Advertisement

Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade

  • Princy Hira
  • Priya Singh
  • Anil Kumar Pinnaka
  • Suresh Korpole
  • Rup LalEmail author
Review article
  • 29 Downloads

Abstract

Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.

Keywords

Microbial taxonomy Classification Niches Novel species Indian biodiversity 

Notes

Acknowledgements

This manuscript was partly written when RL was on INSA-DFG Bilateral Exchange Program-2019. RL is thankful to The National Academy of Sciences, India (NASI) for providing the NASI Senior Scientist Platinum Jubilee Fellowship.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12088_2019_845_MOESM1_ESM.docx (85 kb)
Supplementary file1 (DOCX 84 kb)
12088_2019_845_MOESM2_ESM.docx (92 kb)
Supplementary file2 (DOCX 92 kb)

References

  1. 1.
    Satyanarayana T, Johri BN (2005) Microbial diversity: current perspectives and potential applications. IK International Pvt Ltd., DelhiGoogle Scholar
  2. 2.
    Badhai J, Ghosh TS, Das SK (2015) Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India. Front Microbiol 6:1166.  https://doi.org/10.3389/fmicb.2015.01166 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Mehetre GT, Paranjpe AS, Dastager SG, Dharne MS (2016) Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India. Genom Data 7:140–143.  https://doi.org/10.1016/j.gdata.2015.12.031 CrossRefPubMedGoogle Scholar
  4. 4.
    Shah V, Zakrzewski M, Wibberg D, Eikmeyer F, Schlüter A, Madamwar D (2013) Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. Microb Ecol 66:533–550.  https://doi.org/10.1007/s00248-013-0244-x CrossRefPubMedGoogle Scholar
  5. 5.
    Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, Anand S, Malhotra J, Jindal S, Nigam A, Lal D (2012) Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS ONE 7:e46219.  https://doi.org/10.1371/journal.pone.0046219 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R (2015) Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes. Environ Microbiol Rep 7:812–823.  https://doi.org/10.1111/1758-2229.12297 CrossRefPubMedGoogle Scholar
  7. 7.
    Sharma A, Schmidt M, Kiesel B, Cralle LE, Mahato NK, Singh Y, Richnow HH, Gilbert JA, Arnold W, Lal R (2018) Bacterial and archaeal viruses of Himalayan hot springs at Manikaran modulate host genomes. Front Microbiol 9:3095.  https://doi.org/10.3389/fmicb.2018.03095 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Mahato NK, Sharma A, Singh Y, Lal R (2019) Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Arch Microbiol.  https://doi.org/10.1007/s00203-018-01616-6 CrossRefPubMedGoogle Scholar
  9. 9.
    Verma H, Bajaj A, Kumar R, Kaur J, Anand S, Nayyar N, Puri A, Singh Y, Khurana JP, Lal R (2017) Genome organization of Sphingobium indicum B90A: an archetypal hexachlorocyclohexane (HCH) degrading genotype. Genome Biol Evol 9:2191–2197.  https://doi.org/10.1093/gbe/evx133 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Sangwan N, Verma H, Kumar R, Negi V, Lax S, Khurana P, Khurana JP, Gilbert JA, Lal R (2014) Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data. ISME J 8:398–408.  https://doi.org/10.1038/ismej.2013.153 CrossRefPubMedGoogle Scholar
  11. 11.
    Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P et al (2017) Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques. Antonie Van Leeuwenhoek 110:1357–1371.  https://doi.org/10.1007/s10482-017-0928-1 CrossRefPubMedGoogle Scholar
