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Information on temporal and spatial variations in soil greenhouse gas (GHG) fluxes from tropical peat forests is essential to predict the influence of climate change and estimate the effects of land use on global warming and the carbon (C) cycle. To obtain such basic information, soil carbon dioxide (CO2) and methane (CH4) fluxes, together with soil physicochemical properties and environmental variables, were measured at three major forest types in the Maludam National Park, Sarawak, Malaysia, for eight years, and their relationships were analyzed. Annual soil CO2 fluxes ranged from 860 to 1450 g C m⁻2 yr⁻1 without overall significant differences between the three forest sites, while soil CH4 fluxes, 1.2-10.8 g C m⁻2 yr⁻1, differed. Differences in GHG fluxes between dry and rainy seasons were not necessarily significant, corresponding to the extent of seasonal variation in groundwater level (GWL). The lack of significant differences in soil CO2 fluxes between the three sites could be attributed to set-off between the negative and positive effects of the decomposability of soil organic matter as estimated by pyrophosphate solubility index (PSI) and GWL. The impact of El-Niño on annual CO2 flux also varied between the sites. The variation in soil CH4 fluxes from the three sites was enhanced by variations in temperature, GWL, PSI, and soil iron (Fe) content. A positive correlation was observed between the annual CH4 flux and GWL at only one site, and the influence of soil properties was more pronounced at the site with the lowest GWL and the highest PSI. Variation in annual CH4 fluxes was controlled more strongly by temperature where GWL was the highest and GWL and plant growth fluctuations were the least. Inter-annual variations in soil CO2 and CH4 fluxes confirmed the importance of long-term monitoring of these at multiple sites supporting different forest types.

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The capacity for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis activity in a species depends on the enzymatic activities of fatty acyl desaturase (Fads) and elongation of very long-chain fatty acid (Elovl). The miniaturized fish Paedocypris micromegethes is a developmentally truncated cyprinid living in highly acidic water conditions in tropical peat swamps. The capacity for LC-PUFA biosynthesis in this species, which has a reduced genome size, is unknown. A high-quality de novo transcriptome assembly enabled the identification of a putative Fads2 and four Elovl. The Fads2 was verified as a P. micromegethes Fads2 ortholog with in vitro Δ5 and Δ6 activities. The Elovl sequences were established as an Elovl5, Elovl2, and two Elovl4 paralogs, namely Elovl4a and Elovl4b. These Elovl enzymes, mainly Elovl5 and Elovl2, fulfill the necessary C18, C20, and C22 PUFA elongation steps for LC-PUFA biosynthesis. Collectively, these results validate the presence of a complete repertoire of LC-PUFA biosynthesis enzymes in a peat swamp miniatured freshwater fish.

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A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39' 04.7' N 101° 17' 43.7'' E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA-DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).

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Tropical peat forests are a globally important reservoir of carbon, but little is known about CO2 exchange on an annual basis. We measured CO2 exchange between the atmosphere and tropical peat swamp forest in Sarawak, Malaysia using the eddy covariance technique over 4 years from 2011 to 2014. The CO2 fluxes varied between seasons and years. A small carbon uptake took place during the rainy season at the beginning of 2011, while a substantial net efflux of >600 g C/m2 occurred over a 2 month period in the middle of the dry season. Conversely, the peat ecosystem was a source of carbon during both the dry and rainy seasons in subsequent years and more carbon was lost during the rainy season relative to the dry season. Our results demonstrate that the forest was a net source of CO2 to the atmosphere during every year of measurement with annual efflux ranging from 183 to 632 g C m-2  year-1 , noting that annual flux values were sensitive to gap filling methodology. This is in contrast to the typical view of tropical peat forests which must have acted as net C sinks over time scales of centuries to millennia to create the peat deposits. Path analyses revealed that the gross primary productivity (GPP) and ecosystem respiration (RE) were primarily affected by vapour pressure deficit (VPD). Results suggest that future increases in VPD could further reduce the C sink strength and result in additional net CO2 losses from this tropical peat swamp forest in the absence of plant acclimation to such changes in atmospheric dryness.

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Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.

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Data on ecosystem-scale methane (CH4 ) fluxes in tropical peatlands are currently lacking in the global CH4 budget. Although the waterlogged Indonesian peatlands contain the largest share of peat carbon in South-East Asia, ecosystem-scale CH4 budgets have not yet been reported, although these peatlands have the potential to emit CH4 . We observed 1-year variations in the ecosystem-scale CH4 flux in an undrained secondary peat swamp forest in central Kalimantan, Indonesia, using the eddy covariance method. We found that the peat swamp forest switched from being a CH4 sink during the dry season (as low as -8.9 mg C m-2  day-1 ) to a source of CH4 during the wet season (up to 10.7 mg C m-2  day-1 ), and this was dependent on changes in the groundwater level (GWL). The high GWL during the wet season enhanced the anaerobic CH4 production in the surface layer that had more labile organic matter. However, the CH4 emission also increased when the GWL dropped during dry spells in the wet season. The annual CH4 budget in the studied tropical peat swamp forest (0.09-0.17 g C m-2  year-1 ) was much lower than that in northern, temperate, and subtropical wetlands. We found that CH4 fluxes had almost no effect on the global warming gas budget of the peat swamp forest, and values were only a few percent less than the CO2 fluxes at the same site. In addition, we conducted anaerobic soil incubation experiments to examine the effect of land-use change on CH4 production. The results indicated much higher CH4 production potential in undrained forest soil than in drained or drained and burned ex-forest soils. However, although CH4 production decreased in drained soils relative to undrained soils, conserving pristine peat swamp forests with high GWLs is important to suppress global warming because CO2 emissions increase in drained peatlands.

