Diversity, ecology and biotechnological potential of mangrove sediment microbiomes in Malaysia

Introduction

Mangrove forests are among the world’s most productive and ecologically important ecosystems. They thrive in tropical and subtropical coastal zones where land meets the sea, and they are regularly flooded by tides, exposing them to fluctuating salinity and water levels. Mangrove ecosystems also provide high carbon sequestration capacity (38.3 Tg C year⁻¹), thereby playing an important role in global coastal biogeochemical reactions and climate change.¹ The soil in these ecosystems is layered: the surface is oxygen-rich, while deeper layers are anoxic, creating a unique environment that supports diverse microbial communities. However, previous culture-based methods only managed to identify a small fraction of mangrove microbial diversity, while the bulk of unculturable microorganisms, under standard laboratory conditions, remain unknown. With the ever-increasing anthropogenic activities in recent decades, mangroves are exposed to various pollutants, including hydrocarbons, plastics, pesticides, persistent organic pollutants (POPs), and pharmaceutical waste, which further increases the complexity of the microbial communities’ structure in mangrove sediments. Despite their importance, the microbial communities in mangrove sediments, especially in Malaysia, remain vastly unknown. Mangrove sediments hold a hidden wealth of microbial diversity, uniquely adapted to a saline, anoxic environment rich in organic matter. These microbial communities are vital drivers of carbon sequestration,^2,3 nutrient cycling^4,5 and pollution resilience,⁶ yet they remain underexplored for their biotechnological potential, including in the degradation of pollutants and bioenergy production.

Microbial diversity of mangrove sediments and their ecosystem roles

Due to mangroves’ complex biogeochemical reactions, the microbial structure in mangrove soils is shaped by a complex interplay of biotic and abiotic factors, including vegetation type, soil depth, salinity, tidal cycles, and anthropogenic influences. Recent studies have revealed that mangrove soils harbour a wide array of microbial taxa, many of which are novel or poorly understood.^5,7,8 Microbial communities in mangrove soils are also not uniform; they vary significantly across different ecological niches. Our initial microbial communities screening also showed non-uniformity of microbial community structures in mangrove sediments sampled from six mangrove locations in Northwest Peninsular Malaysia (detailed in Table 1) at three different depths (Fig. 1). Coastal and estuarine mangrove sediments from Kuala Perlis and Matang Mangrove Forest Reserve were chosen to compare the microbial community structures in two different states of Northern Peninsular Malaysia, whereas Pulau Langkawi estuarine mangrove sediments were also examined to determine the effects of anthropogenic activities on microbial community structures.

Fig. 1.

Relative abundance of prokaryotic phyla in mangrove sediment samples from Kuala Perlis coast, Kuala Perlis estuary, Pulau Langkawi anthropogenic estuary, Pulau Langkawi pristine estuary, Matang Mangrove Forest Reserve (MMFR) coast, and MMFR estuary. Sequence reads were taxonomically classified at the family level, and relative abundances were calculated per sample. Taxa contributing >5% in at least one sample are individually shown. Taxa contributing <5% across all samples were grouped as ‘Others <5%’. Shifts in microbial abundance across sites and depths reflect changes in biogeochemical processes such as carbon cycling, nutrient transformation, and pollutant degradation, highlighting the ecological sensitivity of mangrove sediments to environmental conditions.

Dominant phyla characterised using 16S rRNA Illumina sequencing included Firmicutes, Chloroflexota and Proteobacteria among the bacterial community, and Thermoproteota and Asgardachaeota among the archaeal community, with notable shifts in abundance from site to site and with depth within each site (Fig. 1). These microbes were known to be involved in many important biogeochemical reactions in mangrove sediments including hydrocarbons degradation, carbon cycling, nutrients cycling and mercury methylation (Table 2). A recent study⁹ analysing the root-associated microbiomes of four mangrove species (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa), found distinct bacterial distributions in the root, rhizosphere, and non-rhizosphere soils.

Despite their importance, the microbial communities in these mangrove sediments are poorly characterised. However, understanding the microbial community structure in mangrove sediments is essential for conservation and restoration efforts. These microbes not only support mangrove health through nutrient cycling and pollutant degradation but also act as indicators of environmental change, reflecting shifts in salinity, pollution, and hydrology. Systematic monitoring of microbial diversity, combined with advanced analytical tools such as metagenomics and machine learning tools, can inform sustainable management and targeted restoration interventions for mangrove ecosystems.

