Quantification and Diversity of Cultivated Bacteria in Root Endosphere and Rhizosphere of Bamboo Species Fargesia nitida in Association with the Tree Succession
Microbiology Research Journal International, Volume 33, Issue 1,
Page 1-16
DOI:
10.9734/mrji/2023/v33i11358
Abstract
Fargesia nitida is a cold-resistant evergreen bamboo and is a pioneer plant in the secondary succession after the native trees were destroyed in the eastern Tibetan Plateau. However, little is known about the effects of this plant on soil conditions and about its microbiomes. Aiming at learning the interactions among the soil characteristics, the plants and the microbes in relation to the plant succession, a study on cultivated microbes associated with the rhizocompartments of F. nitida was performed in the present study to reveal the preference of this plant to the root associated microbes, in comparison with that associated with the successive spruce (Picea asperata Mast.) trees. The results demonstrated that growth of F. nitida could improve the soil nutrient contents, especially increasing total nitrogen, NH4+-N, total carbon, and microbial biomass carbon, and maintained more soil bacteria than the successive spruce trees. Based upon the study of F. nitida root-associated cultivated microbial community, the nutrient improvement in F. nitida growing soils might be from the root endophytic bacteria, which presented greater abundance (3.8, 1.7, and 12.6 folds) than that of bacteria in its rhizosphere, root zone soil, and spruce root zone soil, respectively. Pseudomonas members, especially species related to P. baetica and P. vancouverensis, were strongly selected by F. nitida as root endophytes.
- Bamboo
- cultivated microbiome
- plant succession
- soil
- pseudomonas
How to Cite
References
Editorial Committee of Chinese Flora. Chinese Flora. 1996; 9(1):425. Science Publishing, Beijing (in Chinese).
Xu B, Wang J, Shi F, Wu N. Relationships between plant colonization and soil characteristics in the natural recovery of an earthquake-triggered debris flow gully in the Wanglang National Nature Reserve, China. J Mt Sci. 2016; 13:59–68.
Wang H, Zhong H, Hou R, Ayala J, Liu G, Yuan S, Yan Z, Zhang W, Liu Y, Cai K, Cai Z, Huang H, Zhang Z, Wu D. A diet diverse in bamboo parts is important for giant panda (Ailuropoda melanoleuca) metabolism and health. Sci Rep. 2017; 7:3377.
Li Z-H, Manfred D. Elevational diversity of arrow bamboo (Fargesia spathacea) communities on Mount Shennongjia in Central China. J Forest Rese. 2002; 13:171–176.
Ramful R, Sunthar TPM, Kamei K, Pezzotti G. Investigating the antibacterial characteristics of Japanese bamboo. Antibiotics. 2022; 11:569.
Liu F, Yuan Z, Zhang X, Zhang G, Xie B. Characteristics and diversity of endophytic bacteria in moso bamboo (Phyllostachys edulis) based on 16S rDNA sequencing. Arch Microbiol. 2017; 199:1259–1266.
Román-Ponce B, Ramos-Garza J, Vásquez-Murrieta MS, Rivera-Orduña FN, Chen WF, Yan J, Estrada-de Los Santos P, Wang ET. Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants. Arch Microbiol. 2016; 198:941–956.
Zhang J, Wang ET, Singh RP, Guo C, Shang Y, Chen J, Liu C. Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China. J Appl Microbiol. 2019; 126:204–214.
Compant S, Clément C, Sessitsch A. Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem. 2010; 42:669e678.
Orozco-Mosqueda M, Rocha-Granados M, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res. 2018; 208:25–31.
Cordero J, de Freitas JR, Germida JJ. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can J Microbiol. 2020; 66:71–85.
Luo L, Guo M, Wang E, Yin C, Wang Y, He H, Zhao C. Effects of mycorrhiza and hyphae on the response of soil microbial community to warming in eastern Tibetan Plateau. Sci Total Environ. 2022; 837:155498.
Zhang YM, Li Y Jr, Chen WF, Wang ET, Tian CF, Li QQ, Zhang YZ, Sui XH, Chen WX. Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol. 2011; 77:6331-6342.
Yu P, Hochholdinger F. The role of host genetic signatures on root–microbe interactions in the rhizosphere and endosphere. Front Plant Sci. 2018; 9:1896.
Zhang YZ, Wang ET, Li M, Li QQ, Zhang YM, Zhao SJ, Jia XL, Zhang LH, Chen WF, Chen WX. Effects of rhizobial inoculation, cropping systems and growth stages on endophytic bacterial community of soybean roots. Plant Soil. 2011; 347:147–161.
Xiao X, Chen W, Zong L, Yang J, Jiao S, Lin Y, Wang E, Wei G. Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments. Mol Ecol. 2017; 26:1641–1651.
Xiao X, Li G, Zai X, Bai W, Wang E, Wei G, Chen W. Compositional response of Phaseolus vulgaris rhizomicrobiome to a changing soil environment is regulated by long-distance plant signaling. Plant Soil. 2019; 442: 257–269.
WRB IWG. World Reference Base for Soil Resources. World Soil Resources Reports. 2006; No. 103. FAO, Rome.
