Bacterial Communitie’s Diversity of Rhizosphere’s Soils of Two Legumes, Cajanus cajan and Milletia laurentii, Revealed by Illumina Miseq Sequencing of 16S rRNA Gene

Alvychelle Benith Banga^{1, 2,} , Augustin Aimé Lebonguy¹, Angélique Espérance Lembella Boumba^{1, 3} and Joseph Goma-Tchimbakala^{1, 3}

¹Institut National de Recherche en Sciences Exactes et Naturelles, Brazzaville République du Congo

²Faculté des Sciences et Techniques, Brazzaville, République du Congo

³Ecole Nationale Supérieure d’Agronomie et de Foresterie, Brazzaville République du Congo

Cite this paper

Alvychelle Benith Banga, Augustin Aimé Lebonguy, Angélique Espérance Lembella Boumba and Joseph Goma-Tchimbakala. Bacterial Communitie’s Diversity of Rhizosphere’s Soils of Two Legumes, Cajanus cajan and Milletia laurentii, Revealed by Illumina Miseq Sequencing of 16S rRNA Gene. World Journal of Agricultural Research. 2022; 10(1):20-29. doi: 10.12691/WJAR-10-1-4

Abstract

Microbial organic fertilizers have been shown to boost plant productivity. These microorganisms of interest are more numerous in the soil around the roots or rhizosphere. Objective of this study was to assess bacterial communities’ diversity of in the rhizosphere of two legumes, Milletia laurentii and Cajanus cajan, growing on the same soil. First of all, the levels Mg, N, Fe, C total, P, NH₄⁺ and particle size were determined by spectrophotometry, Kjeldahl method, Olsen method, Walkey-Black method, Nessler reagent, DEB method and Robinson pipette method, respectively. Next, bacterial diversity was determined by Sequencing Illumina Miseq of 16S rRNA gene. Results showed that contents of carbon, total nitrogen, ammoniacal nitrogen, phosphorus, iron and magnesium were slightly elevated in Milletia rhizosphere compared to Cajanus. According to the USDA's textural triangle, both soils have a sandy loam soil texture. In terms of diversity, all OTUs (1434) were divided into 30 phyla, 50 classes, 158 families and 314 genera for the 2 soils. Proteobacteria (58.62% - 48.71%), Acidobacteria (27.29% - 9.46%), Firmicutes (8.26% - 7.21%) and Bacteroidetes (13.70% - 2.53%) were most dominant phyla in both rhizospheres (Cajanus - Milletia). The most dominant classes were Alphaproteobacteria (51.44% - 38.90%), Acidobacteriia (26.57% - 8.67%), Bacilli (8.19% - 7.18%), Sphingobacteria (9.83% - 2.50%) and Gammaproteobacteria (4.27% - 3.39%). At the family level, Hyphomicrobiaceae (35.05%-24.22%), Bradyrhizobiaceae (17.32%-11.70%) and Bacillaceae (18.98%-6.49%) were most abundant. Finally, Acidobacterium (26.55%-4.58%), Rhodoplanes (21.63%-7.50%), Bradyrhizobium (17.27%-1.96%) and Bacillus (6.43%-6.29%) were the most abundant genera. Thus, bacterial diversity of the rhizosphere of these two legumes encourages their use for the isolation of bacteria with biofertilizing potential.

