We report the draft genome sequence of a bacterial isolate, Paraburkholderia sp. strain C35, which was isolated from a Malaysian tropical peat swamp forest. The putative genes for the biogeochemical processes were annotated and are publicly available in the online databases.
We report here the draft genome of Klebsiella sp. strain C31, a bacterial isolate from the North Selangor peat swamp forest in Malaysia. The putative genes for the biogeochemical processes of the genome were annotated and investigated.
We report here the draft genome sequences of a bacterial isolate, Dyella sp. strain C11, which was isolated from a Malaysian tropical peat swamp forest. The putative genes for the biogeochemical processes were annotated, and the genome was deposited in an online database.
We employ complementary field and laboratory-based incubation techniques to explore the geochemical environment where siderite concretions are actively forming and growing, including solid-phase analysis of the sediment, concretion, and associated pore fluid chemistry. These recently formed siderite concretions allow us to explore the geochemical processes that lead to the formation of this less common carbonate mineral. We conclude that there are two phases of siderite concretion growth within the sediment, as there are distinct changes in the carbon isotopic composition and mineralogy across the concretions. Incubated sediment samples allow us to explore the stability of siderite over a range of geochemical conditions. Our incubation results suggest that the formation of siderite can be very rapid (about two weeks or within 400 hr) when there is a substantial source of iron, either from microbial iron reduction or from steel material; however, a source of dissolved iron is not enough to induce siderite precipitation. We suggest that sufficient alkalinity is the limiting factor for siderite precipitation during microbial iron reduction while the lack of dissolved iron is the limiting factor for siderite formation if microbial sulfate reduction is the dominant microbial metabolism. We show that siderite can form via heated transformation (at temperature 100°C for 48 hr) of calcite and monohydrocalcite seeds in the presence of dissolved iron. Our transformation experiments suggest that the formation of siderite is promoted when carbonate seeds are present.
Mangrove forests play an important role in climate change adaptation and mitigation by maintaining coastline elevations relative to sea level rise, protecting coastal infrastructure from storm damage and storing substantial quantities of carbon (C) in live and detrital pools. Determining the efficacy of mangroves in achieving climate goals can be complicated by difficulty in quantifying C inputs (i.e., differentiating newer inputs from younger trees from older residual C pools), and mitigation assessments rarely consider potential offsets to CO2 storage by methane (CH4 ) production in mangrove sediments. The establishment of non-native Rhizophora mangle along Hawaiian coastlines over the last century offers an opportunity to examine the role mangroves play in climate mitigation and adaptation both globally and locally as novel ecosystems. We quantified total ecosystem C storage, sedimentation, accretion, sediment organic C burial and CH4 emissions from ~70 year old R. mangle stands and adjacent uninvaded mudflats. Ecosystem C stocks of mangrove stands exceeded mudflats by 434 ± 33 Mg C ha-1 , and mangrove establishment increased average coastal accretion by 460%. Sediment organic C burial increased 10-fold (to 4.5 Mg C ha-1 yr-1 ), double the global mean for old growth mangrove forests, suggesting that C accumulation from younger trees may occur faster than previously thought, with implications for mangrove restoration. Simulations indicate that increased CH4 emissions from sediments offset ecosystem CO2 storage by only 2-4%, equivalent to 30-60 Mg CO2 -eq ha-1 over mangrove lifetime (100-year sustained global warming potential). Results highlight the importance of mangroves as novel systems that can rapidly accumulate C, have a net positive atmospheric greenhouse gas removal effect, and support shoreline accretion rates that outpace current sea level rise. Sequestration potential of novel mangrove forests should be taken into account when considering their removal or management, especially in the context of climate mitigation goals.
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.