Wang J, Wu Y, Zhou J, Bing H, Sun H. Carbon demand drives microbial mineralization of organic phosphorus during the early stage of soil development. Biol Fert Soils. 2016; 52:825–839.
Olsen SR, Cole CV. Estimation of available P in soils by extraction with sodium bicarbonate. USDA Circular 939. 1954.
Mc Lean E, Watson M. Soil measurements of plant‐available potassium. In R.D. Munson (ed.) Potassium in Agriculture, pp.277-308. ASA, CSSA, and SSSA Books. 1985.
Vance ED, Brookes PC, Jenkinson DS. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem. 1987; 19: 703–707.
Fließbach A, Oberholzer H, Gunst L, Mader P. Soil organic matter and biological soil quality indicators after 21 years of organic and conventional farming. Agric Ecosyst Environ 2006; 118:273–284.
Wang ET, Tan ZY, Guo XW, Rodriguez-Duran R, Boll G, Martinez-Romero E. Diverse endophytic bacteria isolated from a leguminous tree Conzattia multiflora grown in Mexico. Arch Microbiol. 2006; 186:251–259.
Okon Y, Albrecht SL, Burris RH. Methods for growing Spirillum lipoferum and for counting it in pure culture and in association with plants. Appl Environ Microbiol. 1977; 33:85–88.
Kundu BS, Dadarwal KR, Tauro P. Nitrification and simultaneous denitrification by Azospirillum brasilense 12S. J Biosci. 1987; 12:51–54.
Charlot G. Colorimetric Determination of Elements. Principles and Methods. Elsevier Publishing Co., New York. 1965.
Van Berkum, Beyene D, Eardly BD. Phylogenetic relationships among Rhizobium species nodulating the common bean (Phaseolus vulgaris L.). Int J Syst Bacteriol. 1996; 46:240–244.
Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991;173:697–703.
Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014; 64:346–351
Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006; 33:152–155.
Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016; 33:1870–1874.
Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981; 17:368–376.
Glickmann E, Dessaux Y. A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol. 1995; 61:793–796.
Pikovskaya RI. Mobilization of phosphorus in soil in connection with the vital activity of some microbial species. Mikrobiologiya. 1948; 17:362–370.
Schwyn B, Neilands JB. Universal chemical assay for the detection and determination of siderophores. Anal Biochem. 1987; 160:47–56.
Louden BC, Haarmann D, Lynne AM. Use of blue agar CAS assay for siderophore detection. J Microbiol Biol Educ. 2011; 12:51–53.
Jacoby R, Peukert M, Succurro A, Koprivova A, Kopriva S. The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions. Front Plant Sci. 2017; 8:1617.
Han L-L, Wang Q, Shen J-P, Di HJ, Wang J-T, Wei W-X, Fang Y-T, Zhang L-M, He J-Z. Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China. FEMS Microbiol Ecol. 2019; 95:fiz113.
Xu X, Peter E, Thornton PE, Post WM. A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Global Ecol Biogeogr. 2013; 22:737–749.
Moore JM, Klose S, Tabatabai MA. Soil microbial biomass carbon and nitrogen as affected by cropping systems. Biol Fertil Soils. 2000; 31:200–210.
Silva-Parra A, Mogollón-Ortiz ÁM., Delgado-Huertas H. Soil microbiota: Influence of different land use patterns and soil management factors at Villavicencio Oxisol, East Colombia. Biota Colomb. 2017; 18:1-10.
Vieira FCS, Nahas E. Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiol Res. 2005; 160:197–202.
Tanase C, Cosarca S, Toma F, Mare A, Cosarca A, Man A, Miklos A, Imre S. Antibacterial activities of spruce bark (Picea abies L.) extract and its components against human pathogens. Rev Chim (Bucharest). 2018; 69:1462–1467.
Shi Y, Yang H, Chu M, Niu X, Wang N, Lin Q, Lou K, Zuo C, Wang J, Zou Q, Zhang Y. Differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton (Gossypium sp.). Front Microbiol. 2021; 12:765269.
Szymańska S, Płociniczak T, Piotrowska-Seget Z, Hrynkiewicz K. Endophytic and rhizosphere bacteria associated with the roots of the halophyte Salicornia europaea L. – community structure and metabolic potential. Microbiol Res. 2016; 192: 37–51.
Afrin T., Tsuzuki T., Kanwar R.K. and Wang X. The origin of the antibacterial property of bamboo. J Text Inst 2012. 103:844–849.
Tanaka A, Shimizu K, Kondo R. Antibacterial compounds from shoot skins of moso bamboo (Phyllostachys pubescens). J Wood Sci. 2013; 59:155–159.
Rossi-Tamisier M, Benamar S, Raoult D, Fournier PE. Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. Int J Syst Evol Microbiol. 2015; 65:1929–1934.
Ke X, Feng S, Wang J, Lu W, Zhang W, Chen M, Lin M. Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere. Syst Appl Microbiol. 2019; 42:248–260.
