Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach

1. Thatoi, H., Behera, B. C., Mishra, R. R. & Dutta, S. K. Biodiversity and biotechnological potential of microorganisms from mangrove ecosystems: A review. Ann. Microbiol. 63, 1–19 (2013).

   Google Scholar 

2. Pellegrinetti, T. A. et al. The role of microbial communities in biogeochemical cycles and greenhouse gas emissions within tropical soda lakes. Sci. Total Environ. 947, 174646 (2024).

   Google Scholar 

3. Abdel-Wahab, M. A. Diversity of marine fungi from Egyptian Red Sea mangroves. Bot. Mar. 48, 348 (2005).

   Google Scholar 

4. Sankara Vel, V., Sreeram, S. & Arunprasath, A. Acclimatization on biochemical composition of the true mangrove species in Karankadu Mangrove Forest, Ramanathapuram District. Russ J. Plant. Physiol. 70, 67 (2023).

   Google Scholar 

5. Garbeva, P., van Elsas, J. D. & van Veen, J. A. Rhizosphere microbial community and its response to plant species and soil history. Plant. Soil. 302, 19–32 (2008).

   Google Scholar 

6. Philippot, L., Raaijmakers, J. M., Lemanceau, P. & van der Putten, W. H. Going back to the roots: The microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11, 789–799 (2013).

   Google Scholar 

7. Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant. Sci. 17, 478–486 (2012).

   Google Scholar 

8. Ling, N., Wang, T. & Kuzyakov, Y. Rhizosphere bacteriome structure and functions. Nat. Commun. 13, 836 (2022).

   Google Scholar 

9. Thatoi, H., Mishra, R. R. & Behera, B. C. Biotechnological potentials of halotolerant and halophilic bacteria from mangrove ecosystems. In: (eds Patra, J. K., Mishra, R. R. & Thatoi, H.) Biotechnological Utilization of Mangrove Resources. Elsevier, 413–433 (2020). https://doi.org/10.1016/B978-0-12-819532-1.00020-2

   Google Scholar 

10. Al-Mur, B. A. Biological activities of Avicennia marina roots and leaves regarding their chemical constituents. Arab. J. Sci. Eng. 46, 5407–5419 (2021).

    Google Scholar 

11. Downton, W. Growth and osmotic relations of the mangrove Avicennia marina, as influenced by salinity. Funct. Plant. Biol. 9, 519 (1982).

    Google Scholar 

12. Kumar, V. A., Ammani, K., Siddhardha, B., Sreedhar, U. & Kumar, G. A. Differential biological activities of the solvent extracts of Ceriops decandra (Griff.) and their phytochemical investigations. J. Pharm. Res. 7, 654–660 (2013).

    Google Scholar 

13. Shamsuzzaman, M., Kalaiselvi, K. & Prabakaran, M. Evaluation of antioxidant and anticorrosive activities of Ceriops tagal plant extract. Appl. Sci. 11, 10150 (2021).

    Google Scholar 

14. Prabhu, V. V. & Guruvayoorappan, C. Anti-inflammatory and anti-tumor activity of the marine mangrove Rhizophora apiculata. J. Immunotoxicol. 9, 341–352 (2012).

    Google Scholar 

15. Patra, J., Dhal, N. & Thatoi, H. In vitro bioactivity and phytochemical screening of Suaeda maritima (Dumort): A mangrove associate from Bhitarkanika, India. Asian Pac. J. Trop. Med. 4, 727–734 (2011).

    Google Scholar 

16. Fatnani, D. & Parida, A. K. Unravelling the halophyte Suaeda maritima as an efficient candidate for phytostabilization of cadmium and lead: Implications from physiological, ionomic, and metabolomic responses. Plant. Physiol. Biochem. 212, 108770 (2024).

    Google Scholar 

17. Manojkumar, S. et al. Phytochemical Screening, In silico molecular docking, ADME properties, and in vitro antioxidant, anticancer, and antidiabetic activity of marine halophyte Suaeda maritima (L.) dumort. ACS Omega. 9, 11200–11216 (2024).

    Google Scholar 

18. Jalal, R. S. et al. The microbiome of Suaeda monoica and Dipterygium glaucum from Southern Corniche (Saudi Arabia) reveals different recruitment patterns of bacteria and archaea. Front. Mar. Sci. 9, 865834 (2022).

    Google Scholar 

19. Shakthi, A., Linoj, J., Suresh, V., Hussein, M. A. & Selvamani, M. Evaluation of antibacterial and anti-oxidant activities of Suaeda monoica extract for its potential application. Cureus 16, e53091 (2024).