Keywords

Illumina - Miseq, rhizosphere, bacterial diversity

Copyright

This work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

References

[1]	Kumar S., Satyavir S.D., Kumar R.S., 2022. Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability. Current Research in Microbial Sciences 3(2022) 1000094.
[2]	Buta M., Korzeniewska E., Harnisz M., Hebeny J., Zielinski W., Rolbiecki D., Bajkacz S., Felis E., Kokoszka K., 2021. Microbial and chemical polluants one the manure-crops pathway in the perspective of “One health” holistic approach. Science of the total Environment 785 (2021) 147411.
[3]	Felden B., Cattoira V., 2018. Bacterial adaptation to antibiotics through regulatory RNAs. Antimicrob. Agents Chemother. 62, 1-11.
[4]	Li S., Zou D., Li L., Wu L., Liu F., Zeng X., Wang H., Zhu Y. and Xiao Z. 2020. Evolution of heavy metals during thermal treatment of manure: A critical review and out looks. Chemosphere.
[5]	Borquez C., Frias-Espericueta M.G. and Voltolina D. 2016. Removal of cadmium and lead by adapted strains of Pseudomonas aeruginosa and Enterobacter cloacae. Rev. Int. Contam. Ambient. 32, 407-412.
[6]	Gallego S.M., Pena L.B., Barcia R.A., Azpilicueta C.E., Iannone M.F., Rosales E.P., Benavides M.P. 2012. Unravelling cadmium toxicity and tolerance in plants: insight into regulatory mechanisms. Environ. Exp. Bot 83, 33-46.
[7]	Okafor N. 2011. Pollution of aquatic systems: Pollution through eutrophication, fecal materials, and oil spills. Environmental Microbiology of aquatic and waste systems, 151-187.
[8]	Zhang M.M., Fan S.H., Guan F.Y. and Yin Z.X. 2020. Soil bacterial community structure of mixed bamboo and broad-leaved, Scientific reports, nature research, vol. 1(210). 6522.
[9]	Prashar P., Kapoor N., Sachdeva S. 2013. Rhizosphere: its structure, bacterial diversity and signifiance. Rev Environ Sci Biotechnol.
[10]	Mahanty T., Bhattacharjee S., Goswami M., Bhattacharyya P., Das B., Ghosh A and Tribedy P. 2016. Biofertilizers: a potentiel approach for sustainable agriculture development. Environ. Sci. Poll. Res. 23, 1-21.
[11]	Mazid M. and Khan T.A. 2015. Future of biofertilizers in Indian agriculture: an overview. International Journal of Agricultural and Food Research 3(3): 10-23.
[12]	Babolola O.O. and Igiehon O.N. 2017. Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi. Appl. Microbiol. Biotechnol 101: 4871-4881.
[13]	Aboubacar K., Ousmane Z.M., Amadou H.I., Issaka S., Zoubeirou A.M. 2013. Effect of rhizobial and mycorrhizal co-inoculation on the agronomic performance of cowpea [Vigna unguiculata (L.) Walp. ] in Niger. Journal of Applied Biosciences 72, 5846-5854.
[14]	Murgese P., Santamaria P., Leoni B. and Crecchio C. 2020. Ameliorative effects of PGPB on yield physiological parameters, and nutrient transporters gene expression in Barattiere (Cucumus melo L.). J. Soil. Sci. Plant. Nutr. 20,784-793.
[15]	Fasusi O.A., Cruz C., Babolola O.O. 2021. Agricultural sustainability: Microbial biofertilizers in rhizosphere management. Agriculture 11-163.
[16]	Mabiala S.T., Goma-Tchimbakala J., Goma-Tchimbakala E.J.C.D., Lebonguy A.A and Banga A.B. 2020. Diversity of the Bacterial Community of Three Soils Revealed by Illumina-Miseq Sequencing of 16S rRNA Gene in the South of Brazzaville, Congo. American Journal of Microbiological Research, vol. 8: 141-149.
[17]	Samba-Kimbata M.J. 1978. Le climat du Bas-Congo. Thèse 3ème cycle Géographie, Université de Dijon, Faculté des Sciences Humaines, Centre de recherche de climatologie, 280p.
[18]	Vennetier P. 1977. Climat In Atlas de la République Populaire du Congo. Les Editions Jeune Afrique, Paris (France), 10-15.
[19]	Nelson D.W. and Sommers L.E. 1982. Total carbon, organic carbon and organic matter, in Methods of soil analysis, Part 2 American Society of Agronomy, Madison, 1982, pp. 539-579.
[20]	Bremmer J.M. and Mulvaney C.S. 1982. Nitrogen-Total carbon, chez Methods of soil analysis, Chemical and Microbiological properties, American Society of Agronomy, Soil Science Society of Americana, Madison, 1982, 595-624.
[21]	Murphey J. and Riley P.P. 1962. A modified single solution method for the determination of phosphate in natural water. Anal. Chimim. Acta, vol. 27, pp.31-36.
[22]	Segalen P.P. 1971. La détermination du fer libre dans les sols à sesquioxydes, Cah. ORSTOM, sér. Pédol. Vol. 9(11), pp. 3-27.
[23]	Dabin B. 1967. Application des dosages automatiques à l’analyse des sols; 3ème partie, Cahiers ORSTOM, série Pédologie, vol (3), pp. 257-263.
[24]	Weil A. and Duval J. 2009. Les amendements organiques, fumiers et composts. Dans Guide de gestion globale de la ferme maraichère biologique et diversifiée; Module 7: Amendement et fertilisation. Equiterre; 1-19.
[25]	Alabouvette C. and Cordier C. 2018. Fertilité biologique des sols: des microorganismes utiles à la croissance des plantes. Innovations Agronomiques 69, 61-70.
[26]	Hamarashid N.H., Othman M.A. and Hussain M.A.H. 2010. Effects of soil texture on chemical compositions, microbial populations and carbon mineralization in soil, Egypt. J. Expp. Biol. (Bot), vol. 6(11), pp. 59-64.
