Tropical peat swamp soils: The impact of agricultural and restoration practices on activity and diversity of the soil microbial community
Creators: name: Nurulita, Yuana
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 410603
subject: Soil biology
classificationCode: 410604
subject: Soil chemistry and soil carbon sequestration (excl. carbon sequestration science)
classificationCode: 410605
subject: Soil physics

description: Although occupying just 3-4% of the world’s landmass covering temperate, boreal and tropical areas, peatlands play an important role in conserving biodiversity and as a carbon sink. Current intensification of agricultural activities, especially in tropical areas, has led to increased use of tropical peatlands such as those in Indonesia. There is currently only limited information on the impact of this conversion. This project aimed to examine the effect of agricultural and restoration practices on the physico-chemical characteristics together with the activity and diversity of the microbial community present in tropical peat swamp soils. In addition, the impact of peat swamp restoration on microbial communities was also evaluated in an effort to monitor the success of the restoration process. To achieve this, analyses of physical, chemical and biological characteristics coupled with molecular biological analyses of peat swamp soils exposed to different human practices was carried out within the Giam Siak Kecil – Bukit Batu (GSKBB) Biosphere Reserve, Riau – Indonesia.<br><br>The first component of this study examined the impact of oil palm (burning and without burning) and rubber plantations (5-10 and &gt;40 years old) on both the biotic and abiotic properties of the peatland soil through comparisons with soil from a natural forest. Based on analysis of the physico-chemical properties, soils from plantations demonstrated increased decomposition rates, as shown by a reduction in soil organic matter (4-18%), an increase in bulk density (ρb) (0.08 – 0.17 g cm-3) and an increase in bacterial biomass (0.6 – 5.9 fold) compared with natural forest peat soils. Moreover, drier conditions due to plantation management in peat swamp soil were found, with deeper water tables (45 – 67 cm) and reduced soil water holding capacities (22-53% reduction). However, community level physiological profiling (CLPP) showed impaired microbial community function only in soils from oil palm plantations. Oil palm plantation soil (without burning) showed the lowest microbial activities (50% decrease) and the lowest Shannon diversity values (2.90) compared to natural forest soils. In contrast, soil from young rubber plantations exhibited increased microbial activities (54%) and similar Shannon diversity values (3.13) compared to natural forest soils.<br><br>The second part of this study involved further assessment of the impact of oil palm and rubber plantations on tropical peatland soils using a polyphasic approach involving biochemical and molecular microbial assays. The concentration of ammonium, nitrate and phosphate observed in agricultural soils indicated a substantial increase compared with natural forest. These changes were accompanied by changes in the soil enzyme activity; reduced activities of β-glucosidase, cellobiohydrolase and acid phosphatase activities (50–55% reduction) were detected in agricultural soils while increased chitinase activity was detected in the rubber plantation soil (37% increase). In terms of soil microbial community diversity, PCR-Denaturing Gradient Gel Electrophoresis (DGGE) based analysis showed that the soil bacterial community from agricultural soils exhibited the lowest similarity amongst the different microbial groups (bacteria, fungi and archaea) evaluated, showing only 34% similarity to the natural forest soil. The Shannon diversity index values further confirmed that the conversion of tropical peatland natural forest to agriculture resulted in the greatest impact on microbial diversity being significantly different compared with the natural forest. Overall, this study indicated substantial shifts in soil microbial activity and diversity occured upon conversion of natural peatland forest to agricultural areas.<br><br>The final stage of the study investigated the restoration process of burnt oil palm plantation through revegetation with native peat swamp forest plants and land rewetting through assessment of the activity and diversity of the soil microbial community together with soil chemical and physical characterisation. Overall, the physical-chemical characteristics of the restoration soils remained similar to the soil from the burnt oil palm plantation with increased depth of water table (5-6 times deeper), reduced water holding capacity (23-35%), increased bulk density (ρb) (0.31–.32 g cm-3), an increase the C:N ratio (41:1) and higher ammonium and nitrate concentrations (4-17 times higher) when compared to the forest soil (p&lt;0.05). Restoration, involving revegetation and land rewetting resulted in a significant decrease in the phosphate concentration of the restoration soils (4.722 mg kg-1) (p&lt;0.05) compared with other soil samples. In terms of microbial diversity, PCR-DGGE revealed that the bacterial community of the restoration soil changed significantly (only 10% similarity), amongst the different microbial groups (fungal and archaeal communities). Principal Component Analyses (PCA) showed all three soil samples clustered individually with different dependent parameters. Overall, after 3.5 years of restoration, the degraded burnt oil palm plantation soils did not appear to be similar to the peat swamp natural forest soil.<br><br>Overall, this thesis contributes to our understanding of the impact of agricultural practices, especially oil palm and rubber plantations, on the microbial activity and diversity in tropical peat swamp soil. In addition, soil microbial ecology was found to be a useful indicator for use in the monitoring of the restoration process. Periodic analyses of soils under restoration using molecular microbial techniques are suggested as a useful tool for monitoring the success of the restoration process.