    Google Scholar 

20. Zhang, W., Wang, D., Cao, D., Chen, J. & Wei, X. Exploring the potentials of Sesuvium portulacastrum L. for edibility and bioremediation of saline soils. Front. Plant. Sci. 15, 1387102 (2024).

    Google Scholar 

21. Andreote, F. D. et al. The microbiome of Brazilian mangrove sediments as revealed by metagenomics. PLoS One. 7, e38600 (2012).

    Google Scholar 

22. Chithira, M. S., Aishwarya, P. V., Mohan, A. S. & Antony, S. P. Profiling bacteriome associated with the sediments of a mangrove ecosystem in Kerala, India. Ecol. Genet. Genom. 21, 100103 (2021).

    Google Scholar 

23. Nathan, V. K., Vijayan, J. & Ammini, P. Comparison of bacterial diversity from two mangrove ecosystems from India through metagenomic sequencing. Reg. Stud. Mar. Sci. 35, 101184 (2020).

    Google Scholar 

24. dos Santos, H. F. et al. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: Bacterial proxies for oil pollution. PLoS One. 6, e16943 (2011).

    Google Scholar 

25. Basak, P., Pramanik, A., Roy, R., Chattopadhyay, D. & Bhattacharyya, M. Cataloguing the bacterial diversity of the Sundarbans mangrove, India in the light of metagenomics. Genom Data. 4, 90–92 (2015).

    Google Scholar 

26. Imchen, M. et al. Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. Sci. Rep. 7, 8859 (2017).

    Google Scholar 

27. Imchen, M. et al. Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems. Sci. Rep. 8, 11187 (2018).

    Google Scholar 

28. Wemheuer, B., Wemheuer, F. & Daniel, R. RNA-based assessment of diversity and composition of active archaeal communities in the German bight. Archaea. 2012: 1–8. (2012).

    Google Scholar 

29. Bhattacharyya, A. et al. Diversity and distribution of archaea in the mangrove sediment of Sundarbans. Archaea 2015, 1–14 (2015).

    Google Scholar 

30. Lay, C. Y., Hamel, C. & St-Arnaud, M. Taxonomy and pathogenicity of Olpidium brassicae and its allied species. Fungal Biol. 122, 837–846 (2018).

    Google Scholar 

31. Egamberdieva, D., Wirth, S., Bellingrath-Kimura, S. D., Mishra, J. & Arora, N. K. Salt-tolerant plant growth promoting rhizobacteria for enhancing crop productivity of saline soils. Front. Microbiol. 10, 2791 (2019).

    Google Scholar 

32. Chi, Z. et al. Deciphering edaphic bacterial community and function potential in a Chinese delta under exogenous nutrient input and salinity stress. Catena (Amst). 201, 105212 (2021).

    Google Scholar 

33. Liu, W., Fan, Y., He, P. & Chen, H. Complete genome sequence of a nitrate reducing bacteria, Algoriphagus sp. Y33 isolated from the water of the Indian Ocean. Mar. Genomics. 59, 100861 (2021).

    Google Scholar 

34. Kochhar, N. et al. Perspectives on the microorganism of extreme environments and their applications. Curr. Res. Microb. Sci. 3, 100134 (2022).

    Google Scholar 

35. Craig, H. et al. Nitrogen addition alters composition, diversity, and functioning of microbial communities in mangrove soils: An incubation experiment. Soil. Biol. Biochem. 153, 108076 (2021).

    Google Scholar 

36. Zhang, X., Lin, H., Wang, X. & Austin, B. Significance of Vibrio species in the marine organic carbon cycle—A review. Sci. China Earth Sci. 61, 1357–1368 (2018).

    Google Scholar 

37. Hagaggi, N., Sh, A. & Abdul-Raouf, U. M. Macroalga-associated bacterial endophyte bioactive secondary metabolites twinning: Cystoseira myrica and its associated Catenococcus thiocycli QCm as a model. World J. Microbiol. Biotechnol. 38, 205 (2022).

    Google Scholar 

38. Mahapatra, S., Yadav, R. & Ramakrishna, W. Bacillus subtilis impact on plant growth, soil health and environment: Dr. Jekyll and Mr. Hyde. J. Appl. Microbiol. 132, 3543–3562 (2022).

    Google Scholar 

39. Deryabin, D. G. & Aleshina, E. S. Effect of salts on luminescence of natural and recombinant luminescent bacterial biosensors. Appl. Biochem. Microbiol. 44, 292–296 (2008).