Need for regional economic development and global demand for agro-industrial commodities have resulted in large-scale conversion of forested landscapes to industrial agriculture across South East Asia. However, net emissions of CO2 from tropical peatland conversions may be significant and remain poorly quantified, resulting in controversy around the magnitude of carbon release following conversion. Here we present long-term, whole ecosystem monitoring of carbon exchange from two oil palm plantations on converted tropical peat swamp forest. Our sites compare a newly converted oil palm plantation (OPnew) to a mature oil palm plantation (OPmature) and combine them in the context of existing emission factors. Mean annual net emission (NEE) of CO2 measured at OPnew during the conversion period (137.8 Mg CO2 ha-1 year-1 ) was an order of magnitude lower during the measurement period at OPmature (17.5 Mg CO2 ha-1 year-1 ). However, mean water table depth (WTD) was shallower (0.26 m) than a typical drainage target of 0.6 m suggesting our emissions may be a conservative estimate for mature plantations, mean WTD at OPnew was more typical at 0.54 m. Reductions in net emissions were primarily driven by increasing biomass accumulation into highly productive palms. Further analysis suggested annual peat carbon losses of 24.9 Mg CO2 -C ha-1 year-1 over the first 6 years, lower than previous estimates for this early period from subsidence studies, losses reduced to 12.8 Mg CO2 -C ha-1 year-1 in the later, mature phase. Despite reductions in NEE and carbon loss over time, the system remained a large net source of carbon to the atmosphere after 12 years with the remaining 8 years of a typical plantation's rotation unlikely to recoup losses. These results emphasize the need for effective protection of tropical peatlands globally and strengthening of legislative enforcement where moratoria on peatland conversion already exist.
While wetlands are the largest natural source of methane (CH4 ) to the atmosphere, they represent a large source of uncertainty in the global CH4 budget due to the complex biogeochemical controls on CH4 dynamics. Here we present, to our knowledge, the first multi-site synthesis of how predictors of CH4 fluxes (FCH4) in freshwater wetlands vary across wetland types at diel, multiday (synoptic), and seasonal time scales. We used several statistical approaches (correlation analysis, generalized additive modeling, mutual information, and random forests) in a wavelet-based multi-resolution framework to assess the importance of environmental predictors, nonlinearities and lags on FCH4 across 23 eddy covariance sites. Seasonally, soil and air temperature were dominant predictors of FCH4 at sites with smaller seasonal variation in water table depth (WTD). In contrast, WTD was the dominant predictor for wetlands with smaller variations in temperature (e.g., seasonal tropical/subtropical wetlands). Changes in seasonal FCH4 lagged fluctuations in WTD by ~17 ± 11 days, and lagged air and soil temperature by median values of 8 ± 16 and 5 ± 15 days, respectively. Temperature and WTD were also dominant predictors at the multiday scale. Atmospheric pressure (PA) was another important multiday scale predictor for peat-dominated sites, with drops in PA coinciding with synchronous releases of CH4 . At the diel scale, synchronous relationships with latent heat flux and vapor pressure deficit suggest that physical processes controlling evaporation and boundary layer mixing exert similar controls on CH4 volatilization, and suggest the influence of pressurized ventilation in aerenchymatous vegetation. In addition, 1- to 4-h lagged relationships with ecosystem photosynthesis indicate recent carbon substrates, such as root exudates, may also control FCH4. By addressing issues of scale, asynchrony, and nonlinearity, this work improves understanding of the predictors and timing of wetland FCH4 that can inform future studies and models, and help constrain wetland CH4 emissions.
Pristine tropical peat swamp forests (PSFs) represent a unique wetland ecosystem of distinctive hydrology which support unique biodiversity and globally significant stores of soil carbon. Yet in Indonesia and Malaysia, home to 56% of the world's tropical peatland, they are subject to considerable developmental pressures, including widespread drainage to support agricultural needs. In this article, we review the ecology behind the functioning and ecosystem services provided by PSFs, with a particular focus on hydrological processes as well as the role of the forest itself in maintaining those services. Drawing on this, we review the suitability of current policy frameworks and consider the efficacy of their implementation. We suggest that policies in Malaysia and Indonesia are often based around the narrative of oil palm and other major monocrops as drivers of prosperity and development. However, we also argue that this narrative is also being supported by a priori claims concerning the possibility of sustainability of peat swamp exploitation via drainage-based agriculture through the adherence to best management practices. We discuss how this limits their efficacy, uptake and the political will towards enforcement. Further, we consider how both narratives (prosperity and sustainability) clearly exclude important considerations concerning the ecosystem value of tropical PSFs which are dependent on their unimpacted hydrology. Current research clearly shows that the actual debate should be focused not on how to develop drainage-based plantations sustainably, but on whether the sustainable conversion to drainage-based systems is possible at all.
