of industrial enzymes and medicines, bioengineer of green-nanoparticle, agent of biofertilizer, bioremediation and bio-hydrometallurgy. For the first time, this study discusses the current advances in biotechnological application of Bipolaris and Curvularia species and provide new insights into the prospects of optimizing their bioengineering potential for developing bioeconomy.
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Ma L, Calfee BC, Morris JJ, Johnson ZI, Zinser ER. Degradation of hydrogen peroxide at the ocean's surface: the influence of the microbial community on the realized thermal niche of Prochlorococcus. THE ISME JOURNAL 2018; 12:473-484. [PMID: 29087377 PMCID: PMC5776462 DOI: 10.1038/ismej.2017.182] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 09/14/2017] [Accepted: 09/22/2017] [Indexed: 02/06/2023]
Abstract
Prochlorococcus, the smallest and most abundant phytoplankter in the ocean, is highly sensitive to hydrogen peroxide (HOOH), and co-occurring heterotrophs such as Alteromonas facilitate the growth of Prochlorococcus by scavenging HOOH. Temperature is also a major influence on Prochlorococcus abundance and distribution in the ocean, and studies in other photosynthetic organisms have shown that HOOH and temperature extremes can act together as synergistic stressors. To address potential synergistic effects of temperature and HOOH on Prochlorococcus growth, high- and low-temperature-adapted representative strains were cultured at ecologically relevant concentrations under a range of HOOH concentrations and temperatures. Higher concentrations of HOOH severely diminished the permissive temperature range for growth of both Prochlorococcus strains. At the permissive temperatures, the growth rates of both Prochlorococcus strains decreased as a function of HOOH, and cold temperature increased susceptibility of photosystem II to HOOH-mediated damage. Serving as a proxy for the natural community, co-cultured heterotrophic bacteria increased the Prochlorococcus growth rate under these temperatures, and expanded the permissive range of temperature for growth. These studies indicate that in the ocean, the cross-protective function of the microbial community may confer a fitness increase for Prochlorococcus at its temperature extremes, especially near the ocean surface where oxidative stress is highest. This interaction may play a substantial role in defining the realized thermal niche and habitat range of Prochlorococcus with respect to latitude.
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Affiliation(s)
- Lanying Ma
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Benjamin C Calfee
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - J Jeffrey Morris
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zackary I Johnson
- Nicholas School of the Environment and Biology Department, Duke University Marine Laboratory, Beaufort, NC, USA
| | - Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
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73
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Drage S, Mitter B, Engelmeier D, Chobot V, Gorfer M, Muchugi A, Jamnadass RH, Sessitsch A, Hadacek F. Antimicrobial Drimane Sesquiterpenes Contribute to Balanced Antagonism but Do Not Structure Bacterial and Fungal Endophytes in the African Pepper Bark Tree Warburgia ugandensis. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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74
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Atiphasaworn P, Monggoot S, Gentekaki E, Brooks S, Pripdeevech P. Antibacterial and Antioxidant Constituents of Extracts of Endophytic Fungi Isolated from Ocimum basilicum var. thyrsiflora Leaves. Curr Microbiol 2017; 74:1185-1193. [DOI: 10.1007/s00284-017-1303-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/07/2017] [Indexed: 11/30/2022]
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75
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Köhler JR, Hube B, Puccia R, Casadevall A, Perfect JR. Fungi that Infect Humans. Microbiol Spectr 2017; 5:10.1128/microbiolspec.funk-0014-2016. [PMID: 28597822 PMCID: PMC11687496 DOI: 10.1128/microbiolspec.funk-0014-2016] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 12/18/2022] Open
Abstract
Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as Histoplasma and Coccidioides; the Cryptococcus spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients-Candida, Pneumocystis, and Aspergillus spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.
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Affiliation(s)
- Julia R Köhler
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Rosana Puccia
- Disciplina de Biologia Celular, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - John R Perfect
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710
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76
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Corbin C, Heyworth ER, Ferrari J, Hurst GDD. Heritable symbionts in a world of varying temperature. Heredity (Edinb) 2016; 118:10-20. [PMID: 27703153 DOI: 10.1038/hdy.2016.71] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 12/25/2022] Open
Abstract
Heritable microbes represent an important component of the biology, ecology and evolution of many plants, animals and fungi, acting as both parasites and partners. In this review, we examine how heritable symbiont-host interactions may alter host thermal tolerance, and how the dynamics of these interactions may more generally be altered by thermal environment. Obligate symbionts, those required by their host, are considered to represent a thermally sensitive weak point for their host, associated with accumulation of deleterious mutations. As such, these symbionts may represent an important determinant of host thermal envelope and spatial distribution. We then examine the varied relationship between thermal environment and the frequency of facultative symbionts that provide ecologically contingent benefits or act as parasites. We note that some facultative symbionts directly alter host thermotolerance. We outline how thermal environment will alter the benefits/costs of infection more widely, and additionally modulate vertical transmission efficiency. Multiple patterns are observed, with symbionts being cold sensitive in some species and heat sensitive in others, with varying and non-coincident thresholds at which phenotype and transmission are ablated. Nevertheless, it is clear that studies aiming to predict ecological and evolutionary dynamics of symbiont-host interactions need to examine the interaction across a range of thermal environments. Finally, we discuss the importance of thermal sensitivity in predicting the success/failure of symbionts to spread into novel species following natural/engineered introduction.