Li HB, Singh RK, Singh P, Song QQ, Xing YX, Yang LT, Li YR. Genetic diversity of nitrogen-fixing and plant growth promoting Pseudomonas species isolated from sugarcane rhizosphere. Front Microbiol. 2017; 8:1268.
Samaddar S, Chatterjee P, Choudhury AR, Ahmed S, Sa T. Interactions between Pseudomonas spp. and their role in improving the red T pepper plant growth under salinity stress. Microbiol Res. 2019; 219:66–73.
Xia Q, Rufty T, Shi W. Predominant microbial colonizers in the root endosphere and rhizosphere of turfgrass systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp. Front Microbiol. 2021; 12:643904.
Zhang L, Zhang W, Li Q, Cui R, Wang Z, Wang Y, Zhang Y-Z, Ding W, Shen X. Deciphering the root endosphere microbiome of the desert plant Alhagi sparsifolia for drought resistance-promoting bacteria. Appl Environ Microbiol. 2020; 86:e02863-19.
Afriyani, Maulidia V, Alfizar, Sriwati R. Endophytic bacteria (genus: Pseudomonas spp.) isolated from Aceh bamboo root as biological agent againts nematode Meloidogyne spp. IOP Conf Ser: Earth Environ Sci. 2020; 425:012074.
Singh L, Ruprela N, Dafale N, Thul S.T. Variation in endophytic bacterial communities associated with the rhizomes of tropical bamboos. J Sustain For. 2021; 40:111–123.
López JR, Diéguez AL, Doce A, De la Roca E, De la Herran R, Navas JI, Toranzo AE, Romalde JL. Pseudomonas baetica sp. nov., a fish pathogen isolated from wedge sole, Dicologlossa cuneata (Moreau). Int J Syst Evol Microbiol. 2012; 62:874–888.
Zhang CW, Tian XY, Zhang C-S. Diversity and probiotic activities of endophytic bacteria associated with the coastal halophyte Messerschmidia sibirica. Appl Soil Ecol. 2019; 143:30.
Karimzadeh J, Alikhani HA, Etesami H, Pourbabaei AA. Improved phosphorus uptake by wheat plant (Triticum aestivum L.) with rhizosphere fluorescent pseudomonads strains under water-deficit stress. J Plant Growth Regul. 2021; 40:162–178.
Nongkhlaw FMW, Joshi SR. Epiphytic and endophytic bacteria that promote growth of ethnomedicinal plants in the subtropical forests of Meghalaya, India. Rev Biol Trop. 2014; 62:1295–1308.
Yao R, Dai Q, Wu T, Yang Z, Chen H, Liu G, Zhu Y, Qi D, Yang X, Luo W, Gu X, Yang X, Zhu L. Fly-over phylogeny across invertebrate to vertebrate: The giant panda and insects share a highly similar gut microbiota. Computat Structural Biotechnol J. 2021; 19:4676–4683.
Tvrzová L, Schumann P, Spröer C, Sedláček I, Páčová Z, Šedo O, Zdráhal Z, Steffen M, Lang E. Pseudomonas moraviensis sp. nov. and Pseudomonas vranovensis sp. nov., soil bacteria isolated on nitroaromatic compounds, and emended description of Pseudomonas asplenii. Int J Syst Evol Microbiol. 2006; 56:2657–2663.
Subramanian P, Kim K, Krishnamoorthy R, Mageswari A, Selvakumar G, Sa T. Cold stress tolerance in psychrotolerant soil bacteria and their conferred chilling resistance in tomato (Solanum lycopersicum Mill.) under low temperatures. PLoS ONE. 2016; 11:e0161592.
Mikiciński A, Puławska J, Molzhigitova A, Sobiczewski P. Bacterial species recognized for the first time for its biocontrol activity against fire blight (Erwinia amylovora). Eur J Plant Pathol. 2020; 156:257–272.
Samadi A, Hassani A, Gholamhoseini M. Effect of potassium solubilizing biofertilizers application compared to potassium sulfate on growth and some physiological traits of radish (Raphanus sativus L.) under drought stress. J Hortic Sci. 2021; 34:633–643.
Surhone LM, Tennoe MT, Henssonow SF. Pseudomonas vancouverensis. Betascript Publishing. PP. 68. 2011.
Han JG, Xia DL, Li LB, Sun L, Yang K, Zhang LP. Diversity of culturable bacteria isolated from root domains of Moso bamboo (Phyllostachys edulis). Microb Ecol. 2009; 58:363–373.
Yuan Z-S, Liu F, Zhang G-F. Isolation of culturable endophytic bacteria from moso bamboo (Phyllostachys edulis) and 16S rDNA diversity analysis. Arch Biol Sci Belgrade. 2015; 67:1001–1008.
Moshynets O, Brunet J, Potters G. Identification of endophytic bacteria in Phyllostachys sp. and Fargesia sp. Bamboo Sci Cul. 2012; 25:19–26.
Mohanty P, Singh PK, Chakraborty D, Mishra S, Pattnaik P. Insight into the role of PGPR in sustainable agriculture and environment. Front Sustain Food Syst. 2021; 5:667150.
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