Green leafy vegetables are good sources of carotenoids. Generally, food composition databases related to raw foods are available, but data on cooked foods in Malaysia are still lacking. Since carotenoids are prone to degradation during cooking processes, the present study was undertaken to evaluate the extent of nutrient loss in vegetables subjected to two conventional cooking methods, which were boiling and stir-frying with cooking durations of 4 and 8 minutes. The vegetables selected were Chinese cabbage (Brassica Pekinensis var. cephalata), swamp cabbage (Ipomoea aquatica), spinach (Spinacia oleracea), Ceylon spinach (Basella rubra), red spinach (Amaranthus gangeticus), white spinach (Amaranthus viridis) and tapioca shoots (Manihot utilissima). Percentage losses of nutrients after cooking treatment were calculated based on retention factors. Results obtained showed that stir-frying had reduced lutein content for all vegetables ranging from 8-89% while the effect of boiling for lutein varied (0-428%) with different vegetables at both cooking durations of 4 and 8 min. Boiling for 8 min increased retention of β carotene in all vegetables ranging from 18-380% except for Chinese cabbage and spinach compared with 4 min, while stir-frying generally increased the retention of β-carotene for all vegetables 2-3 times except for spinach. Cooked vegetables have variations in carotenoids composition brought by varying cooking conditions (time and temperature), type of vegetables and the interaction between cooking methods and type of vegetables.
Constructed wetlands (CWs) are affordable and reliable green technologies for the treatment of various types of wastewater. Compared to conventional treatment systems, CWs offer an environmentally friendly approach, are low cost, have fewer operational and maintenance requirements, and have a high potential for being applied in developing countries, particularly in small rural communities. However, the sustainable management and successful application of these systems remain a challenge. Therefore, after briefly providing basic information on wetlands and summarizing the classification and use of current CWs, this study aims to provide and inspire sustainable solutions for the performance and application of CWs by giving a comprehensive review of CWs' application and the recent development of their sustainable design, operation, and optimization for wastewater treatment. To accomplish this objective, thee design and management parameters of CWs, including macrophyte species, media types, water level, hydraulic retention time (HRT), and hydraulic loading rate (HLR), are discussed. Besides these, future research on improving the stability and sustainability of CWs are highlighted. This article provides a tool for researchers and decision-makers for using CWs to treat wastewater in a particular area. This paper presents an aid for informed analysis, decision-making, and communication. The review indicates that major advances in the design, operation, and optimization of CWs have greatly increased contaminant removal efficiencies, and the sustainable application of this treatment system has also been improved.
Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.
The objective of this study is to determine the reduction efficiency of Chemical Oxygen Demand (COD) as well as the removal of color and Amaranth dye metabolites by the Aerobic-anaerobic Baffled Constructed Wetland Reactor (ABCW). The ABCW reactor was planted with common reed (Phragmite australis) where the hydraulic retention time (HRT) was set to 1 day and was fed with synthetic wastewater with the addition of Amaranth dye. Supplementary aeration was supplied in designated compartments of the ABCW reactor to control the aerobic and anaerobic zones. After Amaranth dye addition the COD reduction efficiency dropped from 98 to 91% while the color removal efficiency was 100%. Degradation of azo bond in Amaranth dye is shown by the UV-Vis spectrum analysis which demonstrates partial degradation of Amaranth dye metabolites. The performance of the baffled unit is due to the longer pathway as there is the up-flow and down-flow condition sequentially, thus allowing more contact of the wastewater with the rhizomes and micro-aerobic zones.
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).
