Geographical Isolation and Root-Associated Fungi in the Marine Terrains: A Step Toward Establishing a Strategy for Acquiring Unique Microbial Resources

References

• Ryan MJ, McCluskey K, Verkleij G, et al. Fungal biological resources to support international development: challenges and opportunities. World J Microbiol Biotechnol. 2019;35(9):139.
   Web of Science ®Google Scholar
• Kevin M. A review of living collections with special emphasis on sustainability and its impact on research across multiple disciplines. Biopreserv Biobank. 2017;15(1):20–30.
   Web of Science ®Google Scholar
• Park JM, Hong JW, Son JS, et al. A strategy for securing unique microbial resources—focusing on Dokdo islands-derived microbial resources. Israel J Ecol Evol. 2018;64(1–4):1–11.
   Web of Science ®Google Scholar
• Bloemberg GV, Lugtenberg BJ. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol. 2001;4:343–350.
   PubMed Web of Science ®Google Scholar
• Li HB, Singh RK, Singh P, et al. Genetic diversity of nitrogen-fixing and plant growth promoting Pseudomonas species isolated from sugarcane rhizosphere. Front Microbiol. 2017;14(8):1268.
   Google Scholar
• Rohini S, Aswani R, Kannan M, et al. Culturable endophytic bacteria of ginger rhizome and their remarkable multi-trait plant growth-promoting features. Curr Microbiol. 2017;75:505–511.
   Web of Science ®Google Scholar
• Wang Z, Li T, Wen X, et al. Fungal communities in rhizosphere soil under conservation tillage shift in response to plant growth. Front Microbiol. 2017;11(8):1301.
   Google Scholar
• Park JM, Hong JW, Lee W, et al. Fungal clusters and their uniqueness in geographically segregated wetlands: a step forward to marsh conservation for a wealth of future fungal resources. Mycobiology. 2020;48(5):351–363.
   PubMed Web of Science ®Google Scholar
• Ministry of Environment, Republic of Korea. The Fifth national report to the convention on biological diversity [Internet]. Sejong (South Korea): MoE; 2014 [cited 2019 October 19]. Available from: https://www.cbd.int/nr5/
   Google Scholar
• Ministry of Environment, Republic of Korea. Report: conservation and sustainable use of biological resources [Internet]. Sejong (South Korea): MoE; 2015 [cited 2019 October 19]. Available from: http://hdl.handle.net/20.500.11822/9049
   Google Scholar
• Lucas M, Balbín-Suárez A, Smalla K, et al. Root growth, function, and rhizosphere microbiome analyses show local rather than systemic effects in apple plant response to replant disease soil. PLoS One. 2018;13(10):e0204922.
   Web of Science ®Google Scholar
• Wu L, Chen J, Xiao Z, et al. Barcoded pyrosequencing reveals a shift in the bacterial community in the rhizosphere and rhizoplane of Rehmannia glutinosa under consecutive monoculture. Int J Mol Sci. 2018;19(3):850.
   Web of Science ®Google Scholar
• Yang Y, Dou Y, Huang Y, et al. Links between soil fungal diversity and plant and soil properties on the Loess plateau. Front Microbiol. 2017;78:2198.
   Google Scholar
• Zhang Z, Zhou X, Tian L, et al. Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China. PLoS One. 2017;12(12):e0187575.
   Web of Science ®Google Scholar
• Lee DS. Geology of Korea. Seoul (Republic of Korea): Kyohak-sa; 1987.
   Google Scholar
• Kong WS, David W. The plant geography of Korea with an emphasis on the alpine zones. Berlin (Germany): Springer; 1993.
   Google Scholar
• Thorpe RS, Surget-Groba Y, Johansson H. Genetic tests for ecological and allopatric speciation in anoles on an island archipelago. PLoS Genet. 2010;6(4):e1000929.
   Web of Science ®Google Scholar
• Zhao C, Wang CB, Ma XG, et al. Phylogeographic analysis of a temperate-deciduous forest restricted plant (Bupleurum longiradiatum Turcz.) reveals two refuge areas in China with subsequent refugial isolation promoting speciation. Mol Phylogenet Evol. 2013;68(3):628–643.
   Web of Science ®Google Scholar
• NGII (National Geographic Information Institute). The geography of Dokdo. Suwon (Republic of Korea): Press of National Geographic Information Institute; 2015.
   Google Scholar
• You YH, Park JM, Park JH, et al. Specific rhizobacterial resources: characterization and comparative analysis from contrasting coastal environments of Korea. J Basic Microbiol. 2016;56(1):92–101.
