Abstract
Soil is a primary natural resource that maintains ecosystem functioning, water balance, and supports plant growth. Soil is also a habitat for diverse microflora that is very crucial to soil sustaining activities. Microbial ecology is the study of microbial community dynamics and its functioning in the environmental system. Diversity in any ecological niche is the major descriptor for community structure which decides the dynamics and functioning of a community. Conventionally, microbiome characterization is based on culture-dependent techniques, but due to the insufficiency of appropriate culture media most of the microorganisms are unable to grow; therefore, for microbial community analysis culture-dependent techniques have proven less appropriate. However, over the last few decades, culture-independent techniques are being practiced to assess microbial communities and these approaches appear more satisfactory because they are more advanced and able to determine almost all genomes acclimatized in a variety of environmental samples. Moreover, microbes present in ecological niche participate in the development and maintenance of multiple functioning of ecosystems which include pedosphere development, litter decomposition, nutrient cycling, climate regulation, plant growth promotion, and sustainability maintenance. Therefore, in the present era, the characterization of microbiome is very important. This review provides a wider understanding of the functioning of microbial communities and methods of their assessment in the soil.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Agrawal PK, Agrawal S, Shrivastava R (2015) Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem. Biotech 5(6):853–866
Babikova Z, Gilbert L, Bruce TJ et al (2013) Underground signals carried through common mycelial networks warn neighbouring plants of aphid attack. Ecol Lett 16(7):835–843
Belay-Tedla A, Zhou X, Su B et al (2009) Labile, recalcitrant, and microbial carbon and nitrogen pools of a tall grass prairie soil in the US Great Plains subjected to experimental warming and clipping. Soil Biol Biochem 41(1):110–116
Beneduzi A, Ambrosini A, Passaglia LM (2012) Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents. Genet Mol Biol 35(4):1044–1051
Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17(8):478–486
Bilinski TM, Vargas R, Kenney A (2019) PGPR and water availability effects on plants. Front Microbiol 10:860
Bonk F, Popp D, Harms H et al (2018) PCR-based quantification of taxa-specific abundances in microbial communities: quantifying and avoiding common pitfalls. J Microbiol Methods 153:139–147
Bulgarelli D, Rott M, Schlaeppi K et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488(7409):91
Bulgarelli D, Schlaeppi K, Spaepen S et al (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838
Cohen AC, Bottini R, Pontin M et al (2015) Azospirillum brasilense ameliorates the response of Arabidopsis thaliana to drought mainly via enhancement of ABA levels. Physiol Plant 153(1):79–90
DeSantis TZ, Brodie EL, Moberg JP et al (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53(3):371–383
Franco-Duarte R, Černáková L, Kadam S et al (2019) Advances in chemical and biological methods to identify microorganisms—From past to present. Microorganisms 7(5):130
Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57(8):2351–2359
George TS, Dou D, Wang X (2016) Plant–microbe interactions: manipulating signals to enhance agricultural sustainability and environmental security. Plant Growth Regul 80(1):1–3
Hamarashid NH, Othman MA, Hussain MAH (2010) Effects of soil texture on chemical compositions, microbial populations and carbon mineralization in soil. Egypt J Exp Biol 6(1):59–64
Hawksworth DL, Lücking R (2017) Fungal diversity revisited: 2.2 to 3.8 million species. Fung Kingdom 5(4):79–95
Hiltpold I, Jaffuel G, Turlings TC (2014) The dual effects of root-cap exudates on nematodes: from quiescence in plant-parasitic nematodes to frenzy in entomopathogenic nematodes. J Exp Bot 66(2):603–611
