The First Report of Indigenous Free-Living Diazotroph Kosakonia sacchari Isolated from Himalayan Alder-Based Shifting Cultivation System in Nagaland, India
Tóm tắt
A study was carried out to explore soil bacterial diversity associated with Himalayan Alder (Alnus nepalensis)-based shifting cultivation system in Khonoma Village, Nagaland. This agricultural system is well known for its traditional and sustainable form of shifting cultivation and natural biodiversity conservation in the Eastern Himalayan region of India. Surface soil samples (0–30 cm) were collected from alder-based crop fields in Khonoma, Nagaland, and brought to the laboratory for soil nutrient analysis and isolation of culturable bacteria. Standard methodologies were followed for soil nutrient and bacterial diversity analysis. Isolated bacteria were identified using 16S rDNA spacer sequence analysis. BLAST and phylogenetic analysis of molecular sequences identified a unique bacterial isolate in the soil. 16S rDNA partial sequencing of this bacterial strain showed 99% similarity with Kosakonia sacchari–type strain SP1T which has been named for its association with sugarcane. K. sacchari KhAn is a free-living, aerobic, gram-negative, non-spore-forming, and motile rod-shaped bacterium. This bacterial strain holds diazotrophic potential as it was able to grow in nitrogen-free medium and positive for nifH amplification. Furthermore, it showed positive test for ammonia production in peptone water. The soil under alder-based farming system was rich in organic carbon (3.60 ± 0.17%), available nitrogen (536.67 ± 9.28 kg ha−1), available phosphorous (77.35 ± 4.19 kg ha−1), and exchangeable potassium 127.88 ± 10.62 kg ha−1. The existing literature revealed that K. sacchari has not been reported from India until now; therefore, this is the first novel report from India. This contribution represents Eastern Himalaya, a Biodiversity hotspot of the country.
Tài liệu tham khảo
Ahmad F, Ahmad I, Khan M (2008) Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181
Bevivino A, Paganini P, Bacci G, Florio A, Pellicer MS, Papaleo MC, Mengoni A, Ledda L, Fani R, Benedetti A, Dalmastri C (2014) Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region. PLoS One 9:e105515
Bhattacharjee K, Banerjee S, Joshi SR (2012) Diversity of Streptomyces spp. in Eastern Himalayan region-computational RNomics approach to phylogeny. Bioinformation 8:548–554
Brady C, Cleenwerck I, Venter S, Coutinho T, De Vos P (2013) Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 36:309–319
Castaneda LE, Barbosa O (2017) Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests. PeerJ 5:e3098
Chelius MK, Lepo JE (1999) Restriction fragment length polymorphism analysis of PCR-amplified nifH sequences from wetland plant rhizosphere communities. Environ Technol 20:883–889
Chen M, Zhu B, Lin L, Yang L, Li Y, An Q (2014) Complete genome sequence of Kosakonia sacchari type strain SP1T. Stand Genomic Sci 9:1311–1318
Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Franche C, Lindstrom K, Elmerich C (2009) Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil 321:35–59
Department of Agriculture & Cooperation, Ministry of Agriculture, Government of India (2011)
Franche C, Lindström K, Elmerich C (2009) Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil 321:35–59
Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270
Gardi C, Montanarella L, Arrouays D, Bispo A, Lemanceau P, Jovilet C, Mulder C, Ranjard L, Rombke J, Rutgers M, Menta C (2009) Soil biodiversity monitoring in Europe: ongoing activities and challenges. Eur J Soil Sci 60:807–819
Giri K, Mishra G, Jayaraj RSC, Kumar R (2018) Agrobio-cultural diversity of alder based shifting cultivation practiced by Angami tribe in Khonoma village, Kohima, Nagaland. Curr Sci 115:598–599
Gu CT, Li CY, Yang LJ, Huo GC (2014) Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough and reclassification of Enterobacter sacchari Zhu et al. as Kosakonia sacchari comb. nov. Int J Syst Evol Microbial 64:2650–2656
https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cg
http://www.northeasttourism.gov.in/khonoma.html#sthash.cFZTYDjL.dpbs (Accessed on 23.06.2018)
https://www.ncbi.nlm.nih.gov. National Centre for Biotechnology Information (NCBI). Bethesda, Maryland, US
Jackson ML (1973) Soil chemical analysis. Prentice Hall of India Pvt. Ltd, New Delhi, p 498
Kifle MH, Laing MD (2016) Isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of maize seedlings in greenhouses. Front Plant Sci 6:1225. https://doi.org/10.3389/fpls.2015.01225
Lin L, Li Z, Hu C, Zhang X, Chang S, Yang L, Li Y, An Q (2012) Plant growth-promoting nitrogen-fixing Enterobacteria are in association with sugarcane plants growing in Guangxi, China. Microbes Environ 27:391–398
Meliani A, Bensoltane A, Mederbel K (2012) Microbial diversity and abundance in soil: related to plant and soil type. American J Plant Nut Fert Technol 2:10–18
Myers N, Mittermeier RA, Mittermeier CG, daFonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nat 403:853–858
Olsen SR, Cole CV, Watanabe FS, Dean LA (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. U.S. Department of Agriculture Circular No. 939, Washington D. C.
Piceno YM, Lovell CR (2000) Stability in natural bacterial communities. I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39:32–40
Poly F, Monrozier LJ, Bally R (2001) Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152:95–103
Rennie RJ (1981) A single medium for the isolation of acetylene reducing (dinitrogen-fixing) bacteria from soils. Can J Microbiol 27:8–14
Rosello-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67
Shinjo R, Uesaka K, Ihara K, Loshakova K, Mizuno Y, Yano K, Tanaka A (2016) Complete genome sequence of Kosakonia sacchari strain BO-1, an endophytic diazotroph isolated from a sweet potato. Genome Announc 4:e00868–e00816
Suyal DC, Yadav A, Shouche Y, Goel R (2014) Differential proteomics in response to low temperature diazotrophy of Himalayan psychrophilic nitrogen fixing Pseudomonas migulae S10724 strain. Curr Microbiol 68:543–550
Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
Walkley A, Black IA (1934) An examination of the Degtjareff method for determining organic carbon in soils: effect of variations in digestion conditions and of inorganic soil constituents. Soil Sci 63:251–263
Xu Z, Hansen MA, Hansen LH, Jacquiod S, Sorensen S (2014) Bioinformatic approaches reveal metagenomic characterization of soil microbial community. PLoS One 9:93445
Young JPW (1992) Phylogenetic classification of nitrogen-fixing organisms. In: Stacy G, Burris RH, Evans HJ, (eds) Biological nitrogen fixation. Chapman and Hall, New York, p 43–86
Zehr JP, Mellon MT, Zani S (1998) New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes. Appl Environ Microbiol 64:3444–3450
Zhu B, Zhou Q, Lin L, Hu C, Shen P, Yang L, An Q, Xie G, Li Y (2013) Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.). Int J Syst Evol Microbiol 63:2577–2582