Abstract
The present study is an attempt to understand the impact of bioinoculants, Azotobacter chroococcum (A), Bacillus megaterium (B), Pseudomonas fluorescens (P), on (a) soil and plant nutrient status, (b) total resident and active bacterial communities, and (c) genes and transcripts involved in nitrogen cycle, during cultivation of Cajanus cajan. In terms of available macro- and micro-nutrients, triple inoculation of the bioinoculants (ABP) competed well with chemical fertilizer (CF). Their ‘non-target’ effects were assessed in terms of the abundance and activity of the resident bacterial community by employing denaturing gradient gel electrophoresis (DGGE). The resident bacterial community (16S rRNA gene) was stable, while the active fraction (16S rRNA transcripts) was influenced (in terms of abundance) by the treatments. Quantification of the genes and transcripts involved in N cycle by qPCR revealed an increase in the transcripts of nifH in the soil treated with ABP over CF, with an enhancement of 3.36- and 1.57- fold at flowering and maturity stages of plant growth, respectively. The bioinoculants shaped the resident microflora towards a more beneficial community, which helped in increasing soil N turnover and hence, soil fertility as a whole.
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Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. PNAS USA 105:11512–11519
Babić KH, Schauss K, Hai B, Sikora S, Redzepović S, Radl V, Schloter M (2008) Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.). Environ Microbiol 10:2922–2930
Bakker MG, Schlatter DC, Otto-Hanson L, Kinkel LL (2014) Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome. Mol Ecol 23:1571–1583
Bashan Y, Kloepper JW, de-Bashan LE, Nannipieri P (2016) A need for disclosure of the identity of microorganisms, constituents, and application methods when reporting tests with microbe-based or pesticide-based products. Biol Fertil Soils 52:283–284
Bending GD, Turner MK, Rayns F, Marx MC, Wood M (2004) Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes. Soil Biol Biochem 36:1785–1792
Biswas S (2014) Evaluation of growth, yield and nutrient content with microbial consortia combined with different organic manures in Rumex acetosella L. IOSR-JESTFT 8:1–5
Björklöf K, Sen R, Jørgensen KS (2003) Maintenance and impacts of an inoculated mer/luc-tagged Pseudomonas fluorescens on microbial communities in birch rhizospheres developed on humus and peat. Microb Ecol 45:39–52
Black CA (1965) Methods of soil analysis part II- chemical and micro-biological properties: No 9 series agronomy. American Society of Agronomy Inc Publishers, Medison
Bremner JM (1960) Determination of nitrogen in soil by the Kjeldahl method. J Agr Sci 55:11–33
Bürgmann H, Meier S, Bunge M, Widmer F, Zeyer J (2005) Effects of model root exudates on structure and activity of a soil diazotroph community. Environ Microbiol 7:1711–1724
Ccoscco RA, Sarmiento VH, Villena GK (2018) Microbial diversity assessment by PCR-DGGE analysis in national sanctuary of Ampay in Perú. Adv Biotech & Micro 11:001–006
Chang E, Tian G, Shiau Y, Chen T, Chiu C (2019) Influence of thorny bamboo plantations on soil microbial biomass and community structure in subtropical badland soils. Forests 10:854–865
Chu H, Lin X, Fujii T, Morimoto S, Yagi K, Hu J, Zhang J (2007) Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39:2971–2976
Cleary DFR, Smalla K, Mendonça-Hagler LCS, Gomes NCM (2012) Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. PLoS ONE 7:e29380
Coelho MRR, de Vos M, Carneiro NP, Marriel IE, Paiva E, Seldin L (2008) Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer. FEMS Microbiol Lett 279:15–22
Coelho MRR, Marriel IE, Jenkins SN, Lanyon CV, Seldin L, O’Donnell AG (2009) Molecular detection and quantification of nifH gene sequences in the rhizosphere of sorghum (Sorghum bicolor) sown with two levels of nitrogen fertilizer. Appl Soil Ecol 42:48–53
Dlott G, Maul JE, Buyer J, Yarwood S (2015) Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils. J Micrbiol Meth 115:112–120
Duarte GF, Rosado AS, Seldin L, Keijzer-Wolters AC, van Elsas JD (1998) Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community. J Microbiol Methods 32:21–29
Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of Chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172–178
Ebhin Masto R, Chhonkar P, Singh D, Patra A (2006) Changes in soil biological and biochemical characteristics in a long-term field trial on a sub-tropical inceptisol. Soil Biol Biochem 38:1577–1582
Francioli D, Ascher J, Ceccherini MT, Pietramellara G (2014) Land use and seasonal effects on a Mediterranean soil bacterial community. J Soil Sci Plant Nutr 14:710–722
Ge G, Li Z, Fan F, Chu G, Hou Z, Liang Y (2010) Soil biological activity and their seasonal variations in response to long-term application of organic and inorganic fertilizers. Plant Soil 326:31–44
Ghosh AB, Bajaj JC, Hasan R, Singh D (1983) Soil and water testing methods: a laboratory manual. Sci Res 8:31–36
Goldberg DE, Barton AM (1992) Patterns and consequences of interspecific competition in natural communities: a review of field experiments with plants. Am Nat 139:771–801
Gomez KA, Gomez AA (1984) Statistical procedures for agricultural research. Wiley, New York
Gupta R, Bru D, Bisaria VS, Philippot L, Sharma S (2012) Responses of Cajanus cajan and rhizospheric N-cycling communities to bioinoculants. Plant Soil 358:143–154
Gupta R, Bisaria VS, Sharma S (2013) Bioinoculants: more than just plant growth promoting agents. Endocytobiosis Cell Res 24:8–11
Gupta R, Mathimaran N, Wiemken A, Boller T, Bisaria VS, Sharma S (2014) Non-target effects of bioinoculants on rhizospheric microbial communities of Cajanus cajan. Appl Soil Ecol 76:26–33
Gupta R, Bisaria VS, Sharma S (2015) Effect of agricultural amendments on Cajanus cajan (Pigeon Pea) and its rhizospheric microbial communities—a comparison between chemical fertilizers and bioinoculants. PLoS ONE 10:e0132770
Gupta R, Bisaria VS, Sharma S (2016) Response of rhizospheric bacterial communities of Cajanus cajan to application of bioinoculants and chemical fertilizers: a comparative study. Eur J Soil Biol 75:107–114
Hanson PJ, Edwards NT, Garten CT, Andrews JA (2000) Separating root and soil microbial contributions to soil respiration: a review of methods and observations. Biogeochemistry 48:115–146
He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di H (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:2364–2374
Heuer H, Smalla K (1997) Application of denaturating gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. In: van Elsas JD, Wellington EMH, Trevors JT (eds) Modern soil microbiology. Marcel Dekker, New York, pp 353–373
Huang X, Zhou X, Zhang J, Cai Z (2019) Highly connected taxa located in the microbial network are prevalent in the rhizosphere soil of healthy plant. Biol Fertil Soils 55:299–312
Hugerth LW, Andersson AF (2017) Analysing microbial community composition through amplicon sequencing: from sampling to hypothesis testing. Front Microbiol 8:1561
Iglesias-Rios R, Mazzoni R (2014) Measuring diversity: looking for processes that generate diversity. Nat Conservação 12:156–161
Islam MR, Chauhan PS, Kim Y, Kim M, Sa T (2011) Community level functional diversity and enzyme activities in paddy soils under different long term fertilizer management practices. Biol Fertil Soils 47:599–604
Jackson ML (1973) Soil chemical analysis. Prentice Hall of Englewood Cliffs, New Jersey, p 498
Jia Z, Hu X, Xia W, Fornara D, Nannipieri P, Tiedje J (2019) Community shift of microbial ammonia oxidizers in air-dried rice soils after 22 years of nitrogen fertilization. Biol Fert Soils 55:419–424
Kim TG, Moon KE, Yun J (2012) Comparison of RNA- and DNA-based bacterial communities in a lab-scale methane-degrading biocover. Appl Microbiol Biotechnol 97:3171–3181
Kraková L, Šoltys K, Budiš J, Grivalský T, Ďuriš F, Pangallo D, Szemes T (2016) Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning. Extremophiles 20:795–808
Kumar S, Tamura K, Nei M (2004) MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163
Kumar V, Kumar A, Verma VC, Gond SK, Kharwar RN (2007) Induction of defense enzymes in Pseudomonas fluorescens treated chickpea roots against Macrophomina phaseolina. Indian Phytopath 60:289–295
Kuo J, Wang YW, Chen M, Fuh G, Lin CH (2019) The effect of paclobutrazol on soil bacterial composition across three consecutive flowering stages of mung bean. Folia Microbiol (Praha) 64:197–205