Kaviya N, Upadhayay VK, Singh J et al (2019) Role of microorganisms in soil genesis and functions. In: Varma A, Choudhary DK (eds) Mycorrhizosphere and pedogenesis, 1st edn. Springer, Singapore, pp 25–52
Kenney E, Eleftherianos I (2016) Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol 46(1):13–19
Khan A, Singh J, Upadhayay VK et al (2019) Microbial biofortification: a green technology through plant growth promoting microorganisms. In: Shah S, Venkatramanan V, Prasad R (eds) Sustainable green technologies for environmental management, 1st edn. Springer, Singapore, pp 255–269
Kisiel A, Kępczyńska E (2016) Medicago truncatula Gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa. Planta 243(5):1169–1189
Koller R, Rodriguez A, Robin C (2013) Protozoa enhance foraging efficiency of arbuscular mycorrhizal fungi for mineral nitrogen from organic matter in soil to the benefit of host plants. New Phytol 199(1):203–211
Kumar A, Maurya BR, Raghuwanshi R et al (2017) Co-inoculation with Enterobacter and rhizobacteria on yield and nutrient uptake by wheat (Triticum aestivum L.) in the alluvial soil under indo-gangetic plain of India. J Plant Growth Regul 36(3):608–617
Lacey LA, Georgis R (2012) Entomopathogenic nematodes for control of insect pests above and below ground with comments on commercial production. J Nematol 44(2):218–225
Lenoir I, Fontaine J, Sahraoui ALH (2016) Arbuscular mycorrhizal fungal responses to abiotic stresses: a review. Phytochemistry 123:4–15
Li RX, Cai F, Pang G et al (2015) Solubilisation of phosphate and micronutrients by Trichoderma harzianum and its relationship with the promotion of tomato plant growth. PLoS One 10(6):e0130081
Liu WT, Marsh TL, Cheng H et al (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522
Liu W, Zhang ZHE, Wan S (2009) Predominant role of water in regulating soil and microbial respiration and their responses to climate change in a semiarid grassland. Glob Chang Biol 15(1):184–195
Lyu D, Backer RG, Robinson WG et al (2019) Plant-growth promoting rhizobacteria for cannabis production: yield, cannabinoid profile and disease resistance. Front Microbiol 10:1761
Mahmood K, Xu Z, El-Kereamy A et al (2016a) The Arabidopsis transcription factor ANAC032 represses anthocyanin biosynthesis in response to high sucrose and oxidative and abiotic stresses. Front Plant Sci 7:1548
Mahmood S, Daur I, Al-Solaimani SG et al (2016b) Plant growth promoting rhizobacteria and silicon synergistically enhance salinity tolerance of mung bean. Front Plant Sci 7:876
Montesinos-Navarro A, Segarra-Moragues JG, Valiente-Banuet A et al (2012) Plant facilitation occurs between species differing in their associated arbuscular mycorrhizal fungi. New Phytol 196(3):835–844
Nasreen C, Mohiddin GJ, Srinivasulu M et al (2015) Interaction effects of insecticides on microbial populations and dehydrogenase activity in groundnut (Arachis hypogeae L.) planted black clay soil. Int J Curr Microbiol App Sci 4:135–146
Nema V (2019) The role and future possibilities of next-generation sequencing in studying microbial diversity. In: Das S, Dash HR (eds) Microbial diversity in the genomic era. Academic Press, London, pp 611–630
Nüsslein K, Tiedje JM (1999) Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Appl Environ Microbiol 65(8):3622–3626
Olanrewaju OS, Ayangbenro AS, Glick BR et al (2019) Plant health: feedback effect of root exudates-rhizobiome interactions. Appl Microbiol Biotechnol 103(3):1155–1166
Ongena M, Jourdan E, Adam A et al (2007) Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants. Environ Microbiol 9(4):1084–1090
Parveen H, Singh AV, Khan A, Prasad B, Pareek N (2018) Influence of plant growth promoting rhizobacteria on seed germination and seedling vigor of green gram. Int J Chem Stud 6(4):611–618
Philippot L, Raaijmakers JM, Lemanceau P et al (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11(11):789–799
Purahong W, Wubet T, Lentendu G et al (2016) Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition. Mol Ecol 25(16):4059–4074