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Affiliation(s)
- C Corbin
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - E R Heyworth
- Department of Biology, University of York, York, UK
| | - J Ferrari
- Department of Biology, University of York, York, UK
| | - G D D Hurst
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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77
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Evaluation of the functional roles of fungal endophytes of Phragmites australis from high saline and low saline habitats. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1160-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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78
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Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015; 79:293-320. [PMID: 26136581 PMCID: PMC4488371 DOI: 10.1128/mmbr.00050-14] [Citation(s) in RCA: 1157] [Impact Index Per Article: 115.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Affiliation(s)
- Pablo R. Hardoim
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Stéphane Compant
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Andrea Campisano
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | | | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
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79
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Sharpton TJ. An introduction to the analysis of shotgun metagenomic data. FRONTIERS IN PLANT SCIENCE 2014; 5:209. [PMID: 24982662 PMCID: PMC4059276 DOI: 10.3389/fpls.2014.00209] [Citation(s) in RCA: 304] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/29/2014] [Indexed: 05/19/2023]
Abstract
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
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Affiliation(s)
- Thomas J. Sharpton
- *Correspondence: Thomas J. Sharpton, Department of Microbiology and Department of Statistics, Oregon State University, 220 Nash Hall, Corvallis, OR 97331, USA e-mail:
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80
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Yuan ZL, Zhang CL, Lin FC, Kubicek CP. Identity, diversity, and molecular phylogeny of the endophytic mycobiota in the roots of rare wild rice (Oryza granulate) from a nature reserve in Yunnan, China. Appl Environ Microbiol 2010; 76:1642-52. [PMID: 20038691 PMCID: PMC2832373 DOI: 10.1128/aem.01911-09] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 12/16/2009] [Indexed: 11/20/2022] Open
Abstract
Rice (Oryza sativa L.) is, on a global scale, one of the most important food crops. Although endophytic fungi and bacteria associated with rice have been investigated, little is known about the endophytic fungi of wild rice (Oryza granulate) in China. Here we studied the root endophytic mycobiota residing in roots of O. granulate by the use of an integrated approach consisting of microscopy, cultivation, ecological indices, and direct PCR. Microscopy confirmed the ubiquitousness of dark septate endophytes (DSEs) and sclerotium-like structures in root tissues. Isolations from 204 root segments from 15 wild rice plants yielded 58 isolates, for which 31 internal transcribed spacer (ITS)-based genotypes were recorded. The best BLAST match indicated that 34.5% of all taxa encountered may represent hitherto undescribed species. Most of the fungi were isolated with a very low frequency. Calculation of ecological indices and estimation of taxon accumulation curves indicated a high diversity of fungal species. A culture-independent approach was also performed to analyze the endophytic fungal community. Three individual clone libraries were constructed. Using a threshold of 90% similarity, 35 potentially different sequences (phylotypes) were found among 186 positive clones. Phylogenetic analysis showed that frequently detected clones were classified as Basidiomycota, and 60.2% of total analyzed clones were affiliated with unknown taxa. Exophiala, Cladophialophora, Harpophora, Periconia macrospinosa, and the Ceratobasidium/Rhizoctonia complex may act as potential DSE groups. A comparison of the fungal communities characterized by the two approaches demonstrated distinctive fungal groups, and only a few taxa overlapped. Our findings indicate a complex and rich endophytic fungal consortium in wild rice roots, thus offering a potential bioresource for establishing a novel model of plant-fungal mutualistic interactions.
