The importance of adverse soil microbiomes in the light of omics: Implications for food safety

Akinola S.A., Babalola O.O. (2020): The importance of adverse soil microbiomes in the light of omics: Implications for food safety. Plant Soil Environ., 66: 421–430.


download PDF

One of the most serious threats facing agricultural productivity in the world is unfavourable soil conditions. Several studies have shown that almost half of the world’s land-mass is affected by either natural or human-induced pollution. This, therefore, poses a threat to agricultural improvement needed to tackle the problem of a continuous increase in the world population. The emergence of soil extremophiles with plant growth-promoting trait has proven to be a reliable means to quell the threat posed by some factors limiting soil potency. Adopting these organisms as bio-inoculants will easily proffer a solution to both biotic and abiotic soil stress. As such, the natural bio-fertilisers will help to improve the quality of the soil by making it healthy enough to sustain sufficient plant growth. This review gives an overview of the multifarious importance of extremophiles on plants grown under harsh soil conditions, with the multifaceted application of omics as a means to unveil these organisms and their benefits for environmentally sustainable agricultural systems and food safety.


Aalipour H., Nikbakht A., Etemadi N., Rejali F., Soleimani M. (2020): Biochemical response and interactions between arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria during establishment and stimulating growth of Arizona cypress (Cupressus arizonica G.) under drought stress. Scientia Horticulturae, 261: 108923.
Adam P.S., Borrel G., Brochier-Armanet C., Gribaldo S. (2017): The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. The ISME Journal, 11: 2407–2425.
Asaf L.S., Khan A.L., Waqas M., Kang S.-M., Hamayun M., Lee I.-J., Hussain A. (2019): Growth-promoting bioactivities of Bipolaris sp. CSL-1 isolated from Cannabis sativa suggest a distinctive role in modifying host plant phenotypic plasticity and functions. Acta Physiologiae Plantarum, 41: 65.
Babalola O.O., Odhiambo G.D. (2007): Klebsiella oxytoca (10mkr7) stimulates Striga suicidal germination in Zea mays. Journal of Tropical Microbiology and Biotechnology, 3: 14–19.
Babalola O.O. (2010): Beneficial bacteria of agricultural importance. Biotechnology Letters, 32: 1559–1570.
Bouzid S., Rahmoune C. (2012): Enhancement of saline water for irrigation of Phaseolus vulgaris L. species in presence of molybdenum. Procedia Engineering, 33: 168–173.
Brunel C., Pouteau R., Dawson W., Pester M., Ramirez K.S., van Kleunen M. (2020): Towards unraveling macroecological patterns in rhizosphere microbiomes. Trends in Plant Science, (In Press)
Cherni M., Ferjani R., Mapelli F., Boudabous A., Borin S., Ouzari H.-I. (2019): Soil parameters drive the diversity of Citrus sinensis rhizosphere microbiota which exhibits a potential in plant drought stress alleviation. Applied Soil Ecology, 135: 182–193.
de la Vega M., Sayago A., Ariza J., Barneto A.G., León R. (2016): Characterization of a bacterioruberin-producing Haloarchaea isolated from the marshlands of the Odiel river in the southwest of Spain. Biotechnology Progress, 32: 592–600.
Enagbonma B.J., Babalola O.O. (2020): Unveiling plant-beneficial function as seen in bacteria genes from termite mound soil. Journal of Soil Science and Plant Nutrition, 20: 421–430.
Enebe M.C., Babalola O.O. (2019): The impact of microbes in the orchestration of plants’ resistance to biotic stress: a disease management approach. Applied Microbiology and Biotechnology, 103: 9–25.
Ghorchiani M., Etesami H., Alikhani H.A. (2018): Improvement of growth and yield of maize under water stress by co-inoculating an arbuscular mycorrhizal fungus and a plant growth promoting rhizobacterium together with phosphate fertilizers. Agriculture, Ecosystems and Environment, 258: 59–70.
Goodwin S., McPherson J.D., McCombie W.R. (2016): Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics, 17: 333–351.
Gouda S., Kerry R.G., Das G., Paramithiotis S., Shin H.-S., Patra J.K. (2018): Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiological Research, 206: 131–140.
Igiehon N.O., Babalola O.O. (2017): Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi. Applied Microbiology Biotechnology, 101: 4871–4881.
Igiehon N.O., Babalola O.O., Aremu B.R. (2019): Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress. BMC Microbiology, 19: 159.
Ma Y., Rajkumar M., Oliveira R.S., Zhang C., Freitas H. (2019): Potential of plant beneficial bacteria and arbuscular mycorrhizal fungi in phytoremediation of metal-contaminated saline soils. Journal of Hazardous Materials, 379: 120813.
Ma Y., Rajkumar M., Zhang C., Freitas H. (2016): Inoculation of Brassica oxyrrhina with plant growth promoting bacteria for the improvement of heavy metal phytoremediation under drought conditions. Journal of Hazardous Materials, 320: 36–44.
