Spatiotemporal Analysis of Bacterial Diversity in Sediments of Sundarbans Using Parallel 16S rRNA Gene Tag Sequencing

Microbial Ecology

Volumn 69, Issue 3, 2015, Pages 500-511

  Basak, Pijush ^a   Majumder, Niladri Shekhar ^b   Nag, Sudip ^a   Bhattacharyya, Anish ^a   Roy, Debojyoti ^a   Chakraborty, Arpita ^a   SenGupta, Sohan ^a   Roy, Arunava ^a   Mukherjee, Arghya ^a   Pattanayak, Rudradip ^a   Ghosh, Abhrajyoti ^c   Chattopadhyay, Dhrubajyoti ^a   Bhattacharyya, Maitree ^a  

^a UNIVERSITY OF CALCUTTA   (India)

^b URS Consulting India Pvt Ltd   (India)

^c BOSE INSTITUTE   (India)

Author keywords

16S rRNA gene; 454 amplicon sequencing; Microbial diversity; Sundarbans

Indexed keywords

BACTERIAL DNA; RNA 16S;

BACTERIUM; DNA SEQUENCE; GENETICS; INDIA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; SEDIMENT; SPATIOTEMPORAL ANALYSIS; WETLAND;

BACTERIA; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; INDIA; MICROBIOTA; MOLECULAR SEQUENCE DATA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPATIO-TEMPORAL ANALYSIS; WETLANDS;

EID: 84925534677     PISSN: 00953628     EISSN: 1432184X     Source Type: Journal    
DOI: 10.1007/s00248-014-0498-y     Document Type: Article

References (45)

1. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, Lindquist N, Perez T, Rodrigo A, Schupp PJ, Vacelet J, Webster N, Hentschel U, Taylor MW (2012) Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 6:564–576
2. Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, Tringe SG, Brodie EL, Dominguez-Bello MG (2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6:531–541
3. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103:12115–12120
4. Gomes NC, Cleary DF, Calado R, Costa R (2011) Mangrove bacterial richness. Commun Integr Biol 4:419–423
5. Alongi DM (1988) Bacterial productivity and microbial biomass in tropical mangrove sediments. Microb Ecol 15:59–79
6. Holguin G, Gonzalez-Zamorano P, De-Bashan LE, Mendoza R, Amador E, Bashan Y (2006) Mangrove health in an arid environment encroached by urban development—a case study. Sci Total Environ 363:260–274
7. Duke NC, Meynecke JO, Dittmann S, Ellison AM, Anger K, Berger U, Cannicci S, Diele K, Ewel KC, Field CD, Koedam N, Lee SY, Marchand C, Nordhaus I, Dahdouh-Guebas F (2007) A world without mangroves? Science 317:41–42
8. Bouchez A, Pascault N, Chardon C, Bouvy M, Cecchi P, Lambs L, Herteman M, Fromard F, Got P, Leboulanger C (2013) Mangrove microbial diversity and the impact of trophic contamination. Mar Pollut Bull 66:39–46
9. Feller IC, Lovelock CE, Berger U, McKee KL, Joye SB, Ball MC (2010) Biocomplexity in mangrove ecosystems. Ann Rev Mar Sci 2:395–417
10. Giri C, Ochieng E, Tieszen LL, Zhu Z, Singh A, Loveland T, Masek J, Duke N (2011) Status and distribution of mangrove forests of the world using earth observation satellite data. Glob Ecol Biogeogr 20:154–159
11. Gomes NC, Flocco CG, Costa R, Junca H, Vilchez R, Pieper DH, Krogerrecklenfort E, Paranhos R, Mendonca-Hagler LC, Smalla K (2010) Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia. FEMS Microbiol Ecol 74:276–290
12. Ghosh A, Dey N, Bera A, Tiwari A, Sathyaniranjan K, Chakrabarti K, Chattopadhyay D (2010) Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India. Saline Syst 6:1
13. Yan B, Hong K, Yu ZN (2006) Archaeal communities in mangrove soil characterized by 16S rRNA gene clones. J Microbiol 44:566–571
14. Taketani RG, Yoshiura CA, Dias AC, Andreote FD, Tsai SM (2010) Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove. Antonie Van Leeuwenhoek 97:401–411
15. Dias AC, Pereira Silva Mde EC, Cotta SR, Dini-Andreote F, Soares FL Jr, Salles JF, Azevedo JL, Van Elsas JD, Andreote FD (2012) Abundance and genetic diversity of nifH gene sequences in anthropogenically affected Brazilian mangrove sediments. Appl Environ Microbiol 78:7960–7967
16. Zhang Y, Dong J, Yang Z, Zhang S, Wang Y (2008) Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR-denaturing gradient gel electrophoresis. Arch Microbiol 190:19–28
17. Marcial Gomes NC, Borges LR, Paranhos R, Pinto FN, Mendonca-Hagler LC, Smalla K (2008) Exploring the diversity of bacterial communities in sediments of urban mangrove forests. FEMS Microbiol Ecol 66:96–109
18. Dos Santos HF, Cury JC, Do Carmo FL, Dos Santos AL, Tiedje J, Van Elsas JD, Rosado AS, Peixoto RS (2011) Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS ONE 6:e16943
19. Peixoto R, Chaer GM, Carmo FL, Araujo FV, Paes JE, Volpon A, Santiago GA, Rosado AS (2011) Bacterial communities reflect the spatial variation in pollutant levels in Brazilian mangrove sediment. Antonie Van Leeuwenhoek 99:341–354
20. Taketani RG, Franco NO, Rosado AS, van Elsas JD (2010) Microbial community response to a simulated hydrocarbon spill in mangrove sediments. J Microbiol 48:7–15
21. Brito EM, Guyoneaud R, Goni-Urriza M, Ranchou-Peyruse A, Verbaere A, Crapez MA, Wasserman JC, Duran R (2006) Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 157:752–762
22. Andreote FD, Jimenez DJ, Chaves D, Dias AC, Luvizotto DM, Dini-Andreote F, Fasanella CC, Lopez MV, Baena S, Taketani RG, de Melo IS (2012) The microbiome of Brazilian mangrove sediments as revealed by metagenomics. PLoS ONE 7:e38600
23. Gilbert JA, Meyer F, Bailey MJ (2011) The future of microbial metagenomics (or is ignorance bliss?). ISME J 5:777–779
24. Manna S, Chaudhuri K, Bhattacharyya S, Bhattacharyya M (2010) Dynamics of Sundarban estuarine ecosystem: eutrophication induced threat to mangroves. Saline Syst 6:8
25. Nelson DW, Somers LE (1975) Organic carbon. Academic, London
26. Black CA (1965) Methods of soil analysis. American Society of Agronomy, Wisconsin, USA
27. Knudsen M (1901) Hydrographical tables. G.E.C, Gad Copenhagen
28. Knap A, Michaels A, Close A, Ducklow H, Dickson A (eds.) (1996) Protocols for the Joint global ocean flux study (jgofs) core measurements
29. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
30. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9
31. Clark M (1998) Redox stratification and heavy metal partitioning in Avicennia-dominated mangrove sediments: a geochemical model. Chem Geol 149:147–171
32. Proctor LM (1997) Nitrogen-fixing, photosynthetic, anaerobic bacteria associated with pelagic copepods. Aquat Microb Ecol 12:105–113
33. Sauer JD, Shannon JG, Howe D, Hayes SF, Swanson MS, Heinzen RA (2005) Specificity of Legionella pneumophila and Coxiella burnetii vacuoles and versatility of Legionella pneumophila revealed by coinfection. Infect Immun 73:4494–4504
34. Dang H, Li T, Chen M, Huang G (2007) Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl Environ Microbiol 74:52–60
35. Liang Q, Lloyd-Jones G (2010) Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil. Int J Syst Evol Microbiol 60:413–416
36. Barua S, Tripathi S, Chakraborty A, Ghosh S, Chakrabarti K (2012) Characterization and crop production efficiency of diazotrophic bacterial isolates from coastal saline soils. Microbiol Res 167:95–102
37. Wu J, Guan T, Jiang H, Zhi X, Tang S, Dong H, Zhang L, Li W (2009) Diversity of Actinobacterial community in saline sediments from Yunnan and Xinjiang, China. Extremophiles 13:623–632
38. Arumugam M, Mitra A, Pramanik A, Saha M, Gachhui R, Mukherjee J (2010) Streptomyces Sundarbansensis sp. nov., an actinomycete that produces 2-allyloxyphenol. Int J Syst Evol Microbiol 61:2664–2669
39. Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669
40. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120
41. Schottner S, Pfitzner B, Grunke S, Rasheed M, Wild C, Ramette A (2011) Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea. Environ Microbiol 13:1815–1826
42. Bolhuis H, Stal LJ (2011) Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. ISME J 5:1701–1712
43. Derakshani M, Lukow T, Liesack W (2001) Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl Environ Microbiol 67:623–631
44. Harris JK, Kelley ST, Pace NR (2004) New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol 70:845–849
45. Youssef NH, Blainey PC, Quake SR, Elshahed MS (2011) Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl Environ Microbiol 77:7804–7814