Kutvonen H, Rajala P, Carpén L, Bomberg M (2015) Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms. Front Microbiol 6:1–16
Lanzén A, Jørgensen SL, Bengtsson MM, Jonassen I, Øvreås L, Urich T (2011) Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol 77:577–589
Lee C, Kim J, Shin SG, Hwang S (2008) Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater. FEMS Microbiol Ecol 65:544–554
Lindsay WL, Norvell WA (1978) Development of a DTPA soil test for zinc, iron, manganese, and copper. Soil Sci Soc Am J 42:421–428
Liu E, Yan C, Mei X, He W, Bing S, Ding L, Liu Q, Liu S, Fan T (2009) Organic amendments with reduced chemical fertilizer promote soil microbial development and nutrient availability in a subtropical paddy field: the influence of quantity, type and application time of organic amendments. Appl Soil Ecol 42:166–175
Liu E, Yan C, Mei X, He W, Bing S, Ding L, Liu Q, Liu S, Fan T (2010) Long-term effect of chemical fertilizer, straw, and manure on soil chemical and biological properties in northwest China. Geoderma 158:173–180
Liu M, Tang Y, Zhao K, Liu Y, Guo X, Ren D, Yao W, Tian X, Gu Y, Yi B, Zhang X (2017) Determination of the fungal community of pit mud in fermentation cellars for Chinese strong-flavor liquor, using DGGE and Illumina MiSeq sequencing. Food Res Int 91:80–87
López-Gutiérrez JC, Henry S, Hallet S, Martin-Laurent F, Catroux G, Philippot L (2004) Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. J Microbiol Methods 57:399–407
Lv M, Li Z, Che Y, Han F, Liu M (2011) Soil organic C, nutrients, microbial biomass, and grain yield of rice (Oryza sativa L.) after 18 years of fertilizer application to an infertile paddy soil. Biol Fertil Soils 47:777–783
Maukonen J, Satokari R, Mättö J, Söderlund H, Mattila-Sandholm T, Saarela M (2006) Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J Med Microbiol 55:625–633
Nihorimbere V, Ongena M, Smargiassi M, Thonart P (2011) Beneficial effect of the rhizosphere microbial community for plant growth and health. Biotechnol Agron Soc Environ 15:327–337
Olsen S (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. US Department of Agriculture, Washington, DC
Orlewska K, Piotrowska-Seget Z, Bratosiewicz-Wąsik J, Cycoń M (2018) Characterization of bacterial diversity in soil contaminated with the macrolide antibiotic erythromycin and/or inoculated with a multidrug-resistant Raoultella sp. strain using the PCR-DGGE approach. Appl Soil Ecol 126:57–64
Orr CH, Leifert C, Cummings SP, Cooper JM (2012) Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects. PLoS ONE 7:e52891
Paul EA, Clark FE (1996) Soil microbiology and biochemistry. New Phytol 138:563–566
Peng L, Chaoqun H, Lüping Z, Chunhua R, Qi S (2007) Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water. Chin J Oceanol Limn 25:310–316
Pham VH, Kim J (2012) Cultivation of unculturable soil bacteria. Trends Biotech 30:475–482
Qin H, Tang Y, Shen J, Wang C, Chen C, Yang J, Liu Y, Chen X, Li Y, Hou H (2018) Abundance of transcripts of functional gene reflects the inverse relationship between CH4 and N2O emissions during mid-season drainage in acidic paddy soil. Biol Fertil Soils 54:885–895
Raich JW, Schlesinger WH (1992) The global carbon dioxide flux in soil respiration and its relationship to vegetation and climate. Tellus B 44:81–99
Ramirez KS, Craine JM, Fierer N (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob Chang Biol 18:1918–1927
Samarajeeva AD, Hammad A, Masson L, Khan IU, Scroggins R, Beaudette LA (2015) Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia. J Microbiol Methods 108:103–111
Sarma MVRK, Sahai V, Bisaria VS (2009) Genetic algorithm based medium optimization for enhanced production of fluorescent pseudomonad R81 and siderophores. Biochem Eng J 47:100–108
Savci S (2012) An agricultural pollutant: chemical fertilizer. Int J Environ Sci Dev 3:77–80
Schöler A, Jacquiod S, Vestergaard G, Schulz S, Schloter M (2017) Analysis of soil microbial communities based on amplicon sequencing of marker genes. Biol Fertil Soils 53:485–489
Sharma S, Mehta R, Gupta R, Schloter M (2012) Improved protocol for the extraction of bacterial mRNA from soils. J Microbiol Meth 91:62–64