   Web of Science ®Google Scholar
• CHA (Cultural Heritage Administration), Republic of Korea. Natural heritage of Korea, Dokdo, Cultural Heritage Administration of Korea. Daejeon (Republic of Korea): Cultural Heritage Administration; 2009.
   Google Scholar
• FAO. Guidelines for soil description. 4th ed. Rome (Italy): Food and Agriculture Organisation of the United States; 2006.
   Google Scholar
• Flores-Vargas RD, O’Hara GW. Isolation and characterization of rhizosphere bacterial with potential for biological control of weed in vineyards. J Appl Microbiol. 2006;100(5):946–954.
   Web of Science ®Google Scholar
• Vega NOW. A review on beneficial effects of rhizosphere bacterial on soil nutrient availability and plant nutrient uptake. Rev Fac Nac Agron Medellín. 2007;60(1):3621–3643.
   Google Scholar
• U.S. Salinity Lab Staff. Diagnosis and improvement of saline and alkali soils. In: Richards LA, editor. Agriculture handbook 60. Washington (DC): USDA; 1954. p. 122–124.
   Google Scholar
• FAO, United Nations. Standard operating procedure for soil organic carbon, Walkley-Black method (Titration and colorimetric method). Rome (Italy): Global Soil Laboratory; 2019.
   Google Scholar
• Bremner JM, Mulvaney CS. Nitrogen total. In: Page AL, editor. Methods of soil analysis: part 2 chemical and microbiological properties, 9.2.2. 2nd ed. Madison (WI): American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America; 1983.
   Google Scholar
• Masella AP, Bartram AK, Truszkowski JM, et al. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinf. 2012;13(1):31.
   PubMed Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, et al. Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–7541.
   PubMed Web of Science ®Google Scholar
• Bengtsson Palme J, Ryberg M, Hartmann M, et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4(10):914–919.
   Web of Science ®Google Scholar
• Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–2200.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–2461.
   PubMed Web of Science ®Google Scholar
• Abarenkov K, Nilsson RH, Larsson KH, et al. The UNITE database for molecular identification of fungi—recent updates and future perspectives. New Phytol. 2010;186:281–285.
   PubMed Web of Science ®Google Scholar
• Heck KL, van Belle G, Simberloff D. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology. 1975;56(6):1459–1461.
   Web of Science ®Google Scholar
• Lambshead PJD, Platt HM, Shaw KM. The detection of differences among assemblages of marine benthic species based on an assessment of dominance and diversity. J Nat Hist. 1983;17(6):859–874.
   Web of Science ®Google Scholar
• Chao A, Shen TJ, Ma KH, et al. User's guide for program SPADE (Species Prediction And Diversity Estimation). Taiwan: National Tsing Hua University; 2016 [cited 2019 Dec 18]. Available from: http://chao.stat.nthu.edu
   Google Scholar
• Sonn YK, Park CW, Zhang YS, et al. Characteristics of soils distributed on the Dokdo Island in South Korea. Korean J Soil Sci. 2011;44(2):187–193.
   Google Scholar
• Chapman VJ. Salt marshes and salt deserts of the world. In: Polunin N, editor. Ecology of halophytes. New York (NY): Academic Press; 1974.
   Google Scholar
• Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci USA. 2007;104:11436–11440.
   PubMed Web of Science ®Google Scholar
• Ma B, Gong J. A meta- analysis of the publicly available bacterial and archaeal sequence diversity in saline soils. World J Microbiol Biotechnol. 2013;29:2325–2334.
   PubMed Web of Science ®Google Scholar
• Tazi L, Breakwell DP, Harker AR, et al. Life in extreme environments: microbial diversity in Great Salt Lake, Utah. Extremophiles. 2014;18(3):525–535.
   Web of Science ®Google Scholar
• Zain Ul Arifeen M, Ma YN, Xue YR, et al. Deep-Sea fungi could be the new arsenal for bioactive molecules. Mar Drugs. 2019;18(1):9.
   Web of Science ®Google Scholar
• Blaud A, Lerch TZ, Phoenix GK, et al. Arctic soil microbial diversity in a changing world. Res Microbiol. 2015;166(10):796–813.
   Web of Science ®Google Scholar
• Otlewska A, Migliore M, Dybka-Stępień K, et al. When salt meddles between plant, soil, and microorganisms. Front Plant Sci. 2020;16(11):553087.
   Google Scholar
• Haegeman B, Hamelin J, Moriarty J, et al. Robust estimation of microbial diversity in theory and in practice. ISME J. 2013;7:1092–1101.
   Web of Science ®Google Scholar
• Magurran AE. Measuring biological diversity. Oxford (UK): Blackwell Science; 2004.