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Three strains (DMKU-XE11T, DMKU-XE15 and DMKU-XE20) representing a single novel anamorphic and d-xylose-fermenting yeast species were obtained from three peat samples collected from Khan Thulee peat swamp forest in Surat Thani province, Thailand. The strains differed from each other by one to two nucleotide substitutions in the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and zero to one nucleotide substitution in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the combined sequences of the ITS and the D1/D2 regions showed that the three strains represented a single Candida species that was distinct from the other related species in the Lodderomyces/Candida albicans clade. The three strains form a subclade with the other Candida species including Candida sanyaensis, Candida tropicalis and Candida sojae. C. sanyaensis was the most closely related species, with 2.1-2.4 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 3.8-4.0 % nucleotide substitutions in the ITS region. The three strains (DMKU-XE11T, DMKU-XE15 and DMKU-XE20) were assigned as a single novel species, which was named Candida kantuleensis sp. nov. The type strain is DMKU-XE11T (=CBS 15219T=TBRC 7764T). The MycoBank number for C. kantuleensis sp. nov. is MB 824179.

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To understand the variations in the decomposability of tropical peat soil following deforestation for an oil palm plantation, a field incubation experiment was conducted in Sarawak, Malaysia. Peat soils collected from three types of primary forest, namely Mixed Peat Swamp (MPS; Gonystylus-Dactylocladus-Neoscrotechinia association), Alan Batu (ABt; Shorea albida-Gonstylus-Strenonurus association), and Alan Bunga (ABg; Shorea albida association), were packed in polyvinyl chloride pipes and installed in an oil palm plantation. Carbon dioxide (CO2) and methane (CH4) fluxes from soil were monthly measured for 3years. Environmental variables including soil temperature, soil moisture content, and groundwater table were also monitored. The pH, loss on ignition, and total carbon (C) content were similar among the three soils, while total N content was larger in the MPS than in the ABg soils. Based on 13C nuclear magnetic resonance (NMR) spectroscopy, C composition of the MPS and ABg soils was characterized by the largest proportion of C present as alkyl C and O-alkyl C, respectively. The C composition of the ABt soil was intermediate between the MPS and ABg soils. The CO2 fluxes from the three soils ranged from 78 to 625mgCm-2h-1 with a negative correlation to groundwater level. The CH4 fluxes ranged from -67 to 653µgCm-2h-1. Both total CO2 and CH4 fluxes were larger in the order ABg>ABt>MPS (P<0.05). Annual rate of peat decomposition as was estimated from cumulative C loss differed up to 2 times, and the rate constant in exponential decay model was 0.033y-1 for the MPS soil and 0.066y-1 for the ABg soil. The field incubation results of the three forest peat soils seem to reflect the difference in the labile organic matter content, represented by polysaccharides.

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A novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 µg/ml and 6.26 µg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to be done.

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We report the draft genome sequence of Aeromonas sp. strain HZM, isolated from tropical peat swamp forest soil. The draft genome size is 4,451,364 bp with a G + C content of 61.7% and contains 10 rRNA sequences (eight copies of 5S rRNA genes, single copy of 16S and 23S rRNA each). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JEMQ00000000.

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We report the draft genome sequence of Cellulomonas sp. HZM, isolated from a tropical peat swamp forest. The draft genome size is 3,559,280 bp with a G + C content of 73% and contains 3 rRNA sequences (single copies of 5S, 16S and 23S rRNA).

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Aims: The aims of this study were to isolate and characterize antimicrobial producing bacteria from tropical peat swamp forest soils. Methodology and results: Bacteria isolated from peat soil were screened for antimicrobial properties via agar overlay assay. Broth microdilution was performed using crude-cell free supernatant (CCFS) to determine the minimum inhibitory concentration (MIC). One isolate was selected due to its broad spectrum activity and identified as Burkholderia spp. with a maximum identity of 99% via 16s rRNA gene PCR. This isolate was able to produce antimicrobials that were active against several Gram positive bacteria, Gram negative bacteria and also yeast. The antimicrobial activity of the CCFS was stable at a pH range of 1 to 11, temperatures of −20 °C to 80 °C, and after treatment with several proteolytic enzymes: α-chymotrypsin, proteinase K and trypsin, indicating that the antimicrobial produced might not be proteinaceous in nature. It is possible that the isolate can produce polyketides, a type of antimicrobial compound produced by Burkholderia known to be resistant to proteolytic enzymes. However, further work needs to be done to confirm this. Conclusion, significance and impact of study: The presence of antimicrobial producing bacteria signified that tropical peat swamps are indeed a potential source for antimicrobials to combat infections.

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