The integration of high-throughput sequencing and omics technologies has significantly advanced our understanding of mangrove microbial communities. Long-read sequencing platforms like PacBio have enabled the recovery of high-quality metagenome-assembled genomes (MAGs), revealing novel metabolic pathways and microbial interactions that underpin key biogeochemical processes. However, functional insights remain limited without complementary approaches such as metatranscriptomics, which can link microbial presence to gene expression and activity under varying environmental conditions. The use of RNA stabilisation agents, coupled with AI-driven data analysis, is making such studies increasingly feasible.^15,20

Towards biotechnological applications

Future directions

Future work should prioritise functional validation of candidate taxa and pathways inferred from metagenomic and amplicon data. Approaches such as stable‑isotope probing (e.g. ¹³C, ¹⁵N) coupled to metatranscriptomics, metaproteomics, and metabolomics can directly link taxa to in situ carbon and nitrogen transformations and pollutant degradation. In parallel, generating high-quality MAGs with long‑read assemblies and applying single‑cell genomics will improve recovery of uncultured lineages and resolve novel enzymes relevant to xenobiotic breakdown.

To translate these findings into practical applications, mesocosm and field‑scale pilot studies that replicate mangrove conditions (i.e. salinity, anaerobic zones and root structures) should be set up to test bioaugmentation (introducing pollutant-degrading microbes) and biostimulation (enhancing native microbial functions) for hydrocarbons, plastics, and POPs, while quantifying trade‑offs (e.g. greenhouse gas fluxes, sulfate reduction vs methanogenesis). Bioaugmentation and biostimulation have been successfully tested in such setups, demonstrating accelerated pollutant breakdown and improved ecosystem resilience.¹⁵ Developing eDNA/ddPCR (environmental DNA surveillance coupled with droplet digital PCR) sentinel assays for key indicator taxa and genes could enable routine microbial monitoring to support restoration and compliance programs.

On the data side, the integration of machine learning with harmonised multi‑omics and environmental metadata will enhance the prediction of biodegradation potential. Algorithms trained on large omics datasets can predict biodegradation pathways, identify key microbial players, and estimate pollutant removal efficiencies. This computational approach not only enhances the accuracy of bioremediation models but also enables real-time monitoring and adaptive management of remediation strategies.¹⁵ Additionally, adoption of community metadata standards and open data deposition will increase reproducibility and reuse across sites.

Beyond remediation, mangrove microflora also shows potential in bioenergy applications. Certain anaerobic bacteria and archaea from mangrove sediments are capable of producing biohydrogen²³ and methane through fermentation and methanogenesis.²⁴ For example, sulfate-reducing bacteria and methanogens isolated from mangrove mud have been used in microbial fuel cells (MFCs)²⁵ and anaerobic digesters to generate electricity and biogas from organic waste. These systems not only offer renewable energy solutions but also contribute to waste valorisation in coastal communities.

Together, these innovations underscore the untapped potential of mangrove microbiomes in biotechnology. By combining microbial ecology with cutting-edge genomics and computational tools, researchers can develop sustainable solutions to some of the most pressing environmental challenges, including pollution mitigation and ecosystem restoration. Importantly, these insights can inform policymakers by providing robust, science-based evidence to guide the development of effective conservation strategies, coastal management policies, and climate resilience planning, ensuring that mangrove ecosystems continue to deliver essential services to both nature and society.

Conclusion

Mangrove microbial communities in Northwest Peninsular Malaysia represent a rich resource for environmental biotechnology, from pollutant degradation to bioenergy production. Systematic characterisation, coupled with advanced sequencing and AI analytics, can unlock these microbes’ potential for sustainable remediation strategies and conservation efforts while ensuring the health of mangrove ecosystems against increasing anthropogenic pressures. Future research should focus on functional validation of key microbial taxa and scaling biotechnological applications to support regional conservation and climate adaptation strategies. Importantly, advances in biotechnology ultimately rely on a robust ecological understanding of mangrove microbial communities, as their natural roles in nutrient cycling, carbon sequestration, and pollutant degradation provide the foundation for applied innovations. By explicitly integrating ecological insights with biotechnological development, we can ensure that practical applications remain ecologically relevant and sustainable.