    Google Scholar 

40. Xiao, M., Long, Z., Fu, X. & Zou, L. Versatile applications and mechanisms of genus Exiguobacterium in bioremediating heavy metals and organic pollutants: A review. Int. Biodeterior. Biodegradation. 194, 105884 (2024).

    Google Scholar 

41. Zhong, W. & Agarwal, V. Polymer degrading marine Microbulbifer bacteria: An un(der)utilized source of chemical and biocatalytic novelty. Beilstein J. Org. Chem. 20, 1635–1651 (2024).

    Google Scholar 

42. Kadri, T., Magdouli, S., Rouissi, T. & Brar, S. K. Ex-situ biodegradation of petroleum hydrocarbons using Alcanivorax borkumensis enzymes. Biochem. Eng. J. 132, 279–287 (2018).

    Google Scholar 

43. Wu, Z. et al. A slow-release reduction material of Escherichia sp. F1 coupled with micron iron powder achieves the remediation of trichloroethylene-contaminated soil. J. Environ. Manage. 370, 122765 (2024).

    Google Scholar 

44. McLeish, A. G., Greenfield, P., Midgley, D. J. & Paulsen, I. T. Desulfuromonas sp. ‘CSMB_57’, isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals. Microb. Genom. 8, 000857 (2022).

    Google Scholar 

45. Logan, L. K. & Weinstein, R. A. The epidemiology of carbapenem-resistant enterobacteriaceae: The impact and evolution of a global menace. J. Infect. Dis. 215, S28–S36 (2017).

    Google Scholar 

46. Tacconelli, E. et al. Discovery, research, and development of new antibiotics: The WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318–327 (2018).

    Google Scholar 

47. Miller, W. R. & Arias, C. A. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat. Rev. Microbiol. 22, 598–616 (2024).

    Google Scholar 

48. Findlay, J., Poirel, L., Kessler, J., Kronenberg, A. & Nordmann, P. New Delhi metallo-β-lactamase–producing Enterobacterales bacteria, Switzerland, 2019–2020. Emerg. Infect. Dis. 27, 2628–2637 (2021).

    Google Scholar 

49. Lee, M. R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638 (2015).

    Google Scholar 

50. Araghi, A., Hashemi, S., Akhavan Sepahi, A., Faramarzi, M. A. & Amin, M. Purification and study of anti-cancer effects of Serratia marcescens serralysin. Iran. J. Microbiol. 11, 320–327 (2019).

    Google Scholar 

51. Selan, L. et al. Serratiopeptidase: A well-known metalloprotease with a new non-proteolytic activity against S. aureus biofilm. BMC Microbiol. 15, 207 (2015).

    Google Scholar 

52. Marzhoseyni, Z. et al. Designing a novel fusion protein from Streptococcus agalactiae with apoptosis induction effects on cervical cancer cells. Microb. Pathog. 169, 105670 (2022).

    Google Scholar 

53. Broberg, C. A., Calder, T. J. & Orth, K. Vibrio parahaemolyticus cell biology and pathogenicity determinants. Microbes Infect. 13, 992–1001 (2011).

    Google Scholar 

54. Price, C. E., Zeyniyev, A., Kuipers, O. P. & Kok, J. From meadows to milk to mucosa—Adaptation of Streptococcus and Lactococcus species to their nutritional environments. FEMS Microbiol. Rev. 36, 949–971 (2012).

    Google Scholar 

55. Wang, Y. & Huang, Y. Effect of Lactobacillus acidophilus and Bifidobacterium bifidum supplementation to standard triple therapy on Helicobacter pylori eradication and dynamic changes in intestinal flora. World J. Microbiol. Biotechnol. 30, 847–853 (2014).

    Google Scholar 

56. Raghavan, P. U. M. & Vivekanandan, M. Bioremediation of oil-spilled sites through seeding of naturally adapted Pseudomonas putida. Int. Biodeterior. Biodegrad. 44, 29–32 (1999).

    Google Scholar 

57. Smith, M. et al. Pseudomonas and Xanthomonas. in European Handbook of Plant Diseases 136–175 (Wiley, 1988).

58. Li, L. et al. Comparative genomic analysis of Pseudomonas amygdali pv. lachrymans NM002: Insights into its potential virulence genes and putative invasion determinants. Genomics 111, 1493–1503 (2019).

    Google Scholar 

59. Cremonesi, A. S. et al. The citrus plant pathogen Xanthomonas citri has a dual polyamine-binding protein. Biochem. Biophys. Rep. 28, 101171 (2021).

    Google Scholar 

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