Physicochemical properties and bacterial diversity of pristine and stressed Malaysian mangrove ecosystems

Coastal mangroves: role, threats and associated microbiomes

Tropical coastal mangrove forests are biogeochemically active zones susceptible to tidal change and salinity, enabling exchange of sediments and organic matter between water and land.¹ Besides serving to protect coastlines and impede erosion, these coastal wetlands support various key functions which includes biogeochemical cycling, ecosystem remediation, carbon sequestration, flood mitigation, breeding and nursing grounds for aquatic species, and providing bioresources for local community, industries and tourism.² Malaysia has among the largest extents of mangrove forests in South East Asia. Despite having significant impact on environment protection, biodiversity conservation and socio-economic benefits, this unique ecosystem is constantly threatened by a multitude of stress factors such as intensive harvesting, pollution from excessive anthropogenic activities, rise in sea level, sediment salinisation and other natural disasters.³ Over the years, reports showed a drastic decline in Malaysian coastal mangrove areas from approximately 700,000 ha in 1975 to 572,000 ha in 2000.⁴ This raised an urgent need for close monitoring of soil quality status of microsites within affected stands in the country, for establishing soil restoration, rehabilitation and sustainable management strategies in coastal mangrove forests.⁵

Mangrove forests harbour a highly dynamic and diverse microbiome composition and structure, including bacteria, archaea, viruses, fungi and protists, due to the environmental conditions and nutrient contents in these ecosystems.⁶ With high organic matter as well as anaerobic and reduced condition of soil, mangrove sediments have high capacity to accumulate pollutants discharged from anthropogenic activities to the near shore marine environment. These constant changes have repercussions, as alterations to the mangrove sediment physicochemical properties can influence microbiome diversity and composition within the ecosystem.⁷ Therefore, it is likely that there will be a difference in the mangrove microbiome structure influenced by anthropogenic pressures, and knowing the indicator species is useful for monitoring the impact of these stresses over time.⁸

Metagenomics research using high throughput next-generation sequencing (NGS) to identify microbial taxa from environmental samples, have expanded our understanding of the mangrove microbiome, its diversity, abundance and potential functional roles.⁹ Prokaryotic communities associated with mangrove sediments and the rhizosphere, which includes bacteria and archaea, play crucial roles in nutrient cycling to maintain soil fertility and ecological balance in the productive mangrove ecosystems.¹⁰ While the relevance of mangrove prokaryotic processes to carbon, nitrogen and phosphorus cycling are known, information on the influence of stress factors on the changes in bacterial diversity and community structure is still lacking in Malaysia.¹¹ Here, we present a study which examined bacterial communities in two contrasting Malaysian coastal mangrove areas, Tanjung Piai and Matang mangroves, using 16S rRNA gene amplicon sequencing. The idea was to generate a baseline data set on mangrove habitat specificity to changes in the microbiome of both ecosystems, with regards to interaction with different sediment physicochemical properties.

Sediment physicochemical properties in stressed and pristine mangrove ecosystems

Mangrove forests act as important carbon sinks, providing a niche for bacterial communities crucial in regulating nutrient cycles.¹² Variables such as erosion, flooding, agricultural activities, industrial and sewage effluents, and urban development can heavily impact the physicochemical properties of mangrove sediments.¹³ Tanjung Piai National Park is located in the Johor State land comprising of coastal mangroves and intertidal mudflats, at the southernmost tip of continental Asia. Studies in Tanjung Piai mangroves outlined its importance in biodiversity as a Bruguiera-Rhizophora dominated forest.¹⁴ Although being awarded as a Ramsar site (wetlands of international importance), this coastal mangrove area of 526 ha has been impacted by various factors hampering the efforts in conservation strategies and eco-tourism.¹⁴ An oil slick contamination incident reported previously¹⁵ highlights its geographical location as an important waterway of the Straits of Malacca for cargo ships. Thus presents potential hydrocarbon and heavy metal contamination risks, and shoreline retreat caused by hydrodynamic conditions and regular ship traffic, which further impacts mangrove health.¹¹