  12. 12.
    Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL (2015) Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 197:359–370.  https://doi.org/10.1007/s00203-014-1071-2 CrossRefPubMedGoogle Scholar
  13. 13.
    Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad MN, Negi RK, Singh Y, Khurana JP (2017) Comparative genomic analysis reveals habitat-specific genes and regulatory hubs within the genus Novosphingobium. mSystems 2:e00020–17. https://doi.org/10.1128/mSystems.00020-17 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R (2014) Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics 15:1014.  https://doi.org/10.1186/1471-2164-15-1014 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Sharma A, Sangwan N, Negi V, Kohli P, Khurana JP, Rao DL, Lal R (2015) Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite. BMC Genomics 16:313.  https://doi.org/10.1186/s12864-015-1488-2 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Gupta V, Haider S, Sood U, Gilbert JA, Ramjee M, Forbes K, Singh Y, Lopes BS, Lal R (2016) Comparative genomic analysis of novel Acinetobacter symbionts: a combined systems biology and genomics approach. Sci Rep 6:29043.  https://doi.org/10.1038/srep29043 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Tripathi C, Mishra H, Khurana H, Dwivedi V, Kamra K, Negi RK, Lal R (2017) Complete genome analysis of Thermus parvatiensis and comparative genomics of Thermus spp. provide insights into genetic variability and evolution of natural competence as strategic survival attributes. Front Microbiol 8:1410. https://doi.org/10.3389/fmicb.2017.01410 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Sood U, Hira P, Kumar R, Bajaj A, Rao DL, Lal R, Shakarad M (2019) Comparative genomic analyses reveal core-genome-wide genes under positive selection and major regulatory hubs in outlier strains of Pseudomonas aeruginosa. Front Microbiol 10:53.  https://doi.org/10.3389/fmicb.2019.00053 CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Bhatia S, Batra N, Pathak A, Green SJ, Joshi A, Chauhan A (2015) Metagenomic evaluation of bacterial and archaeal diversity in the geothermal hot springs of Manikaran, India. Genome Announc 3:e01544–e1614.  https://doi.org/10.1128/genomeA.01544-14 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Dudhagara P, Ghelani A, Patel R, Chaudhari R, Bhatt S (2015) Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India. Genomic Data 4:8–11.  https://doi.org/10.1016/j.gdata.2015.01.010 CrossRefGoogle Scholar
  21. 21.
    Mangrola AV, Dudhagara P, Koringa P, Joshi CG, Patel RK (2015) Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India. Genomic Data 4:73–75.  https://doi.org/10.1016/j.gdata.2015.03.005 CrossRefGoogle Scholar
  22. 22.
    Saxena R, Dhakan DB, Mittal P, Waiker P, Chowdhury A, Ghatak A, Sharma VK (2017) Metagenomic analysis of hot springs in Central India reveals hydrocarbon degrading thermophiles and pathways essential for survival in extreme environments. Front Microbiol 7:2123.  https://doi.org/10.3389/fmicb.2016.02123 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Gupta RS (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367–402.  https://doi.org/10.1111/j.1574-6976.2000.tb00547.x CrossRefPubMedGoogle Scholar
  24. 24.
    Krieg NR, Brenner DJ, Staley JT (2005) Bergey's manual of systematic bacteriology: the proteobacteria. Springer, Berlin. ISBN 978–0–387–95040–2.Google Scholar
