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Volume 7, Issue 6

Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia Open Access

Abstract

The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed (67–69%), (6–8%), (5–8%), (4–5%), (3–4%), (2–4%) and (1–2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the ‘Shannon’ index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of , and suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S sequencing , coastal Malaysia , ecosystem , mangrove microbiome , microbial diversity and soil bacteria
Funding
This study was supported by the:
  • NUMed Internal Research Grant (Award 226900-IG2)
    • Principle Award Recipient: ROSHANMASCARENHAS
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-06-18
2025-07-10
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References

  1. Carugati L, Gatto B, Rastelli E, Lo Martire M, Coral C et al. Impact of mangrove forests degradation on biodiversity and ecosystem functioning. Sci Rep 2018; 8:13298 [View Article] [PubMed]
     [Google Scholar]
  2. Nagelkerken I, Blaber SJM, Bouillon S, Green P, Haywood M et al. The habitat function of mangroves for terrestrial and marine fauna: a review. Aquatic Botany 2008; 89:155–185 [View Article]
     [Google Scholar]
  3. Nellemann C, Corcoran E, Duarte CM, Valdés L, De Young C et al. Blue carbon. A rapid response assessment. Arendal, Norway: GRID-Arendal; 2009
  4. Alongi DM. Carbon cycling and storage in mangrove forests. Annu Rev Mar Sci 2014; 6:195–219 [View Article]
     [Google Scholar]
  5. Sasmito SD, Kuzyakov Y, Lubis AA, Murdiyarso D, Hutley LB et al. Organic carbon burial and sources in soils of coastal mudflat and mangrove ecosystems. CATENA 2020; 187:104414 [View Article]
     [Google Scholar]
  6. Feller IC, Friess DA, Krauss KW, Lewis RR III. The state of the world’s mangroves in the 21st century under climate change. Hydrobiologia 2017; 803:1–12 [View Article]
     [Google Scholar]
  7. Howard J, Sutton-Grier A, Herr D, Kleypas J, Landis E et al. Clarifying the role of coastal and marine systems in climate mitigation. Frontiers in Ecol & Environ 2017; 15:42–50 [View Article]
     [Google Scholar]
  8. Trevathan-Tackett SM, Sherman CDH, Huggett MJ, Campbell AH, Laverock B et al. A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 2019; 3:1509–1520 [View Article]
     [Google Scholar]
  9. Hamilton SE, Casey D. Creation of a high spatio‐temporal resolution global database of continuous mangrove forest cover for the 21st century (CGMFC‐21). Global Ecol Biogeogr 2016; 25:729–738 [View Article]
     [Google Scholar]
  10. Bryan-Brown DN, Connolly RM, Richards DR, Adame F, Friess DA et al. Global trends in mangrove forest fragmentation. Sci Rep 2020; 10:7117 [View Article] [PubMed]
     [Google Scholar]
  11. Ramli SF, Caihong Z. National mangrove restoration project in malaysia. J Environ Earth Sci 2017; 7:119–125
     [Google Scholar]
  12. Wainwright BJ, Millar T, Bowen L, Semon L, Hickman KJE et al. The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival. Environ Microbiome 2023; 18:47 [View Article] [PubMed]
     [Google Scholar]
  13. Fadzil MF, Yun PS, Razal AR, Chee PS, Suratman S et al. Oil and grease and total petroleum hydrocarbons in the waters of ramsar gazetted mangrove area. Johor J Sustain Sci Manag 2017; 12:30–39
     [Google Scholar]
  14. Gonsilou AP, Azman S, Isharunizam NIA, Mohamed Najib MZ, Syafiuddin A et al. Microplastic uptake by mud creepers (Cerithidea obtusa) at Kukup, Johor. J Sustain Sci Manag 2023; 18:1–23 [View Article]
     [Google Scholar]
  15. Halim NHA, Abdullah R, Kadir WR, Ajeng AA, Zawawi NZB. Heavy metals distribution and fractionation in mangrove sediments linked to organic deposits vis-à-vis accumulation in Rhizophora spp. at Tanjung Piai, Johor, Malaysia. Appl Ecol Env Res 2022; 20:4011–4030 [View Article]
     [Google Scholar]
  16. Kanniah K, Sheikhi A, Cracknell A, Goh H, Tan K et al. Satellite images for monitoring mangrove cover changes in a fast growing economic region in southern Peninsular Malaysia. Remote Sens 2015; 7:14360–14385 [View Article]
     [Google Scholar]
  17. de Araujo JE, Taketani RG, Pylro VS, Leite LR, Pereira E Silva M de C et al. Genomic analysis reveals the potential for hydrocarbon degradation of Rhodopirellula sp. MGV isolated from a polluted Brazilian mangrove. Braz J Microbiol 2021; 52:1397–1404 [View Article] [PubMed]
     [Google Scholar]
  18. Gong B, Cao H, Peng C, Perčulija V, Tong G et al. High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China. Sci Rep 2019; 9:9377 [View Article] [PubMed]
     [Google Scholar]
  19. Sepúlveda-Correa A, Daza-Giraldo LV, Polanía J, Arenas NE, Muñoz-García A et al. Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities. Marine Pollution Bulletin 2021; 171:112740 [View Article]
     [Google Scholar]
  20. Imchen M, Kumavath R, Barh D, Azevedo V, Ghosh P et al. Searching for signatures across microbial communities: metagenomic analysis of soil samples from mangrove and other ecosystems. Sci Rep 2017; 7:8859 [View Article] [PubMed]