The Matang Mangrove Forest Reserve (MMFR), located in the districts of Krian, Larut Matang and Manjung in the State of Perak on the northwest coast of Peninsular Malaysia, is known worldwide as an exemplary sustainably managed tropical mangrove forest with an area of 40,288 ha. Most areas are covered by pure stands of the economically valuable Bakau Forest (Rhizophora apiculata and R. mucronata). The MMFR provides ecosystem services such as coastal protection, biodiversity conservation, ecotourism, wood provision for charcoal production, fishery maintenance and mangrove propagule production. For 115 years, the mangroves in the productive zones have been harvested under a 30-year rotation cycle, indicating a long-standing sustainable management regime.¹⁶

Systematic sampling of sediments at 5–20 cm depth was carried out by establishing five transects at each mangrove site. Sediment samples from Tanjung Piai were collected from transects facing seawards on the intertidal mudflats with sparse vegetation (Fig. 1), and also facing landwards in an old growth forest parallel to the intertidal mudflats. In Matang, samples were collected from undisturbed pristine mangrove forest patches or the Virgin Jungle Reserve areas (Fig. 2). Overall, soil physicochemical analysis showed a significantly higher organic carbon (OC) content which correlates with organic matter (OM) value of 2.9-fold higher in the pristine Matang site compared to Tanjung Piai. We found that despite having comparative levels of nitrogen (N), the available phosphorus (Av. P) level was significantly higher in Tanjung Piai (Table 1).

Fig. 1.

Mangrove sediment collected at 5–20 cm depth using augers in one of the five transects established for sampling in Tanjung Piai mangrove; figure shows one of the transect area facing seawards on the intertidal mudflats with sparse vegetation (source: Forest Research Institute Malaysia).

Fig. 2.

Pristine mangrove forest patches within Matang Mangroves are showcases of the rich biological diversity of this unique ecosystem (source: Forest Research Institute Malaysia).

Most mangrove ecosystems are known to be rich in C and OM but poor in nutrients which includes N and P. The inputs from litterfall alters the OC, OM and N values as microbes utilise these elements for various processes such as decomposition, nitrification, denitrification and transformation.¹⁷ Our findings indicated that there are several aquaculture farming activities upstream of the Tanjung Piai mangroves. The effluent from these aquaculture farms flows downstream and resides in the intertidal enclave of Tanjung Piai, presenting a potential source of the high Av. P observed in the sediments. Effluents from shrimp and aquaculture farming are known to contain high P.¹⁸ Similar studies on mangroves in South America and Asia showed that areas impacted by anthropogenic activities may result in up to 17-fold higher N and P accumulation rates in comparison with values under conserved conditions. While others reported that these differences may by up to 5-fold higher in impacted as compared to the conserved mangrove ecosystems.¹⁹ Thus, there is a high possibility that besides influx of sediment rich nutrients from the open sea facing the Straits of Malacca, upstream influx may have also altered the nutrient dynamics of Tanjung Piai mangroves.

Mangrove–microbiome interactions in different ecosystems

Outcomes of the amplicon sequencing analysis showed higher number of unique amplicon sequence variants (ASVs) in the Tanjung Piai mangroves. Unique site-specific ASVs may serve as indicators of core microbial community components shaping mangrove sediment microbiomes.¹² Additionally, alpha diversity indices dataset measured significant differences in bacterial communities between Matang and Tanjung Piai, with the latter exhibiting higher species richness and diversity. Tanjung Piai experiences higher levels of external nutrient inputs from human settlements, shrimp farming activities and the waterways of the Straits of Malacca. Oil spills and illegal water ballast dumping,²⁰ and high lead and zinc contents,²¹ have also been reported. Increased nutrient levels such as Av. P and other confounding factors due to anthropogenic activities, may have favoured a more diverse bacterial population and higher unique ASVs in Tanjung Piai. External nutrient inputs from anthropogenic disturbances are known to shift the ecosystem equilibrium forcing microorganisms to adapt to the new habitat. This indirectly causes disturbed mangrove areas to have higher unique bacterial taxa, promoting a variety of microbes to thrive and survive in the ecosystem.¹² Conversely, Matang mangroves appears to support a more stable and less variable bacterial community structure. This is likely due to minimal human and tidal disturbances, and ecological stability where well-established bacterial populations dominate, leading to lower species turnover. For example, areas closer to seafront with continuous tidal buffering and sediment turnover tend to have higher microbial diversity compared to more stable areas such as Matang, with less frequent water exchange and salinity variations.²²