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Affiliation(s)
- Zhi-lin Yuan
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China, Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China, Institute of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, 1060 Vienna, Austria
| | - Chu-long Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China, Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China, Institute of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, 1060 Vienna, Austria
| | - Fu-cheng Lin
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China, Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China, Institute of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, 1060 Vienna, Austria
| | - Christian P. Kubicek
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China, Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China, Institute of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, 1060 Vienna, Austria
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81
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82
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Porras-Alfaro A, Herrera J, Sinsabaugh RL, Odenbach KJ, Lowrey T, Natvig DO. Novel root fungal consortium associated with a dominant desert grass. Appl Environ Microbiol 2008; 74:2805-13. [PMID: 18344349 PMCID: PMC2394874 DOI: 10.1128/aem.02769-07] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 03/01/2008] [Indexed: 11/20/2022] Open
Abstract
The broad distribution and high colonization rates of plant roots by a variety of endophytic fungi suggest that these symbionts have an important role in the function of ecosystems. Semiarid and arid lands cover more than one-third of the terrestrial ecosystems on Earth. However, a limited number of studies have been conducted to characterize root-associated fungal communities in semiarid grasslands. We conducted a study of the fungal community associated with the roots of a dominant grass, Bouteloua gracilis, at the Sevilleta National Wildlife Refuge in New Mexico. Internal transcribed spacer ribosomal DNA sequences from roots collected in May 2005, October 2005, and January 2006 were amplified using fungal-specific primers, and a total of 630 sequences were obtained, 69% of which were novel (less than 97% similarity with respect to sequences in the NCBI database). B. gracilis roots were colonized by at least 10 different orders, including endophytic, coprophilous, mycorrhizal, saprophytic, and plant pathogenic fungi. A total of 51 operational taxonomic units (OTUs) were found, and diversity estimators did not show saturation. Despite the high diversity found within B. gracilis roots, the root-associated fungal community is dominated by a novel group of dark septate fungi (DSF) within the order Pleosporales. Microscopic analysis confirmed that B. gracilis roots are highly colonized by DSF. Other common orders colonizing the roots included Sordariales, Xylariales, and Agaricales. By contributing to drought tolerance and nutrient acquisition, DSF may be integral to the function of arid ecosystems.
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Affiliation(s)
- Andrea Porras-Alfaro
- Department of Biology, MSC03 2020, 1 The University of New Mexico, Albuquerque, NM 87131-0001, USA.
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83
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Márquez LM, Redman RS, Rodriguez RJ, Roossinck MJ. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science 2007; 315:513-5. [PMID: 17255511 DOI: 10.1126/science.1136237] [Citation(s) in RCA: 481] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. We characterized a virus from this fungus that is involved in the mutualistic interaction. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants.
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Affiliation(s)
- Luis M Márquez
- Plant Biology Division, Samuel Roberts Noble Foundation, Post Office Box 2180, Ardmore, OK 73402, USA
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84
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Gunatilaka AAL. Natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence. JOURNAL OF NATURAL PRODUCTS 2006; 69:509-26. [PMID: 16562864 PMCID: PMC3362121 DOI: 10.1021/np058128n] [Citation(s) in RCA: 539] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A growing body of evidence suggests that plant-associated microorganisms, especially endophytic and rhizosphere bacteria and fungi, represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological relevance. A diverse array of bioactive small molecule natural products has been encountered in these microorganisms. The structures of over 230 metabolites isolated and characterized from over 70 plant-associated microbial strains during the past four years are presented with information on their hosts, culture conditions, and biological activities. Some significant biological and ecological implications of their occurrence are also reviewed.
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Affiliation(s)
- A A Leslie Gunatilaka
- Southwest Center for Natural Products Research and Commercialization, Office of Arid Lands Studies, College of Agriculture and Life Sciences, University of Arizona, Tucson, 85706-6800, USA.
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85
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Rodriguez R, Redman R. Balancing the generation and elimination of reactive oxygen species. Proc Natl Acad Sci U S A 2005; 102:3175-6. [PMID: 15728396 PMCID: PMC552941 DOI: 10.1073/pnas.0500367102] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rusty Rodriguez
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA.
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86
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Ganley RJ, Brunsfeld SJ, Newcombe G. A community of unknown, endophytic fungi in western white pine. Proc Natl Acad Sci U S A 2004; 101:10107-12. [PMID: 15220484 PMCID: PMC454172 DOI: 10.1073/pnas.0401513101] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The endophytic fungi of woody plants may be diverse as often claimed, and likewise, they may be functionally novel as demonstrated in a few studies. However, the endophyte taxa that are most frequently reported tend to belong to fungal groups composed of morphologically similar endophytes and parasites. Thus, it is plausible that endophytes are known (i.e., described) parasites in a latent phase within the host. If this null hypothesis were true, endophytes would represent neither additional fungal diversity distinct from parasite diversity nor a symbiont community likely to be novel ecologically. To be synonymous with parasites of the host, endophytes should at least be most closely related to those same parasites. Here we report that seven distinct parasites of Pinus monticola do not occur as endophytes. The majority of endophytes of P. monticola (90% of 2,019 cultures) belonged to one fungal family, the Rhytismataceae. However, not a single rhytismataceous endophyte was found to be most closely related by sequence homology to the three known rhytismataceous parasites of P. monticola. Similarly, neither endophytic Mycosphaerella nor endophytic Rhizosphaera isolates were most closely related to known parasites of P. monticola. Morphologically, the endophytes of P. monticola can be confounded with the parasites of the same host. However, they are actually most closely related to, but distinct from, parasites of other species of Pinus. If endophytes are generally unknown species, then estimates of 1 million endophytes (i.e., approximately 1 in 14 of all species of life) seem reasonable.
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Affiliation(s)
- Rebecca J Ganley
- Department of Forest Resources, University of Idaho, Moscow, 83844, USA
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