     [Google Scholar]
  21. Zhang C-J, Pan J, Duan C-H, Wang Y-M, Liu Y et al. Prokaryotic diversity in mangrove sediments across southeastern china fundamentally differs from that in other biomes. mSystems 2019; 4:e00442-19 [View Article] [PubMed]
     [Google Scholar]
  22. Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R et al. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): drivers and potential bioindicators. Sci Total Environ 2022; 807:150667 [View Article]
     [Google Scholar]
  23. Liu M, Huang H, Bao S, Tong Y. Microbial community structure of soils in Bamenwan mangrove wetland. Sci Rep 2019; 9:8406 [View Article] [PubMed]
     [Google Scholar]
  24. Quintero IJ, Castillo AM, Mejía LC. Diversity and taxonomy of soil bacterial communities in urban and rural mangrove forests of the Panama Bay. Microorganisms 2022; 10:11 [View Article] [PubMed]
     [Google Scholar]
  25. Bhattacharyya A, Haldar A, Bhattacharyya M, Ghosh A. Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India. Sci Total Environ 2019; 647:1626–1639 [View Article]
     [Google Scholar]
  26. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
     [Google Scholar]
  27. Nygaard AB, Tunsjø HS, Meisal R, Charnock C. A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. Sci Rep 2020; 10:3209 [View Article] [PubMed]
     [Google Scholar]
  28. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 2018; 34:2666–2669 [View Article] [PubMed]
     [Google Scholar]
  29. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261–5267 [View Article] [PubMed]
     [Google Scholar]
  30. Schloss PD. Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses. mSphere 2024; 9:e0035423 [View Article] [PubMed]
     [Google Scholar]
  31. Basak P, Pramanik A, Sengupta S, Nag S, Bhattacharyya A et al. Bacterial diversity assessment of pristine mangrove microbial community from Dhulibhashani, Sundarbans using 16S rRNA gene tag sequencing. Genom Data 2016; 7:76–78 [View Article] [PubMed]
     [Google Scholar]
  32. Jeyanny V, Norlia B, Getha K, Nur-Nabilah A, Lee SL et al. Bacterial communities in a newly regenerated mangrove forest of Sungai Haji Dorani mangroves in the West Coast of Selangor, Malaysia. J Trop Forest Sci 2020; 32:268–282 [View Article]
     [Google Scholar]
  33. Ma X-X, Jiang Z-Y, Wu P, Wang Y-F, Cheng H et al. Effect of mangrove restoration on sediment properties and bacterial community. Ecotoxicology 2021; 30:1672–1679 [View Article]
     [Google Scholar]
  34. De Santana CO, Spealman P, Melo V, Gresham D, de Jesus T et al. Large-scale differences in diversity and functional adaptations of prokaryotic communities from conserved and anthropogenically impacted mangrove sediments in a tropical estuary. PeerJ 2021; 9:e12229 [View Article] [PubMed]
     [Google Scholar]
  35. Mughini-Gras L, van der Plaats RQJ, van der Wielen PWJJ, Bauerlein PS, de Roda Husman AM. Riverine microplastic and microbial community compositions: a field study in the Netherlands. Water Res 2021; 192:116852 [View Article] [PubMed]
     [Google Scholar]
  36. Nogueira VLR, Rocha LL, Colares GB, Angelim AL, Normando LRO et al. Microbiomes and potential metabolic pathways of pristine and anthropized Brazilian mangroves. Reg Stud Mar Sci 2015; 2:56–64 [View Article]
     [Google Scholar]
  37. Rampadarath S, Bandhoa K, Puchooa D, Jeewon R, Bal S. Metatranscriptomics analysis of mangroves habitats around Mauritius. World J Microbiol Biotechnol 2018; 34:59 [View Article]
     [Google Scholar]
  38. Manan NMR, Yuh YS, Theng LW, Zakaria MP. Distribution of petroleum hydrocarbons in aquaculture fish from selected locations in the straits of malacca, malaysia. World Appl Sci J 2011; 14:14–21
     [Google Scholar]
  39. Keshavarzifard M, Zakaria MP, Keshavarzifard S. Evaluation of polycyclic aromatic hydrocarbons contamination in the sediments of the Johor Strait, Peninsular Malaysia. Polycyclic Aromat Compd 2019; 39:44–59 [View Article]
     [Google Scholar]
  40. Samsudin et al. River water quality assessment using APCS-MLR and statistical process control in johor river basin, malaysia. Int J Adv Appl Sci 2017; 4:84–97 [View Article]
     [Google Scholar]
  41. Ghaderpour A, Mohd Nasori KN, Chew LL, Chong VC, Thong KL et al. Detection of multiple potentially pathogenic bacteria in Matang mangrove estuaries, Malaysia. Mar Pollut Bull 2014; 83:324–330 [View Article]
     [Google Scholar]
  42. Meng S, Peng T, Pratush A, Huang T, Hu Z. Interactions between heavy metals and bacteria in mangroves. Marine Pollution Bulletin 2021; 172:112846 [View Article]
     [Google Scholar]
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Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia
Access Microbiology 7, 000902.v3 (2025); https://doi.org/10.1099/acmi.0.000902.v3
/content/journal/acmi/10.1099/acmi.0.000902.v3
/content/journal/acmi/10.1099/acmi.0.000902.v3
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