Rashid MI, Mujawar LH, Shahzad T et al (2016) Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils. Microbiol Res 183:26–41
Rawat S, Mushtaq A (2015) Plant growth promoting rhizobacteria, a formula for sustainable agriculture: a review. Asian J Plant Sci Res 5(4):43–46
Rytioja J, Hildén K, Yuzon J et al (2014) Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Mol Biol Rev 78(4):614–649
Salam MD, Varma A (2019) A review on impact of e-waste on soil microbial community and ecosystem function. Pollution 5(4):761–774
Schouteden N, DeWaele D, Panis B et al (2015) Arbuscular mycorrhizal fungi for the biocontrol of plant-parasitic nematodes: a review of the mechanisms involved. Front Microbiol 6:1280
Silva-Sánchez A, Soares M, Rousk J (2019) Testing the dependence of microbial growth and carbon use efficiency on nitrogen availability, pH, and organic matter quality. Soil Biol Biochem 134:25–35
Singh AV, Sharma A, Johri BN (2012) Phylogenetic profiling of culturable bacteria associated with early phase of mushroom composting assessed by amplified rDNA restriction analysis. Ann Microbiol 62(2):675–682
Singh AV, Prasad B, Goel R (2018) Plant growth promoting efficiency of phosphate solubilizing Chryseobacterium sp. PSR 10 with different doses of N and P fertilizers on Lentil (Lens culinaris var. PL-5) growth and yield. Int J Curr Microbiol App Sci 7(5):2280–2289
Tisserant E, Malbreil M, Kuo A et al (2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci 110(50):20117–20122
Tlaskal V, Voriskova J, Baldrian P (2016) Bacterial succession on decomposing leaflitter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia. FEMS Microbiol Ecol 92:177
Tran H, Ficke A, Asiimwe T et al (2007) Role of the cyclic lipopeptidemassetolide A in biological control of Phytophthora infestans and in colonization of tomato plants by Pseudomonas fluorescens. New Phytol 175(4):731–742
Vivas A, Voros I, Biro B et al (2003) Symbiotic efficiency of autochthonous arbuscular mycorrhizal fungus (G. mosseae) and Brevibacillus sp. isolated from cadmium polluted soil under increasing cadmium levels. Environ Pollut 126(2):179–189
Vlcek V, Pohanka M (2020) Glomalin—an interesting protein part of the soil organic matter. Soil Water Res 15(2):67–74
Voges MJ, Bai Y, Schulze-Lefert P et al (2019) Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proc Natl Acad Sci 116(25):12558–12565
Walder F, Boller T, Wiemken A et al (2016) Regulation of plants' phosphate uptake in common mycorrhizal networks: role of intraradical fungal phosphate transporters. Plant Signal Behav 11(2):e1131372
Weyens N, Thijs S, Popek R et al (2015) The role of plant–microbe interactions and their exploitation for phytoremediation of air pollutants. Int J Mol Sci 16(10):25576–25604
Xiaoping TIAN, Lei WANG, Yahong HOU (2019) Responses of soil microbial community structure and activity to incorporation of straws and straw biochars and their effects on soil respiration and soil organic carbon turnover. Pedosphere 29(4):492–503
Yang J, Kloepper JW, Ryu CM (2008) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14(1):1–4
Yi HS, Ahn YR, Song GC et al (2016) Impact of a bacterial volatile 2, 3-butanediol on Bacillus subtilis rhizosphere robustness. Front Microbiol 7:993
Zhang F, Ge H, Zhang F et al (2016) Biocontrol potential of Trichoderma harzianum isolate T-aloe against Sclerotinia sclerotiorum in soybean. Plant Physiol Biochem 100:64–74
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Khan, A., Joshi, M., Singh, A.V. (2020). Rhizospheric Microbial Community: Ecology, Methods, and Functions. In: Sharma, S.K., Singh, U.B., Sahu, P.K., Singh, H.V., Sharma, P.K. (eds) Rhizosphere Microbes. Microorganisms for Sustainability, vol 23. Springer, Singapore. https://doi.org/10.1007/978-981-15-9154-9_5
Download citation
DOI: https://doi.org/10.1007/978-981-15-9154-9_5
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-9153-2
Online ISBN: 978-981-15-9154-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)