Abstract
Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3–V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Availability of data and materials
GenBank submission All the Next-generation sequences have been submitted to GenBank and have appeared in the public database.
References
Abdul MS, Graw MF, Chatziefthimiou AD, Nguyen H, Richer R, Louge M, Hay AG (2016) Microbial characterization of Qatari Barchan sand dunes. PLoS ONE 11:1–22. https://doi.org/10.1371/journal.pone.0161836
Almeida J, Mohanty A, Dharini N, Hoti SL, Kerkar S, Kumar A (2020) A report on novel mosquito pathogenic Bacillus Spp. isolated from a beach in Goa. India Int J Mosq Res 7:21–29
Arun AB, Sridhar KR (2004) Symbiotic performance of fast-growing rhizobia isolated from the coastal sand dune legumes of west coast of India. Biol Fert Soils 40:435–439. https://doi.org/10.1007/s00374-004-0800-0
Aureen G, Ramesh R, Saroj B (2010) Bacteria from sand dunes of Goa promoting growth in eggplant. World J Agric Res 6:555–564
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. https://doi.org/10.1038/ismej.2011.52
Chandel S, Allan EJ, Woodward S (2010) Biological control of Fusarium oxysporum f. sp. lycopersici on tomato by Brevibacillus brevis. J Phytopathol 158:470–478. https://doi.org/10.1111/j.1439-0434.2009.01635.x
Chen WM, Cho NT, Yang SH, Arun AB, Young CC, Sheu SY (2012) Aquabacterium limnoticum sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 62:698–704. https://doi.org/10.1099/ijs.0.030635-0
Desai KN (2005) Significance of Sand Dune Vegetation in the Shelter Belt Development. Pollution in Urban Industrial Environment 229. Thesis. Goa University
Eder W, Peplies J, Wanner G, Frühling A, Verbarg S (2015) Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water. Int J Syst Evol Microbiol 65:920–926. https://doi.org/10.1099/ijs.0.000040
Fernandes GL, Shenoy BD, Menezes LD, Meena RM, Damare SR (2019) Prokaryotic diversity in oxygen depleted waters of the Bay of Bengal inferred using culture-dependent and independent methods. Indian J Microbiol 59:193–199. https://doi.org/10.1007/s12088-019-00786-1
Gaonkar T, Bhosle S (2013) Effect of metals on a siderophore producing bacterial isolate and its implications on microbial assisted bioremediation of metal contaminated soils. Chemosphere 93:1835–1843. https://doi.org/10.1016/j.chemosphere.2013.06.036
Gaonkar T, Nayak PK, Garg S, Bhosle S (2012) Siderophore-producing bacteria from a sand dune ecosystem and the effect of sodium benzoate on siderophore production by a potential isolate. Sci World J 2012:1–8. https://doi.org/10.1100/2012/857249
Glick BR (2012) Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:1–15. https://doi.org/10.6064/2012/963401
Godinho AL, Bhosle S (2009) Sand aggregation by exopolysaccharide-producing Microbacterium arborescens AGSB. Curr Microbiol 58:616–621. https://doi.org/10.1007/s00284-009-9400-4
Godinho AL, Bhosle S (2013) Microbacterium arborescens AGSB sp. nov., isolated from the rhizosphere of sand dune plant, Ipomoea pes caprae. Afr J Microbiol Res 7:5154–5158. https://doi.org/10.5897/ajmr10.198
Graeber I, Kaesler I, Borchert MS et al (2008) Spongiibacter marinus gen. nov., sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1. Int J Syst Evol Microbiol 58:585–590. https://doi.org/10.1099/ijs.0.65438-0
Hammer Ø, Harper DA, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontol 4:1–9
Imhoff JF (2015) Rhodovibrio. Bergey’s Manual Syst Archaea Bacteria. https://doi.org/10.1002/9781118960608.gbm00898
Kedar A, Rathod D, Yadav A, Agarkar G, Rai M (2014) Endophytic Phoma sp. isolated from medicinal plants promote the growth of Zea mays. Nus Biosci 6:1–7. https://doi.org/10.13057/nusbiosci/n060205
Khoshoo TN (1996) India needs a national biodiversity conservation board. Curr Sci 71:506–513
l’Haridon S, Miroshnichenko ML, Kostrikina NA, Tindall BJ, Spring S, Schumann P, Jeanthon C (2006) Vulcanibacillus modesticaldus gen. nov., sp. nov., a strictly anaerobic, nitrate-reducing bacterium from deep-sea hydrothermal vents. Int J Syst Evol Micr 56:1047–1053. https://doi.org/10.1099/ijs.0.64012-0
