Vol.:(0123456789) 1 3 Archives of Microbiology (2020) 202:17–29 https://doi.org/10.1007/s00203-019-01715-y ORIGINAL PAPER Diversity of endophytic bacterial community inhabiting in tropical aerobic rice under aerobic and fooded condition Pranjali Vishwakarma 1,2  · Suresh Kumar Dubey 3 Received: 27 February 2019 / Revised: 3 August 2019 / Accepted: 13 August 2019 / Published online: 23 August 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract The role and activity of bacterial endophytes remains largely unexplored and detail insight into Indian rice agro ecosystem is still little explored. In this study, we examined the diversity of endophytic bacteria in aerobic rice (variety ARB6) under aerobic and fooded feld conditions. Based on 16S rRNA gene RFLP cloning sequencing, 900 clones with 144 representa- tives (72 aerobic and 72 fooded) revealed majority of clones afliated to Gammaproteobacteria (64.58%), Betaproteobacteria (9.72%), Alphaproteobacteria (17.36), Firmicutes (6.26%) and Bacteroidetes (2.08). The study suggests that the aerobic rice variety harbours plant growth promoting (PGP) genera (viz. Pantoea, Enterobacter, Paenibacillus, etc). Investigations on aerobic rice under aerobic and fooded conditions revealed high richness and diversity of endophytic bacteria under aerobic condition inferring that the endophytic bacteria are benefcial for rice growth and productivity, and hence, would be helpful in designing better strategies for rice cultivation under drought or water scarce conditions. Keywords Aerobic rice · Dry (aerobic) feld · Flooded feld · Endophytic bacteria · Uncultured bacteria · Diversity · Tropical Introduction Rice is the major crop to feed more than a billion world’s population. It is also the biggest consumer of the available freshwater. Around 700 million of the world’s poor, live in rice-growing areas of Asia (IRRI 2008). With the rapid pop- ulation growth and urbanization, leading to environmental degradation, water will soon become a scarce commodity. UNESCO (2007) predicted that by 2025, over a billion peo- ple will be living in countries with absolute water scarcity, and two-third of the world population could be under stress. Based on such predictions, agriculture could be severely affected in South and Southeast Asia which may suffer “economic water scarcity”. For this reason, researchers around the world are developing water-saving technologies; one such technology is the aerobic rice system. In India, the University of Agricultural Sciences, GKVK, Banga- lore, has developed three aerobic rice varieties viz. ARB6, MAS946-1 and MAS26 through breeding (Shashidhar 2013). Aerobic rice carries relevance to small farm holders where the availability of fooded lowland is relatively poor. Water consumption is 30–70% less than in the fooded rice, depending on irrigation water management, and anticipated rice yield (Bouman et al. 2005). Compared to the fooded counterpart, aerobic rice releases 80–85% lesser methane to the environment thus keeping the environment relatively safer (Sashidhar 2007). Aerobic rice is cultivated under non-fooded conditions where the root zone gets exposed to aerobic conditions for most of the time. This means that the soil water content in a signifcant part of the root zone is allowed to dry down to less than the feld capacity. Therefore, special rice cul- tivars are being developed with greater drought tolerance along with the in ability to respond to inputs, especially the nutrients. The approach of aerobic rice cultivation involves growing such specially developed cultivars under aerobic condition. The rice variety IR64 was used in the current Communicated by Jorge Membrillo-Hernández. * Suresh Kumar Dubey skdubey@bhu.ac.in 1 Department of Microbiology and Biotechnology, Bangalore University, Bengaluru 560056, India 2 Present Address: Bio-Safety Support Unit, Regional Centre of Biotechnology, Faridabad 121001, India 3 Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India