  25. 25.
    Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A (2017) Proteobacteria: a common factor in human diseases. BioMed Res Int.  https://doi.org/10.1155/2017/9351507 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Sharma A, Gilbert JA, Lal R (2016) (Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans. Sci Rep 6:25527.  https://doi.org/10.1038/srep25527 CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Tilak KV, Ranganayaki N, Pal KK, De R, Saxena AK, Nautiyal CS, Mittal S, Tripathi AK, Johri BN (2005) Diversity of plant growth and soil health supporting bacteria. Curr Sci 10:136–150. https://pdfs.semanticscholar.org/345a/779e00266360d055e69787586e1edf473c4b.pdf
  28. 28.
    Binda C, Lopetuso LR, Rizzatti G, Gibiino G, Cennamo V, Gasbarrini A (2018) Actinobacteria: a relevant minority for the maintenance of gut homeostasis. Dig Liver Dis 50:421–428.  https://doi.org/10.1016/j.dld.2018.02.012 CrossRefPubMedGoogle Scholar
  29. 29.
    Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266.  https://doi.org/10.1099/ijs.0.016949-0 CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Shivaji S, Chaturvedi P, Begum Z, Pindi PK, Manorama R, Padmanaban DA, Shouche YS, Pawar S, Vaishampayan P, Dutt CB, Datta GN, Manchanda RK, Rao UR, Bhargava PM, Narlikar JV (2009) Janibacter hoylei sp. nov., Bacillus isronensis sp. nov. and Bacillus aryabhattai sp. nov., isolated from cryotubes used for collecting air from the upper atmosphere. Int J Syst Evol Microbiol 59:2977–2986.  https://doi.org/10.1099/ijs.0.002527-0 CrossRefPubMedGoogle Scholar
  31. 31.
    Dadhwal M, Jit S, Kumari H, Lal R (2009) Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int J Syst Evol Microbiol 59:3140–3144.  https://doi.org/10.1099/ijs.0.005553-0 CrossRefPubMedGoogle Scholar
  32. 32.
    Lai Q, Yuan J, Shao Z (2009) Maribaculum marinum gen. nov., sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 59:3083–3087.  https://doi.org/10.1099/ijs.0.008177-0 CrossRefPubMedGoogle Scholar
  33. 33.
    Lai Q, Yuan J, Shao Z (2009) Altererythrobacter marinus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 59:2973–2976.  https://doi.org/10.1099/ijs.0.008193-0 CrossRefPubMedGoogle Scholar
  34. 34.
    Lakshmi KV, Sasikala C, Ramana CV (2009) Rhodoplanes pokkaliisoli sp. nov., a phototrophic alphaproteobacterium isolated from a waterlogged brackish paddy soil. Int J Syst Evol Microbiol 59:2153–2157.  https://doi.org/10.1099/ijs.0.008185-0 CrossRefPubMedGoogle Scholar
  35. 35.
    Ramana VV, Kumar PA, Srinivas TNR, Sasikala C, Ramana CV (2009) Rhodobacter aestuarii sp. nov., a phototrophic alphaproteobacterium isolated from an estuarine environment. Int J Syst Evol Microbiol 59:1133–1136.  https://doi.org/10.1099/ijs.0.004507-0 CrossRefPubMedGoogle Scholar
  36. 36.
    Bandyopadhyay S, Schumann P, Das SK (2013) Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India. Arch Microbiol 195:1–8.  https://doi.org/10.1007/s00203-012-0840-z CrossRefPubMedGoogle Scholar
  37. 37.
    Rakshak K, Ravinder K, Nupur STNR, Kumar PA (2013) Caldimonas meghalayensis sp. nov., a novel thermophillic betaproteobacterium isolated from a hot spring of Meghalaya in northeast India. Antonie Van Leeuwenhoek 104:1217–1225.  https://doi.org/10.1007/s10482-013-0043-x CrossRefPubMedGoogle Scholar
  38. 38.