   Google Scholar
• Chao A, Gotelli NJ, Hsieh TC, et al. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol Monogr. 2014;84(1):45–67.
   Web of Science ®Google Scholar
• Gong Y, Son SJ. A study of oceanic thermal fronts in the Southern Japan Sea. Bull Fish Res Dev Agency. 1982;28:25–54.
   Google Scholar
• Park B, Kang GW, Song GM, et al. Ten newly recorded species of insect on Dokdo Island, South Korea. J Species Res. 2017;6(3):280–290.
   Google Scholar
• Johnson NC, Graham JH, Smith FA. Functioning of mycorrhizal associations along the mutualism–parasitism continuum. New Phytol. 1997;135(4):575–585.
   Web of Science ®Google Scholar
• Bäumler A, Fang FC. Host specificity of bacterial pathogens. Cold Spring Harb Perspect Med. 2013;3(12):a010041.
   PubMed Web of Science ®Google Scholar
• Morris CE, Moury B. Revisiting the concept of host range of plant pathogens. Annu Rev Phytopathol. 2019;57:63–90.
   PubMed Web of Science ®Google Scholar
• Sati SC, Belwal M. Aquatic hyphomycetes as endophytes of riparian plant roots. Mycologia. 2005;97(1):45–49.
   Web of Science ®Google Scholar
• Quilliam RS, Jones DL. Fungal root endophytes of the carnivorous plant Drosera rotundifolia. Mycorrhiza. 2010;20(5):341–348.
   Web of Science ®Google Scholar
• Sapkota R, Jørgensen LN, Nicolaisen M. Spatiotemporal variation and networks in the mycobiome of the wheat canopy. Front Plant Sci. 2017;8:1357.
   Web of Science ®Google Scholar
• Renker C, Blanke V, Börstler B, et al. Diversity of Cryptococcus and Dioszegia yeasts (Basidiomycota) inhabiting arbuscular mycorrhizal roots or spores. FEMS Yeast Res. 2004;4(6):597–603.
   PubMed Web of Science ®Google Scholar
• Nehls U. Review Mastering ectomycorrhizal symbiosis: the impact of carbohydrates. J Exp Bot. 2008;59(5):1097–1108.
   Web of Science ®Google Scholar
• Chen K, Wu XQ, Huang MX, et al. First report of brown culm streak of Phyllostachys praecox caused by Arthrinium arundinis in Nanjing, China. Plant Dis. 2014;98(9):1274.
   Web of Science ®Google Scholar
• Palenzuela J, Barea JM, Ferrol N, et al. Entrophospora nevadensis, a new arbuscular mycorrhizal fungus from Sierra Nevada National Park (southeastern Spain). Mycologia. 2010;102(3):624–632.
   Web of Science ®Google Scholar
• Amna T, Puri SC, Verma V, et al. Bioreactor studies on the endophytic fungus Entrophospora infrequens for the production of an anticancer alkaloid camptothecin. Can J Microbiol. 2006;52(3):189–196.
   PubMed Web of Science ®Google Scholar
• Busby PE, Ridout M, Newcombe G. Fungal endophytes: modifiers of plant disease. Plant Mol Biol. 2016;90(6):645–655.
   PubMed Web of Science ®Google Scholar
• Araújo CAS, Dias LP, Ferreira PC, et al. Responses of entomopathogenic fungi to the mutagen 4-nitroquinoline 1-oxide. Fungal Biol. 2018;122(6):621–628.
   Web of Science ®Google Scholar
• Toju H, Tanabe AS, Sato H. Network hubs in root-associated fungal metacommunities. Microbiome. 2018;6(1):116.
   Google Scholar
• Jaber E, Xiao C, Asiegbu FO. Comparative pathobiology of Heterobasidion annosum during challenge on Pinus sylvestris and Arabidopsis roots: an analysis of defensin gene expression in two pathosystems. Planta. 2014;239(3):717–733.
   PubMed Web of Science ®Google Scholar
• Barelli L, Waller AS, Behie SW, et al. Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil. PLoS One. 2020;15(4):e0231150.
   Web of Science ®Google Scholar
• Lovett B, St Leger RJ. Stress is the rule rather than the exception for Metarhizium. Curr Genet. 2015;1(3):253–261.
   Google Scholar
• Karakkat BB, Hockemeyer K, Franchett M, et al. Data for designing two isothermal amplification assays for the detection of root-infecting fungi on cool-season turfgrasses. Data Brief. 2018;20:471–479.