Sharma R, Paliwal JS, Chopra P, Dogra D, Pooniya V, Bisaria VS, Swarnalakshmi K, Sharma S (2017) Survival, efficacy and rhizospheric effects of bacterial inoculants on Cajanus cajan. Agric Ecosyst Environ 240:244–252
Singh D, Raghuvanshi K, Chaurasiya A, Dutta SK, Dubey SK (2018) Enhancing the nutrient uptake and quality of Pearlmillet (Pennisetum glaucum L.) through use of biofertilizers. Int J Curr Microbiol Appl Sci 7:3296–3306
Solomon L, Ogugbue CJ, Okpokwasili GC (2018) Influence of biostimulation treatment using composted plant biomass on bacterial diversity of an aged petroleum contaminated soil as determined by culture-dependent and 16S rRNA gene PCR-DGGE based identification methods. South Asian J Res Microbiol 1:1–16
Son TTN, Thu VV, Man LH, Kobayashi H, Yamada R (2004) Effect of long-term application of organic and bio-fertilizer on soil fertility under rice-soyabean-rice cropping system. OmonRice 12:45–51
Stamford NP, da Silva JS, Santos CERS, Freitas ADS, Lira Junior MA, Barros MFC (2013) Cowpea nodulation, biomass yield and nutrient uptake, as affected by biofertilizers and rhizobia, in a sodic soil amended with Acidithiobacillus. Acta Sci Agron 35:453–459
Stotzky G (1997) Soil as an environment for microbial life. In: Van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil microbiology. Marcel Dekker, New York, pp 1–20
Subbiah BV, Asija GL (1956) A rapid procedure for the determination of available nitrogen in soil. Curr Sci 25:259–260
Sultana S, Sharma N, Shirkot CK (2004) Production of antifungal antibiotic by a newly isolated strain of Bacillus megaterium. J Microbiol World 6:8–15
Trabelsi D, Mhamdi R (2013) Microbial inoculants and their impact on soil microbial communities: a review. BioMed Res Intl 2013:862340
Timms-Wilson TM, Kilshaw K, Bailey MJ (2005) Risk assessment for engineered bacteria used in biocontrol of fungal disease in agricultural crops. Plant Soil 266:57–67
Vestergaard G, Schulz S, Schöler A, Schloter M (2017) Making big data smart–how to use metagenomics to understand soil quality. Biol Fertil Soils 53:479–484
Walkely A, Black IA (1934) An examination of Degtjareff methods for determining soil organic matter and a proposed modification of the chromic acid titration method. Soil Sci 37:29–38
Wei L, Ma F, Wang XY, Liu YL, Wang LN, Li WG (2008) Influence of different 16S rDNA target sequence on analysis of microbial diversity in anaerobic ABR reactor. J Environ Sci (China) 29:776–780
Xing DF, Ren NQ, Song JX, Qu M, Xu XL (2006) Community of activated sludge based on different target sequence of 16S rDNA by denaturing gradient gel electrophoresis. Environ Sci 27:1424–1428
Yong X, Cui Y, Chen L, Ran W, Shen Q, Yang X (2011) Dynamics of bacterial communities during solid-state fermentation using agro-industrial wastes to produce poly-γ-glutamic acid, revealed by real-time PCR and denaturing gradient gel electrophoresis (DGGE). Appl Microbiol Biotechnol 92:717–725
Yu WT, Bi ML, Xu YG, Zhou H, Ma Q, Jiang CM (2013) Microbial biomass and community composition in a Luvisol soil as influenced by long-term land use and fertilization. CATENA 107:89–95
Yuen SH, Pollard AG (1953) Determination of nitrogen in soil and plant materials: use of boric acid in the micro-kjeldahl method. J Sci Food Agric 4:490–496
Zhao Y, Bian SM, Zhou HN, Huang JF (2006) Diversity of nitrogenase systems in diazotrophs. J Integr Plant Biol 48:745–755
Zhong WH, Cai ZC (2007) Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl Soil Ecol 36:84–91
Acknowledgements
This work was supported by Department of Biotechnology, Govt. of India (Grant No. BT/PR5499/AGR/21/355/2012). RS acknowledges Council of Scientific and Industrial Research, India for the award of fellowship to carry out this doctoral work.
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Sharma, R., Pooniya, V., Bisaria, V.S. et al. Bioinoculants play a significant role in shaping the rhizospheric microbial community: a field study with Cajanus cajan. World J Microbiol Biotechnol 36, 44 (2020). https://doi.org/10.1007/s11274-020-02818-1
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DOI: https://doi.org/10.1007/s11274-020-02818-1