    Srinivas A, Sasikala C, Ramana CV (2014) Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy. Int J Syst Evol Microbiol 64:2198–2203.  https://doi.org/10.1099/ijs.0.063347-0 CrossRefPubMedGoogle Scholar
  39. 39.
    Patil VS, Salunkhe RC, Patil RH, Husseneder C, Shouche YS, Ramana VV (2015) Enterobacillus tribolii gen. nov., sp. nov., a novel member of the family Enterobacteriaceae, isolated from the gut of a red flour beetle Tribolium castaneum. Antonie van Leeuwenhoek 107:1207–1216.  https://doi.org/10.1007/s10482-015-0412-8 CrossRefPubMedGoogle Scholar
  40. 40.
    Ramaprasad EVV, Tushar L, Dave B, Sasikala C, Ramana CV (2016) Rhodovulum algae sp. nov., isolated from an algal mat. Int J Syst Evol Microbiol 66:3367–3371.  https://doi.org/10.1099/ijsem.0.001203 CrossRefPubMedGoogle Scholar
  41. 41.
    Ojha AK, Verma A, Pal Y, Bhatt D, Mayilraj S, Krishnamurthi S (2017) Marinomonas epiphytica sp. nov., isolated from a marine intertidal macroalga. Int J Syst Evol Microbiol 67:2746–2751.  https://doi.org/10.1099/ijsem.0.002014 CrossRefPubMedGoogle Scholar
  42. 42.
    Pal D, Kaur N, Sudan SK, Bisht B, Krishnamurthi S, Mayilraj S (2018) Acidovorax kalamii sp. nov., isolated from a water sample of the river Ganges. Int J Syst Evol Microbiol 68:1719–1724.  https://doi.org/10.1099/ijsem.0.002736 CrossRefPubMedGoogle Scholar
  43. 43.
    Parag B, Sasikala Ch, Ramana ChV (2013) Molecular and culture dependent characterization of endolithic bacteria in two beach sand samples and description of Rhizobium endolithicum sp. nov. Antonie Van Leeuwenhoek 104:1235–1244.  https://doi.org/10.1007/s10482-013-0046-7 CrossRefPubMedGoogle Scholar
  44. 44.
    Reddy SV, Aspana S, Tushar DL, Sasikala C, Ramana CV (2013) Spirochaeta sphaeroplastigenens sp. nov., a halo-alkaliphilic, obligately anaerobic spirochaete isolated from soda lake Lonar. Int J Syst Evol Microbiol 63:2223–2228.  https://doi.org/10.1099/ijs.0.046292-0 CrossRefPubMedGoogle Scholar
  45. 45.
    Sravanthi T, Tushar L, Sasikala C, Ramana CV (2015) Spirochaeta odontotermitis sp. nov., an obligately anaerobic, cellulolytic, halotolerant, alkaliphilic spirochaete isolated from the termite Odontotermes obesus (Rambur) gut. Int J Syst Evol Microbiol 65:4589–4594.  https://doi.org/10.1099/ijsem.0.000616 CrossRefPubMedGoogle Scholar
  46. 46.
    Shivani Y, Subhash Y, Tushar L, Sasikala Ch, Ramana CV (2015) Spirochaeta lutea sp. nov., isolated from marine habitats and emended description of the genus Spirochaeta. Syst Appl Microbiol 38:110–114.  https://doi.org/10.1016/j.syapm.2014.11.002 CrossRefPubMedGoogle Scholar
  47. 47.
    Shivani Y, Subhash Y, Sasikala C, Ramana CV (2016) Description of ‘Candidatus Marispirochaeta associata’ and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov. Int J Syst Evol Microbiol 66:5485–5492.  https://doi.org/10.1099/ijsem.0.001545 CrossRefPubMedGoogle Scholar
  48. 48.
    Sravanthi T, Tushar L, Sasikala C, Ramana CV (2016) Alkalispirochaeta cellulosivorans gen. nov., sp. nov., a cellulose-hydrolysing, alkaliphilic, halotolerant bacterium isolated from the gut of a wood-eating cockroach (Cryptocercus punctulatus), and reclassification of four species of Spirochaeta as new combinations within Alkalispirochaeta gen. nov. Int J Syst Evol Microbiol 66:1612–1619.  https://doi.org/10.1099/ijsem.0.000865 CrossRefPubMedGoogle Scholar
  49. 49.
    Anand S, Bala K, Saxena A, Schumann P, Lal R (2012) Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site. Int J Syst Evol Microbiol 62:2114–2120.  https://doi.org/10.1099/ijs.0.034439-0 CrossRefPubMedGoogle Scholar