   Web of Science ®Google Scholar
• Xu F, Yang G, Wang J, et al. Spatial distribution of root and crown rot fungi associated with winter wheat in the north china plain and its relationship with climate variables. Front Microbiol. 2018;25:9.
   Google Scholar
• Xu J, Saunders CW, Hu P, et al. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci USA. 2007;104(47):18730–18735.
   Web of Science ®Google Scholar
• Kamel NM, Abdel-Motaal FF, El-Zayat SA. Endophytic fungi from the medicinal herb Euphorbia geniculata as a potential source for bioactive metabolites. Arch Microbiol. 2020;202(2):247–255.
   Web of Science ®Google Scholar
• Zhong X, Peng QY, Li SS, et al. Detection of Ophiocordyceps sinensis in the roots of plants in alpine meadows by nested-touchdown polymerase chain reaction. Fungal Biol. 2014;118(4):359–363.
   Web of Science ®Google Scholar
• Wang JB, St LR. Wang C. Advances in genomics of entomopathogenic fungi. Adv Genet. 2016;94:67–105.
   Web of Science ®Google Scholar
• Cullings K, Makhija S. Ectomycorrhizal fungal associates of Pinus contorta in soils associated with a hot spring in Norris Geyser Basin, Yellowstone National Park, Wyoming. Appl Environ Microbiol. 2001;67(12):5538–5543.
   Web of Science ®Google Scholar
• Barton LL, Northup DE. Microbial ecology. Hoboken (NJ): Wiley-Blackwell; 2011.
   Google Scholar
• Park JM, You YH, Back CG, et al. Fungal load in Bradysia agrestis, a phytopathogen-transmitting insect vector. Symbiosis. 2018;74(2):145–158.
   Web of Science ®Google Scholar
• Park JM, You YH, Park JH, et al. Cutaneous microflora from geographically isolated groups of Bradysia agrestis, an insect vector of diverse plant pathogens. Mycobiology. 2017;45(3):160–171.
   PubMed Web of Science ®Google Scholar
• Baker DK, Rice SJ, Leemon DM, et al. Horizontal transmission of Metarhizium anisopliae (Hypocreales: Clavicipitacea) and the effects of infection on oviposition rate in laboratory populations of Musca domestica (Diptera: Muscidae). Pest Manag Sci. 2017;74(4):987–991.
   Web of Science ®Google Scholar
• Liao X, Lovett B, Fang W, et al. Metarhizium robertsii produces indole-3-acetic acid, which promotes root growth in Arabidopsis and enhances virulence to insects. Microbiology. 2017;163(7):980–991.
   Web of Science ®Google Scholar
• Masoudi A, Koprowski JL, Bhattarai UR, et al. Elevational distribution and morphological attributes of the entomopathogenic fungi from forests of the Qinling mountains in China. Appl Microbiol Biotechnol. 2017;102(3):1483–1499.
   Web of Science ®Google Scholar
• Mukherjee K, Vilcinskas A. The entomopathogenic fungus Metarhizium robertsii communicates with2the insect host Galleria mellonella during infection. Virulence. 2017;9(1):402–413.
   Web of Science ®Google Scholar
• Pelizza SA, Schalamuk S, Simón MR, et al. Compatibility of chemical insecticides and entomopathogenic fungi for control of soybean defoliating pest, Rachiplusia nu. Rev Argent Microbiol. 2017;50(2):189–201.
   Web of Science ®Google Scholar
• Wilke AB, Marrelli MT. Paratransgenesis: a promising new strategy for mosquito vector control. Parasit Vectors. 2015;8:342.
   PubMed Web of Science ®Google Scholar
• Ashraf M, Farooq M, Shakeel M, et al. Influence of entomopathogenic fungus, Metarhizium anisopliae, alone and in combination with diatomaceous earth and thiamethoxam on mortality, progeny production, mycosis, and sporulation of the stored grain insect pests. Environ Sci Pollut Res Int. 2017;24(36):28165–28174.
   PubMed Web of Science ®Google Scholar
• Kabaluk T, Li-Leger E, Nam S. Metarhizium brunneum - An enzootic wireworm disease and evidence for its suppression by bacterial symbionts. J Invertebr Pathol. 2017;150:82–87.
   Web of Science ®Google Scholar
• Alexopoulos CJ, Mims CW, Blackwell M. Introductory mycology. 4th ed. Hoboken (NJ): John Wiley & Sons, Inc.; 1996.
   Google Scholar
• Hameed A, Gulzar S, Aziz I, et al. Effects of salinity and ascorbic acid on growth, water status, and antioxidant system in a perennial halophyte. AoB Plants. 2015;7:1–11.
   Web of Science ®Google Scholar