Magallon-Servín P., Antoun H., Taktek S., Bashan Y., de-Bashan L. (2019): The maize mycorrhizosphere as a source for isolation of arbuscular mycorrhizae-compatible phosphate rock-solubilizing bacteria. Plant and Soil, 451: 169–186.
Mingma R., Pathom-aree W., Trakulnaleamsai S., Thamchaipenet A., Duangmal K. (2014): Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine. World Journal of Microbiology and Biotechnology, 30: 271–280.
Nayfach S., Bradley P.H., Wyman S.K., Laurent T.J., Williams A., Eisen J.A., Pollard K.S., Sharpton T.J. (2015): Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLoS Computational Biology, 11: e1004573.
Ojuederie O.B., Olanrewaju O.S., Babalola O.O. (2019): Plant growth promoting rhizobacterial mitigation of drought stress in crop plants: implications for sustainable agriculture. Agronomy, 9: 712.
Omomowo O.I., Babalola O.O. (2019): Bacterial and fungal endophytes: tiny giants with immense beneficial potential for plant growth and sustainable agricultural productivity. Microorganisms, 7: 481.
Patel S., Jinal H.N., Amaresan N. (2017): Isolation and characterization of drought resistance bacteria for plant growth promoting properties and their effect on chilli (Capsicum annuum) seedling under salt stress. Biocatalysis and Agricultural Biotechnology, 12: 85–89.
Pehlivan N., Yesilyurt A.M., Durmus N., Karaoglu S.A. (2017): Trichoderma lixii ID11D seed biopriming mitigates dose dependent salt toxicity in maize. Acta Physiologiae Plantarum, 39: 79.
Piromyou P., Songwattana P., Greetatorn T., Okubo T., Kakizaki K.C., Prakamhang J., Tittabutr P., Boonkerd N., Teaumroong N., Minamisawa K. (2015): The type III secretion system (T3SS) is a determinant for rice-endophyte colonization by non-photosynthetic Bradyrhizobium. Microbes and Environments, 30: 291–300.
Samaddar S., Chatterjee P., Choudhury A.R., Ahmed S., Sa T.M. (2019): Interactions between Pseudomonas spp. and their role in improving the red pepper plant growth under salinity stress. Microbiological Research, 219: 66–73.
Sharpton T.J. (2014): An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science, 5: 209.
Shivlata L., Tulasi S. (2015): Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Frontiers in Microbiology, 6: 1014.
Suksaard P., Srisuk N., Duangmal K. (2018): Saccharopolyspora maritima sp. nov., an actinomycete isolated from mangrove sediment. International Journal of Systematic Evolutionary Microbiology, 68: 3022–3027.
Taffner J., Erlacher A., Bragina A., Berg C., Moissl-Eichinger C., Berg G. (2018): What is the role of Archaea in plants? New insights from the vegetation of alpine bogs. mSphere, 3: e00122-18.
Thanh D.T.N., Diep C.N. (2014): Isolation and identification of rhizospheric bacteria in Acrisols of maize (Zea mays L.) in the eastern of South Vietnam. American Journal of Life Sciences, 2: 82–89.
Treusch A.H., Leininger S., Kletzin A., Schuster S.C., Klenk H.-P., Schleper C. (2005): Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology, 7: 1985–1995.
Verma P., Yadav A.N., Khannam K.S., Mishra S., Kumar S., Saxena A.K., Suman A. (2019): Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from peninsular zone of India. Saudi Journal of Biological Sciences, 26: 1882–1895.
Verma P., Yadav A.N., Kumar V., Singh D.P., Saxena A.K. (2017): Beneficial plant-microbes interactions: biodiversity of microbes from diverse extreme environments and its impact for crop improvement. In: Singh D.P., Singh H.B., Prabha R. (eds.): Plant-Microbe Interactions in Agro-Ecological Perspectives. Singapore, Springer, 543–580. ISBN: 978-981-10-6592-7
Weselowski B., Nathoo N., Eastman A.W., MacDonald J., Yuan Z.-C. (2016): Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production. BMC Microbiology, 16: 244.
Xia M., Chakraborty R., Terry N., Singh R.P., Fu D.F. (2020): Promotion of saltgrass growth in a saline petroleum hydrocarbons contaminated soil using a plant growth promoting bacterial consortium. International Biodeterioration and Biodegradation, 146: 104808.
Yadav A.N. (2017): Agriculturally important microbiomes: biodiversity and multifarious PGP attributes for amelioration of diverse abiotic stresses in crops for sustainable agriculture. Biomedical Journal of Scientific and Technical Research, 1: 861–864.
Yadav A.N., Sachan S.G., Verma P., Saxena A.K. (2016): Bioprospecting of plant growth promoting psychrotrophic Bacilli from the cold desert of north western Indian Himalayas. Indian Journal of Experimental Biology, 52: 142–150.
Yooyongwech S., Samphumphuang T., Tisarum R., Theerawitaya C., Cha-Um S. (2017): Water-deficit tolerance in sweet potato [Ipomoea batatas (L.) Lam.] by foliar application of paclobutrazol: role of soluble sugar and free proline. Frontiers in Plant Science, 8: 1400.
download PDF

© 2022 Czech Academy of Agricultural Sciences | Prohlášení o přístupnosti