  50. 50.
    Dastager SG, Qiang ZL, Damare S, Tang SK, Li WJ (2012) Agromyces indicus sp. nov., isolated from mangroves sediment in Chorao Island, Goa, India. Antonie van Leeuwenhoek 102:345–352.  https://doi.org/10.1007/s10482-012-9744-9 CrossRefPubMedGoogle Scholar
  51. 51.
    Nimaichand S, Zhang YG, Cheng J, Li L, Zhang DF, Zhou EM, Dong L, Ningthoujam DS, Li WJ (2013) Micromonospora kangleipakensis sp. nov., isolated from a sample of limestone quarry. Int J Syst Evol Microbiol 63:4546–4551.  https://doi.org/10.1099/ijs.0.052746-0 CrossRefPubMedGoogle Scholar
  52. 52.
    Singh PK, Kumari A, Chawla N, Pinnaka AK, Korpole S (2015) Rhodococcus lactis sp. nov., an actinobacterium isolated from sludge of a dairy waste treatment plant. Int J Syst Evol Microbiol 65:4215–4220.  https://doi.org/10.1099/ijsem.0.000565 CrossRefPubMedGoogle Scholar
  53. 53.
    Sultanpuram VR, Mothe T, Mohammed F (2015) Nocardioides solisilvae sp. nov., isolated from a forest soil. Antonie Van Leeuwenhoek 107:1599–1606.  https://doi.org/10.1007/s10482-015-0455-x CrossRefPubMedGoogle Scholar
  54. 54.
    Chen RW, Wang KX, Zhou XF, Long C, Tian XP, Long LJ (2018) Indioceanicola profundi gen. nov., sp. nov., isolated from Indian Ocean sediment. Int J Syst Evol Microbiol 68:3707–3712.  https://doi.org/10.1099/ijsem.0.003016 CrossRefPubMedGoogle Scholar
  55. 55.
    Ramaprasad EVV, Sasikala C, Ramana CV (2015) Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva. Int J Syst Evol Microbiol 65:4627–4631.  https://doi.org/10.1099/ijsem.0.000624 CrossRefPubMedGoogle Scholar
  56. 56.
    Prakash O, Nimonkar Y, Munot H, Sharma A, Vemuluri VR, Chavadar MS, Shouche YS (2014) Description of Micrococcus aloeverae sp. nov., an endophytic actinobacterium isolated from Aloe vera. Int J Syst Evol Microbiol 64:3427–3433.  https://doi.org/10.1099/ijs.0.063339-0 CrossRefPubMedGoogle Scholar
  57. 57.
    Kaur G, Mual P, Kumar N, Verma A, Kumar A, Krishnamurthi S, Mayilraj S (2016) Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish. Int J Syst Evol Microbiol 66:4665–4670.  https://doi.org/10.1099/ijsem.0.001407 CrossRefPubMedGoogle Scholar
  58. 58.
    Rahi P, Kurli R, Pansare AN, Khairnar M, Jagtap S, Patel NB, Dastager SG, Lawson PA, Shouche YS (2018) Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone. Int J Syst Evol Microbiol 68:1052–1058.  https://doi.org/10.1099/ijsem.0.002622 CrossRefPubMedGoogle Scholar
  59. 59.
    Ramaswamy M, Nair S, Soumya VP, Thomas GV (2013) Phylogenetic analysis identifies a ‘Candidatus Phytoplasma oryzae’-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India. Int J Syst Evol Microbiol 63:1376–1382.  https://doi.org/10.1099/ijs.0.043315-0 CrossRefPubMedGoogle Scholar
  60. 60.
    Kumar PA, Srinivas TNR, Sasikala C, Ramana CV, Suling J, Imhoff J (2009) Prosthecochloris indica sp. nov., a novel green sulfur bacterium from marine aquaculture pond of Kakinada, India. J Gen Appl Microbiol 55:163–169.  https://doi.org/10.2323/jgam.55.163 CrossRefGoogle Scholar
  61. 61.
    Suradkar A, Villanueva C, Gaysina LA, Casamatta DA, Saraf A, Dighe G, Mergu R, Singh P (2017) Nostoc thermotolerans sp. nov., a soil-dwelling species of Nostoc (Cyanobacteria). Int J Syst Evol Microbiol 67:1296–1305.  https://doi.org/10.1099/ijsem.0.001800 CrossRefPubMedGoogle Scholar
  62. 62.