Distribution and dominance of specific bacterial taxa varied significantly between the pristine Matang and anthropogenically-disturbed Tanjung Piai mangroves (Fig. 3). Proteobacteria and Gammaproteobacteria emerged as the dominant phylum and class, respectively, across both sites. This is consistent with previous studies on mangrove ecosystems worldwide.²³ Proteobacteria is linked to several processes, notably carbon, nitrogen and sulfur cycling,²⁴ and thrives in high nutrient conditions.²⁵ Gammaproteobacteria are well known for their role in sulfur oxidation, particularly in mangrove environments where anaerobic respiration is crucial for organic matter decomposition.²⁶ Notable variations were observed with Alphaproteobacteria, another major class of Proteobacteria. A significantly higher abundance in Matang, aligns with previous reports of Alphaproteobacteria as a key bacterial group in well-preserved mangrove ecosystems.²⁷ Its lower abundance in Tanjung Piai could be linked to higher sediment Av. P level. Negative correlation between Alphaproteobacteria abundance and Av. P level was observed by others,²⁸ explaining its lower prevalence in the P-enriched environment in Tanjung Piai. Conversely, Chloroflexi (class Dehalococcoidia) and Bacteroidota (class Bacteroidia), which were positively correlated with Av. P,²⁸ were significantly abundant in Tanjung Piai.

Fig. 3.

Bacterial phyla composition in composite replicate samples of Matang (M1–M5) and Tanjung Piai (P1–P5) mangrove sediments.

Actinomycetota (mostly Acidimicrobiia and Actinomycetes) were significantly dominant in the pristine mangrove ecosystem. Genomic data mining of uncultured Acidimicrobiia species suggested that they display metabolic versatility indicating their important role in biogeochemical cycling.²⁹ High abundance of actinomycetes in the Matang sediments suggest a potential role in enhancing mangrove health through phytohormone production, nitrogen fixation and mineral solubilisation.³⁰ The significantly lower abundance of this taxa in Tanjung Piai suggests potential ecological stressors or anthropogenic disturbances affecting their survival. Members of the phylum Desulfobacterota, including Desulfobacteria, are known for sulfate and nitrate reduction under anaerobic conditions and play a key role in anoxic organic matter mineralisation. The elevated abundance of Desulfobacteria in Tanjung Piai may be linked to contamination, as they are also often associated with the degradation of anthropogenic hydrocarbons and pollutants.³¹

Conclusion

Although the interactions between environmental settings and sediment microbes have not been fully studied yet, the present study suggested that increased bacterial diversity in Tanjung Piai most likely reflects anthropogenic stress-induced opportunism in the mangrove ecosystem. The significant reduction in beneficial bacterial taxa such as Actinomycetes and Alphaproteobacteria, along with the increased abundance of pollution-associated groups such as Desulfobacteria and Bacteroidia, provides evidence that disturbances in Tanjung Piai may impact soil microbial health. These findings support the idea that microbial diversity can serve as a bioindicator of ecosystem health, providing valuable insights into the extent of environmental degradation. Despite the knowledge gained from this work, there are several considerations to be addressed in future studies. Sampling done in both areas at different times is important to enrich our understanding of the relationship between changing environmental inputs, such as seasonal or tidal variability, and the mangrove microbial communities. Functional pathway analysis using bioinformatics tools such as PICRUSt2 for predicting bacterial metabolic specialisations, will also be included in future studies to validate ecological roles of key taxa in the microbiomes.