[27]	Robin D. 1997. Interest of biochemical characterization for the evaluation of the proportion of stable organic matter after decomposition in soil and the classification of organomeral products. Agronomy, EDP Sciences 17(3), pp. 157-171.
[28]	Lauber C.L., Hamady M., Knight R. and Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol, vol. 75, pp. 5111-5120.
[29]	Janssen P.H. 2006. Identifying the dominant Soil Bacterial Taxa in Librairies of 16S rRNA Genes. Applied and Environmental Microbiology, 72, 1719-1728.
[30]	Putrie R.F.W., Aryantha I.P. and Antonius I.S. 2020. Diversity of endophytic and rhizosphere bacteria from pineaple (Ananas comosus) plant in semi arid ecosystem. Biodiversitas Vol 21, Number 7, pp: 3084-3093.
[31]	Ek-Ramos M.J., Gomez-Flores R., Orozco-Flores A.A., Rodriguez-Padilla C., Gonzalez-Ochoa G. and Tamez-Guerra P. 2009. Bioactive products from plant-endophytic Gram-Positive bacteria. Front Microbiol 10: 463
[32]	Klein E., Katan J. and Gamliel A. 2016. Soil suppressiveness by organic amendement to Fusarium disease in cucumber: Effect on pathogen and host. Phytoparasitica, vol. 44, pp. 239-249.
[33]	Qiu M., Zhang R., Xue C., Zhang S., Li S., Zhang N. and Shen Q. 2012. Application of bio-organic fertilizers can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil, Biol. Fertil. Soils, vol. 48, pp. 807-816.
[34]	Sun B., Dong Z.X., Zhang X.X., Li Y., Cao H. and Cui Z.L. 2011. Rice to Vegetables: Short-Versus Long-term Impact of Land-Use Change on the Indigenous Soil Microbial Community, Microb. Ecol. Vol. 1(262), pp. 474-485.
[35]	Alami M.M., Xue J., Ma Y., Zhu D., Gong Z., Shu S. and Wang X. 2020. Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields, Diversity, vol, 1(212), 57.
[36]	Kennedy A.C. and Smith K.L. 1995. Soil microbial diversity and the sustainability of agriculture soil, Plant Soil, vol. 170, pp. 75-86.
[37]	Antoun S.A. 2016. Bacterial Diversity in hyperarid Atacama Desert Soils. Journal of Geophysical Research: Biogeo sciences, 112, G04S17.
[38]	Francesco P., Frascella A., Santopolo L., Bazzicalupo M., Biondi E.G., Scotti C. and Mengoni A. 2012. Exploring the plant-associated bacterial communities in Medicago sativa L. BCM Microbiology 12: 78.
[39]	Uroz S., Marc B., Claude M., Pascal F.K. and Francis M. 2010. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environmental Microbiology Reports 2(2), 281-288.
[40]	Wang Q., Jiang X., Guan D., Wei D., Zhao B., Ma M., Chen S., Li L., Cao F. and Li L. 2017. Long-term fertilization changes bacterial communities in the maize rhizosphere of Chinese Mollisols. Applied Soil Ecology.
[41]	Xuan X., Liu L., He X., Wang K., Xie Q., O’Donnell A.G. and Chen C. 2015. The Bradyrhizobium-legume symbiosis is dominant in shrubby ecosystem of the karst region Southwest China. European Journal of Soil Biology 68 (2015) 1-8.
[42]	Barelli F., Santos F.L., 2021. Plant microbiome structure and benefits for sustainable agriculture. Current Plant Biology 26, 100198, 2021.
[43]	Yin P., Shi P., Zhang Y., Hu Z., Ma K., Wang H. and Chai T. 2017. The Response of Soil Bacterial communities to Mining Subsidence in the West China Aeolian Sand Area. Applied Soil Ecology 121, 1-10.
[44]	Zubair M., Hamif A., Farzand A., Sheikh M.M.T., Khan R.A., Suleman M., Ayaz M. and Gao X. 2019. Genetic Screening and Expression Analysis of Psychrophilic Bacillus spp. Reveal Their Potentiel to Alleviate Cold Stress and Modulate Phytohormones in Wheat. Microorganisms 2019, 7, 337.
[45]	Verma J.P., Yadav J., Tiwari N.K. 2012. Enhancement of nodulation and yield of chickpea by co-inoculation of indigenous Mesorhizobium spp. and plant growth promoting rhizobacteria on nodulation Plant growth-promoting rhizobacteria in eastern Uttar Pradesh. Commun. Soil Sci. Plant Anal. 43, 605-621.
[46]	Valverde A., Burgos A., Friscella T., Rivas R., Velaz-quez E., Rodriguez-Barrueco C., Cervantes E., Chamber M. and Igual J.M. 2006. Deferential effects of coinoculations with Pseudomonas jessenii PS06 (a phosphate-solubilizing bacteria) and Mesorhizobium ciceri C-2/2 strains on the growth and seed yield of chickpea under greenhouse and field conditions. Plant Soil 287, 43-50.
[47]	Marques A.P.G.C, Pires C., Moreira H., Rangel A.O.S.S., Castro P.M.L. 2010. Assessment of the plant growth promotion abilities of six bacterial isolates using zeamays as indicator plants. Soil Biol. Biochem. 42, 1229-1235.
[48]	Tian F., Ding Y., Zhu H., Yao L. and Du B. 2009. Genetic Diversity of Siderophore producing bacteria of Tobacco rhizosphere. Brazilian Journal of Microbiology (2009): 40: 276-284.
[49]	Hu D., Li S., Li Y., Peng J., Wei X., Ma J., Zhang C., Jia N., Wang E. and Wang Z. 2020. Streptomyces sp. Strain TOR3209: a rhizosphere bacterium promoting growth of tomato by affecting the rhizosphere microbial communities.
[50]	Zheng Z.H., Qiao Y.J., Li Z.Z., Wang X., Zhu B. and Hu Y.G. 2019. Effect of legume-cereal mixtures on the diversity of bacterial communities in the rhizosphere, Plant Soil Environ 58. (4): 174-180.