    Shashidhar R, Bandekar JR (2009) Deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish. Int J Syst Evol Microbiol 59:2714–2717.  https://doi.org/10.1099/ijs.0.003046-0 CrossRefPubMedGoogle Scholar
  63. 63.
    Yadav S, Vaddavalli R, Siripuram S, Eedara RVV, Yadav S, Rabishankar O, Lodha T, Chintalapati S, Chintalapati V (2018) Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis. J Antibiot 71:575.  https://doi.org/10.1038/s41429-018-0035-1 CrossRefGoogle Scholar
  64. 64.
    Lai Q, Cao J, Dupont S, Shao Z, Jebbar M, Alain K (2016) Thermodesulfatator autotrophicus sp. nov., a thermophilic sulfate-reducing bacterium from the Indian Ocean. Int J Syst Evol Microbiol 66:3978–3982.  https://doi.org/10.1099/ijsem.0.001297 CrossRefPubMedGoogle Scholar
  65. 65.
    Jayasinghearachchi HS, Lal B (2011) Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells. Int J Syst Evol Microbiol 61:554–560.  https://doi.org/10.1099/ijs.0.018036-0 CrossRefPubMedGoogle Scholar
  66. 66.
    Rajasabapathy R, Mohandass C, Dastager SG, Liu Q, Khieu T-N, Son CK, Li W-J, Colaco A (2014) Roseovarius azorensis sp. nov., isolated from seawater at Espalamaca Azores. Antonie van Leeuwenhoek 105:571–578.  https://doi.org/10.1007/s10482-013-0109-9 CrossRefPubMedGoogle Scholar
  67. 67.
    Shivaji S, Reddy VVP, Rao SSS, Begum Z, Manasa P, Srinivas TNR (2012) Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment. Int J Syst Evol Microbiol 62:2133–2139.  https://doi.org/10.1099/ijs.0.038661-0 CrossRefPubMedGoogle Scholar
  68. 68.
    Srinivas TNR, Reddy VVP, Begum Z, Manasa P, Shivaji S (2012) Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera. Int J Syst Evol Microbiol 62:1926–1931.  https://doi.org/10.1099/ijs.0.036475-0 CrossRefPubMedGoogle Scholar
  69. 69.
    Srinivas TNR, Manasa P, Begum Z, Sunil B, Sailaja B, Singh SK, Prasad S, Shivaji S (2013) Iodobacter arcticus sp. nov., a psychrotolerant bacterium isolated from a meltwater stream sediment of an Arctic glacier. Int J Syst Evol Microbiol 63:2800–2805.  https://doi.org/10.1099/ijs.0.044776-0 CrossRefPubMedGoogle Scholar
  70. 70.
    Prasad S, Manasa BP, Buddhi S, Pratibha MS, Begum Z, Bandi S, Tirunagari P, Shivaji S (2013) Arcticibacter svalbardensis gen. nov., sp. nov., of the family Sphingobacteriaceae in the phylum Bacteroidetes, isolated from Arctic soil. Int J Syst Evol Microbiol 63:1627–1632.  https://doi.org/10.1099/ijs.0.044420-0 CrossRefPubMedGoogle Scholar
  71. 71.
    Begum Z, Srinivas TNR, Manasa P, Sailaja B, Sunil B, Prasad S, Shivaji S (2013) Winogradskyella psychrotolerans sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from Arctic sediment. Int J Syst Evol Microbiol 63:1646–1652.  https://doi.org/10.1099/ijs.0.044669-0 CrossRefPubMedGoogle Scholar
  72. 72.
    Srinivas TNR, Prasad S, Manasa P, Sailaja B, Begum Z, Shivaji S (2013) Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment of Kongsfjorden, Svalbard, Arctic and emended description of the genus Lacinutrix. Int J Syst Evol Microbiol 63:729–734.  https://doi.org/10.1099/ijs.0.040907-0 CrossRefPubMedGoogle Scholar
  73. 73.
    Chaturvedi P, Prabahar V, Manorama R, Pindi PK, Bhadra B, Begum Z, Shivaji S (2008) Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo Dry Valleys, Antarctica. Int J Syst Evol Microbiol 58:2447–2453.  https://doi.org/10.1099/ijs.0.2008/000067-0 CrossRefPubMedGoogle Scholar
  74. 74.
