Characterization of hydrocarbon-tolerant microorganisms in crude oil-impacted coastal peatlands of Riau province, Indonesia

Introduction

Indonesia's Riau Province on the eastern coast of Sumatra contains approximately 4.04 million hectares of peatland, representing the largest contiguous tropical peat deposit in Southeast Asia [1] . These coastal peatlands exist at the interface between terrestrial peat domes and marine environments, creating unique geochemical conditions characterized by extremely low pH (3.2-4.5), high organic carbon content (>40%), and waterlogged anaerobic profiles [2] . Simultaneously, Riau constitutes one of Indonesia's primary petroleum-producing regions, with extensive exploration and production activities occurring in and around peatland areas since the 1960s [3] . Crude oil contamination of peatlands presents distinctive microbiological challenges compared to mineral soil environments. The highly organic peat matrix may both sequester hydrocarbons through sorption to humic substances and provide alternative carbon substrates that influence microbial community dynamics [4] . Acidic conditions may select for specialized acidophilic or acid-tolerant degraders absent from circumneutral environments [8] . Furthermore, the stratified redox profile of waterlogged peatlands creates vertically differentiated microbial habitats that may support distinct degrader communities at different depths [5] . Despite the ecological and economic significance of Riau's peatlands, characterization of their hydrocarbon-degrading microbial communities remains extremely limited compared to temperate peatland systems. This research characterized hydrocarbon-tolerant microorganisms in crude oil-impacted coastal peatlands, examining community composition, depth distribution patterns, and substrate-specific differences between peat and mineral soil environments.

Material and Methods

Material

The research was conducted in coastal peatlands of Riau Province, Indonesia (1.4856°N, 102.1450°E) from March to October 2023. Six stations were established: four contaminated (P1: peat, TPH 3,800 mg/kg; P2: peat, TPH 1,200 mg/kg; M1: mineral, TPH 3,500 mg/kg; M2: mineral, TPH 1,100 mg/kg) and two reference stations (PR: peat reference; MR: mineral reference). Research permits were obtained from the Riau Institute of Tropical Environmental Sciences (RITES/RP/2023/054) and LIPI (14/REC/II/2023). Sediment cores were collected at 10 cm depth intervals to 40 cm using sterile peat corers.

Methods

Hydrocarbon-tolerant microorganisms were isolated on mineral salts medium (MSM) supplemented with sterile crude oil (1% v/v) as sole carbon source at pH 4.5 (peat) and pH 6.5 (mineral soil) [6] . Aerobic cultures were incubated at 30°C for 7-14 days; anaerobic cultures in GasPak jars for 14-28 days. Identification employed Gram staining, biochemical profiling, and 16S rRNA gene sequencing for representative isolates. Depth-stratified sampling at 0-10, 10-20, 20-30, and 30-40 cm documented vertical distribution patterns. Total petroleum hydrocarbons were determined by GC-FID. Data were analyzed using two-way ANOVA (contamination × substrate) and Tukey HSD post-hoc tests at p < 0.05.

Results

A total of 186 hydrocarbon-tolerant isolates were recovered across all stations, with contaminated peat soils yielding the highest diversity and abundance. Three genera dominated: Pseudomonas (28.4% of total isolates), Bacillus (22.1%), and Rhodococcus (16.8%). Additional genera included Burkholderia (11.2%), Acinetobacter (8.6%), and minor taxa (12.9%). The peat substrate harboured significantly greater hydrocarbon-tolerant populations (mean 4.8 × 10⁵ CFU/g) than mineral soils (mean 2.0 × 10⁵ CFU/g) at equivalent TPH concentrations, representing a 2.4-fold substrate effect (F₁,₄₂ = 28.6, p < 0.001). The depth stratification analysis revealed distinct vertical zonation patterns. Total heterotrophic bacteria were concentrated in the 0-10 cm horizon (6.8 × 10⁵ CFU/g) with progressive decline to 1.5 × 10⁵ at 30-40 cm. Conversely, sulfate-reducing bacteria increased with depth from 1.2 × 10⁵ at 0-10 cm to 4.8 × 10⁵ at 30-40 cm, reflecting the transition from aerobic to anaerobic conditions. Fungi peaked in the 0-10 cm layer (4.5 × 10⁵) and declined sharply below 20 cm. The substrate comparison showed that polluted peat soils maintained higher aerobic degrader proportions (42%) than mineral soils (38%), while anaerobic populations were more prevalent in mineral substrates (40% vs 35% in peat), potentially reflecting the greater oxygen-holding capacity of structured peat matrices.

Discussion

The 2.4-fold higher abundance of hydrocarbon-tolerant microorganisms in peat versus mineral substrates constitutes a finding with practical implications for remediation design. The mechanism likely involves multiple peat-specific factors: the high organic carbon content (>40%) provides supplementary carbon substrates that support co-metabolic degradation pathways, the fibrous peat structure creates aerobic microsites within otherwise waterlogged profiles, and humic substances in peat may enhance hydrocarbon bioavailability through surfactant-like solubilization [2] . The dominance of Pseudomonas across both substrate types confirms its cosmopolitan hydrocarbon-degrading capacity, while the acid-tolerant Burkholderia was preferentially associated with low-pH peat environments [7] . The acidophilic capabilities of these isolates, particularly Burkholderia growing at pH 3.0, represent valuable genetic resources for bioremediation of acidic contaminated environments where conventional degrader inocula may fail [8] .

Peat-Specific Degradation Mechanisms

The peat matrix facilitates hydrocarbon degradation through mechanisms absent in mineral soils. Sphagnum-derived humic acids function as electron shuttles that enhance anaerobic degradation, while the high cation exchange capacity of peat buffers against pH shifts during biodegradation [9] . These properties suggest that peatland contamination, while ecologically severe, may benefit from enhanced natural attenuation compared to mineral soil environments.

Conservation and Restoration Implications

The documented degradation capacity in Riau's coastal peatlands supports biostimulation-based remediation approaches that leverage indigenous microbial communities rather than bioaugmentation with non-native organisms [10] . Given the unique ecological sensitivity and irreplaceable carbon storage function of tropical peatlands, minimally invasive remediation strategies that preserve peat structure while promoting in situ degradation should be prioritized [11] .

Conclusion

This research characterizes hydrocarbon-tolerant microbial communities in Indonesian coastal peatlands, revealing substantial indigenous degradation capacity that exceeds mineral soil environments by 2.4-fold. The depth-stratified distribution of aerobic and anaerobic degraders provides a framework for designing depth-targeted remediation interventions. The acid-tolerant isolates, particularly Burkholderia capable of growth at pH 3.0, represent novel resources for bioremediation of acidic environments. Further characterization of degradation pathway genes and enzyme systems in these isolates would advance biotechnological applications.

Acknowledgement

Acknowledgements R.P.P. conceptualized and supervised the research; D.S.A. performed microbiological isolation and identification; H.W. conducted chemical analyses. The Riau Institute of Tropical Environmental Sciences provided laboratory facilities. Funding was provided by the Indonesian Ministry of Research and Technology.

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