Lee MS, Do JO, Park MS, Jung S, Lee KH, Bae KS, Kim SB (2006) Dominance of Lysobacter sp. in the rhizosphere of two coastal sand dune plant species, Calystegia soldanella and Elymus mollis. Anton Leeuw 90:19–27. https://doi.org/10.1007/s10482-006-9056-z
Li X, Ma J, Yang Y, Hou H, Liu GJ, Chen F (2019) Short-term response of soil microbial community to field conversion from dryland to paddy under the land consolidation process in North China. Agriculture 9:216. https://doi.org/10.3390/agriculture9100216
Lin YT, Whitman WB, Coleman DC, Chen TH, Chiu CY (2014) Composition of bacterial communities in sand dunes of subtropical coastal forests. Biol Fert Soils 50:809–814. https://doi.org/10.1007/s00374-014-0900-4
Mascarenhas A, Jayakumar S (2008) An environmental perspective of the post-tsunami scenario along the coast of Tamil Nadu, India: role of sand dunes and forests. J Environ Manage 89:24–34. https://doi.org/10.1016/j.jenvman.2007.01.053
May RM (1988) How many species are there on Earth? Science 241:1441–1449. https://doi.org/10.1126/science.241.4872.1441
McLachlan A, Brown AC (2006) Interstitial Ecology. Ecol Sandy Shores. https://doi.org/10.1016/b978-012372569-1/50009-4
Mhamdi R, Laguerre G, Aouani ME, Mars M, Amarger N (2002) Different species and symbiotic genotypes of field rhizobia can nodulate Phaseolus vulgaris in Tunisian soils. FEMS Microbiol Ecol 41:77–84. https://doi.org/10.1111/j.1574-6941.2002.tb00968.x
Mohammadipanah F, Wink J (2016) Actinobacteria from arid and desert habitats: diversity and biological activity. Front Microbiol 6:1541. https://doi.org/10.3389/fmicb.2015.01541
Muthukumar K, Samuel AS (2011) Coastal sand dune flora in the Thoothukudi District, Tamil Nadu, southern India. J Threat Taxa. https://doi.org/10.11609/jott.o2634.2211-6
Narsing Rao MP, Xiao M, Li WJ (2017) Fungal and bacterial pigments: secondary metabolites with wide applications. Front Microbiol 8:1113. https://doi.org/10.3389/fmicb.2017.01113
Nayak PK, Mohanty AK, Gaonkar T, Kumar A, Bhosle SN, Garg S (2013) Rapid identification of polyhydroxyalkanoate accumulating members of Bacillales using internal primers for phaC gene of Bacillus megaterium. ISRN Bacteriol. https://doi.org/10.1155/2013/562014
Nayak S, Behera S, Dash PK (2019) Potential of microbial diversity of coastal sand dunes: need for exploration in Odisha Coast of India. Sci World J 2019:1–9. https://doi.org/10.1155/2019/2758501
Park MS, Jung SR, Lee MS, Kim KO, Do JO, Lee KH, Bae KS (2005) Isolation and characterization of bacteria associated with two sand dune plant species, Calystegia soldanella and Elymus mollis. J Microbiol 43:219–227
Poyyamoli G, Padmavathy K, Balachandran N (2012) Coastal sand dunes vegetation structure, diversity and disturbance in Nallavadu Village, Puducherry, India. In: Subramanian V (ed) Coastal environments: focus on Asian regions. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3002-3_14
Prabhu N, Borkar S, Garg S (2018) Phosphate solubilization mechanisms in alkaliphilic bacterium Bacillus marisflavi FA7. Curr Sci 114:845–853. https://doi.org/10.18520/cs/v114/i04/845-853
Pradella S, Hans A, Spröer C et al (2002) Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56. Arch Microbiol 178:484–492. https://doi.org/10.1007/s00203-002-0479-2
Qiu Z, Wang J, Delgado-Baquerizo M, Trivedi P, Egidi E, Chen YM, Singh BK (2020) Plant microbiomes: do different preservation approaches and primer sets alter our capacity to assess microbial diversity and community composition? Front Plant Sci 11:993. https://doi.org/10.3389/fpls.2020.00993
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Glöckner FO (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. https://doi.org/10.1093/nar/gks1219
Ramarajan S, Murugesan AG (2014) Plant diversity on coastal sand dune flora, Tirunelveli, District, Tamil Nadu. Indian J Plant Physiol 3:42–48
Rodgers WA, Panwar SH (1988) Biogeographical classification of India. New Forest, Dehra Dun, India.
Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (2014) The Prokaryotes: Actinobacteria 201–238. Springer, Berlin Heidelberg
Sangeetha S, Jaffar Hussain A, Jayaprakashvel M (2012) Antagonistic activity of salt tolerant Actinobacteria against phytopathogens. In: Manoharan V (ed) National Conference on Marine Environmental Challenges and coastal zone management strategy. Bharathidasan University Press, Trichirappalli
Sauder LA, Engel K, Stearns JC, Masella AP, Pawliszyn R, Neufeld JD (2011) Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters. PLoS ONE 6:23281. https://doi.org/10.1371/journal.pone.0023281
Seena S, Sridhar KR, Arun AB (2007) Canavalia cathartica of the south-west coast of India-A neglected wild legume. Plant Genet Resour Newsl 150:16
Sharma A, Dhar SK, Prakash O, Vemuluri VR, Thite V, Shouche YS (2014) Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus. Int J Syst Evol Microbiol 64:3010–3015. https://doi.org/10.1099/ijs.0.064295-0
Shin D, Park MS, Jung S, Lee MS, Lee KH, Bae KS, Kim SB (2007) Plant growth-promoting potential of endophytic bacteria isolated from roots of coastal sand dune plants. J Microbiol Biotechnol 17:1361
Shinde VL, Suneel V, Rathore C, Shenoy BD (2020) Degradation of tarballs using associated bacterial consortia. 3 Biotech 10:109. https://doi.org/10.1007/s13205-020-2095-8
Speirs LBM, Rice DTF, Petrovski S, Seviour RJ (2019) The phylogeny, biodiversity, and ecology of the chloroflexi in activated sludge. Front Microbiol 10:2015. https://doi.org/10.3389/fmicb.2019.02015
Suneel V, Vethamony P, Naik BG, Krishna MS, Jadhav L (2015) Identifying the source of tar balls deposited along the beaches of Goa in 2013 and comparing with historical data collected along the west coast of India. Sci Total Environ 527:313–321. https://doi.org/10.1016/j.scitotenv.2015.04.102
Verma M, Lal D, Kaur J, Saxena A, Kaur J, Anand S, Lal R (2013) Phylogenetic analyses of phylum Actinobacteria based on whole-genome sequences. Res Microbiol 164:718–728. https://doi.org/10.1016/j.resmic.2013.04.002
Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W (2016) Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition. Biotechnol Biofuels 9:22. https://doi.org/10.1186/s13068-016-0440-2
Warnock AM, Hagen SC, Passeri DL (2015) Marine tar residues: a review. Water Air Soil Poll 226:68. https://doi.org/10.1007/s11270-015-2298-5
Wasserstrom H, Kublik S, Wasserstrom R, Schulz S, Schloter M, Steinberger Y (2017) Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland. Sci Rep 7:1–7. https://doi.org/10.1038/srep40266
Whittaker RH (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecol Monographs 30:279–338. https://doi.org/10.2307/1943563
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. https://doi.org/10.1101/gr.074492.107
Zhang L, He J (2012) A novel archaeal phylum: Thaumarchaeota–a review. Wei Sheng Wu Xue Bao. Acta Microbiol Sin 52:411
Zhang L, Wu GL, Wang Y, Dai J, Fang CX (2011) Bacillus deserti sp. nov., a novel bacterium isolated from the desert of Xinjiang, China. Anton Leeuw 99:221–229. https://doi.org/10.1007/s10482-010-9479-4
Acknowledgements
This work was supported by University Grant Commission (UGC), National Fellowship for Students to pursue a Ph.D. degree [award letter number: F./2014-15/NFO-2014-15-OBC-GOA-486/(SA-III/website)]. The authors would like to thank Dr. Priya Mallika D’Costa, faculty at Goa University for going through the manuscript and giving valuable suggestions.
Funding
This work was supported by the University Grant Commission (UGC), National Fellowship for Students to pursue a Ph.D. degree [award letter number: F./2014-15/NFO-2014-15-OBC-GOA-486/(SA-III/website)].
Author information
Authors and Affiliations
Contributions
All authors contributed to the study conception and design. Materials preparation, data collection, and analysis were performed by SAS and SG. The draft of the manuscript was written by SAS and SG commented on previous versions of the manuscript. All the authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Shet, S.A., Garg, S. Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics. 3 Biotech 11, 252 (2021). https://doi.org/10.1007/s13205-021-02809-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-021-02809-5