    Pindi PK, Kishore KH, Reddy GSN, Shivaji S (2009) Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov. Int J Syst Evol Microbiol 59:1348–1352.  https://doi.org/10.1099/ijs.0.006643-0 CrossRefPubMedGoogle Scholar
  75. 75.
    Pindi PK, Manorama R, Begum Z, Shivaji S (2010) Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment. Int J Syst Evol Microbiol 60:2263–2266.  https://doi.org/10.1099/ijs.0.012989-0 CrossRefPubMedGoogle Scholar
  76. 76.
    Shivaji S, Reddy GS (2014) Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. Int J Syst Evol Microbiol 64:3264–3275.  https://doi.org/10.1099/ijs.0.065409-0 CrossRefPubMedGoogle Scholar
  77. 77.
    Shivaji S, Sathyanarayana RG, Sundareswaran VR, Thomas C (2015) Description of Thalassospira lohafexi sp. nov., isolated from Southern Ocean, Antarctica. Arch Microbiol 197:627–637.  https://doi.org/10.1007/s00203-015-1092-5 CrossRefPubMedGoogle Scholar
  78. 78.
    Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL (2013) Microbial genomic taxonomy. BMC Genomics 14:913.  https://doi.org/10.1186/1471-2164-14-913 CrossRefPubMedPubMedCentralGoogle Scholar
  79. 79.
    Meier-Kolthoff JP, Klenk HP, Göker M (2014) Taxonomic use of DNA G+ C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356.  https://doi.org/10.1099/ijs.0.056994-0 CrossRefPubMedPubMedCentralGoogle Scholar
  80. 80.
    Hahn MW, Jezberová J, Koll U, Beck-Saueressig T, Schmidt J (2016) Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences. ISME J 10:1642–1655.  https://doi.org/10.1038/ismej.2015.237 CrossRefGoogle Scholar
  81. 81.
    Teeling H, Waldmann J, Lombardot T, Bauer M, Glöckner FO (2004) TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinform 5:163.  https://doi.org/10.1186/1471-2105-5-163 CrossRefGoogle Scholar
  82. 82.
    Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264.  https://doi.org/10.1128/JB.187.18.6258-6264.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  83. 83.
    Ran W, Kristensen DM, Koonin EV (2014) Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea. MBio 5:e00956–e1014.  https://doi.org/10.1128/mBio.00956-14 CrossRefPubMedPubMedCentralGoogle Scholar
  84. 84.
    Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Commun 10:2182.  https://doi.org/10.1038/s41467-019-10210-3 CrossRefGoogle Scholar
  85. 85.
    Tsai MH, Liu YY, Soo VW, Chen CC (2019) A new genome-to-genome comparison approach for large-scale revisiting of current microbial taxonomy. Microorganisms 7:161.  https://doi.org/10.3390/microorganisms7060161 CrossRefPubMedCentralGoogle Scholar
  86. 86.
    Rosselló-Móra R, Whitman WB (2019) Dialogue on the nomenclatura and clasification of prokaryotes. Syst Appl Microbiol 42:5–14.  https://doi.org/10.1016/j.syapm.2018.07.002 CrossRefPubMedGoogle Scholar
  87. 87.
    Singh DN, Kumar A, Sarbhai MP, Tripathi AK (2012) Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane. Appl Microbiol Biotechnol 93:1337–1350.  https://doi.org/10.1007/s00253-011-3778-1 CrossRefPubMedGoogle Scholar
  88. 88.
    Mani K, Salgaonkar BB, Braganca JM (2012) Culturable halophilic archaea at the initial and crystallization stages of salt production in a natural solar saltern of Goa, India. Aquat Biosyst 8:15.  https://doi.org/10.1186/2046-9063-8-15 CrossRefPubMedPubMedCentralGoogle Scholar
  89. 89.
    Antony CP, Murrell JC, Shouche YS (2012) Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments. FEMS Microbiol Ecol 81:43–51.  https://doi.org/10.1111/j.1574-6941.2011.01274.x CrossRefPubMedGoogle Scholar
  90. 90.
    Upasani VN (2008) Microbiological studies on Sambhar Lake (Salt of Earth) Rajasthan, India. In: Proceedings of Taal 2007: the 12th world lake conference, vol 448, p 450Google Scholar
  91. 91.
    Krishnamurthi S, Chakrabarti T (2013) Diversity of bacteria and archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches. Syst Appl Microbiol 36:56–68.  https://doi.org/10.1016/j.syapm.2012.08.009 CrossRefPubMedGoogle Scholar
  92. 92.
    Panda AK, Bisht SS, De Mandal S, Kumar NS (2016) Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India. AMB Express 6:111.  https://doi.org/10.1186/s13568-016-0284-y CrossRefPubMedPubMedCentralGoogle Scholar
  93. 93.
    Chaudhuri B, Chowdhury T, Chattopadhyay B (2017) Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India. Genomic Data 12:122–129.  https://doi.org/10.1016/j.gdata.2017.04.001 CrossRefGoogle Scholar
  94. 94.
    Mukherjee D, Selvi VA, Ganguly J, Ram LC, Masto RE (2018) Exploratory study of archaebacteria and their habitat in underground, opencast coal mines and coal mine fire areas of Dhanbad. J Geo Soc India 91:575–582.  https://doi.org/10.1007/s12594-018-0907-9 CrossRefGoogle Scholar
  95. 95.
    Kalia VC, Patel SK, Kang YC, Lee JK (2019) Quorum sensing inhibitors as antipathogens: biotechnological applications. Biotechnol Adv 37:68–90.  https://doi.org/10.1016/j.biotechadv.2018.11.006 CrossRefPubMedGoogle Scholar
  96. 96.
    Kalia VC, Prakash J, Koul S, Ray S (2017) Simple and rapid method for detecting biofilm forming bacteria. Ind J Microbiol 57:109–111.  https://doi.org/10.1007/s12088-016-0616-2 CrossRefGoogle Scholar
  97. 97.
    Sood U, Singh DN, Hira P, Lee JK, Kalia VC, Lal R, Shakarad M (2019) Rapid and solitary production of mono-rhamnolipid biosurfactant and biofilm inhibiting pyocyanin by a taxonomic outlier Pseudomonas aeruginosa strain CR1. J Biotechnol 307:98–106.  https://doi.org/10.1016/j.jbiotec.2019.11.0044 CrossRefPubMedGoogle Scholar
  98. 98.
    Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad MN, Negi RK, Singh Y, Khurana JP (2017) Comparative genomic analysis reveals habitat-specific genes and regulatory hubs within the genus Novosphingobium. mSystems 2:e00020–17. https://doi.org/10.1128/mSystems.00020-17
  99. 99.
    Verma H, Dhingra GG, Sharma M, Gupta V, Negi RK, Singh Y, Lal R (2019) Comparative genomics of Sphingopyxis spp. unravelled functional attributes. Genomics S0888–7543:30371–30374.  https://doi.org/10.1016/j.ygeno.2019.11.008 CrossRefGoogle Scholar
  100. 100.
    Yu Y, Zeng Y, Li J, Yang C, Zhang X, Luo F, Dai X (2019) An algicidal Streptomyces amritsarensis strain against Microcystis aeruginosa strongly inhibits microcystin synthesis simultaneously. Sci Total Environ 650:34–43.  https://doi.org/10.1016/j.scitotenv.2018.08.433 CrossRefPubMedGoogle Scholar

Copyright information

© Association of Microbiologists of India 2019

Authors and Affiliations

  • Princy Hira
    • 1
  • Priya Singh
    • 2
  • Anil Kumar Pinnaka
    • 3
  • Suresh Korpole
    • 3
  • Rup Lal
    • 4
    Email author
  1. 1.Department of ZoologyMaitreyi College (University of Delhi)ChanakyapuriIndia
  2. 2.Department of ZoologyAcharya Narendra Dev College (University of Delhi)New DelhiIndia
  3. 3.CSIR-Institute of Microbial TechnologyChandigarhIndia
  4. 4.The Energy and Resource InstituteNew DelhiIndia

Personalised recommendations