A novel, rod-shaped, Gram-stain-negative, halophilic and non-motile bacterium, designated CCB-MM1T, was isolated from a sample of estuarine sediment collected from Matang Mangrove Forest, Malaysia. The cells possessed a rod-coccus cell cycle in association with growth phase and formed aggregates. Strain CCB-MM1T was both catalase and oxidase positive, and able to degrade starch. Optimum growth occurred at 30 °C and pH 7.0 in the presence of 2-3 % (w/v) NaCl. The 16S rRNA gene sequence of strain CCB-MM1T showed 98.12, 97.46 and 97.33 % sequence similarity with Microbulbifer rhizosphaerae Cs16bT, Microbulbifer maritimus TF-17T and Microbulbifergwangyangensis GY2T respectively. Strain CCB-MM1T and M. rhizosphaerae Cs16bT formed a cluster in the phylogenetic tree. The major cellular fatty acids were iso-C17 : 1 ω9c and iso-C15 : 0, and the total polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoaminolipid, two unidentified lipids, an unidentified glycolipid and an unidentified aminolipid. The major respiratory quinone was ubiquinone Q-8 and the genomic DNA G+C content of the strain was 58.9 mol%. On the basis of the phylogenetic, phenotypic and genotypic data presented here, strain CCB-MM1T represents a novel species of the genus Microbulbifer, for which the name Microbulbiferaggregans sp. nov. is proposed. The type strain is CCB-MM1T (=LMG 29920T=JCM 31875T).
Mineral elemental uptake by Colocasia esculenta growing in swamp agroecosystem was studied following 14, 18 or 28 months of field spraying (MAT, months after treatment) with herbicide Gramoxone ® (paraquat). In overall, Al (68226.67 + 24066.56 μg/g dw) was the major element in riverine alluvial swamp soil, followed by micronutrient Fe (22280.00 + 6328.87 μg/g dw).
Concentration of macronutrient K (20733.33 + 7371.82 μg/g dw) was the highest in swamp taro leaf followed by macronutrient Ca (7050.00 + 3767.26 μg/g dw). In overall, the order of importance of the average mineral concentration in swamp taro leaf was K > Ca > Mn > Al > Na > Fe > Zn > Br > Co. However at 14 MAT, the order of importance of mineral content concentration in swamp taro leaf was K > Ca > Al > Na > Mn > Fe > Zn > Br > Co. At 18 MAT, the order of importance of mineral content concentration in swamp taro leaf was K > Ca > Mn > Al > Fe > Na > Zn > Br > Co. At 28 MAT, the order of importance of mineral content concentration in swamp taro leaf was K > Ca > Mn > Fe > Al > Zn > Na > Br > Co. In overall, the average order of importance of mineral elemental uptake or the soil plant transfer coefficient was Mn > K > Na > Zn > Co > Fe > Al; similar with the order at 28 MAT. However, at 14 MAT the order of importance of the soil plant transfer coefficient was different at Mn > K > Na > Co > Zn > Al > Fe.
The composition of fish larvae and their diversity in different habitats are very important for fisheries management. Larval fishes were investigated in a mangrove estuary of Marudu Bay, Sabah, Malaysia from October 2012 to September 2013 at five different sites. Monthly samples of fish larvae were collected at five sampling sites by a plankton net with a mouth opening of 40.5 cm in diameter. In total, 3879 larval fish were caught in the investigated area. The mean density of ichthyoplankton at this area was 118 larvae/100 m(3). The fish larval assemblage comprised of 20 families whereas 13 families occurred at St1, 16 at St2, 16 at St3, 12 at St4 and 16 at St5. The top major families were Sillaginidae, Engraulidae, Mugilidae and Sparidae with Sillaginidae consisted 44% of total larval composition. St3 with 143 larvae/100 m(3) had the highest density amongst the stations which was due to higher abundance of Sillaginidae. Shannon-Wiener diversity index represented significant variation during monsoon and inter-monsoon seasons, peaking in the months December-January and May-June. However, Shannon-Wiener index, evenness and family richness showed significant differences among stations and months (p < 0.05).
Horizontal subsurface-flow (HSF) constructed wetland incorporating baffles was developed to facilitate upflow and downflow conditions so that the treatment of pollutants could be achieved under multiple aerobic, anoxic and anaerobic conditions sequentially in the same wetland bed. The performances of the baffled and conventional HSF constructed wetlands, planted and unplanted, in the removal of azo dye Acid Orange 7 (AO7) were compared at the hydraulic retention times (HRT) of 5, 3 and 2 days when treating domestic wastewater spiked with AO7 concentration of 300 mg/L. The planted baffled unit was found to achieve 100%, 83% and 69% AO7 removal against 73%, 46% and 30% for the conventional unit at HRT of 5, 3 and 2 days, respectively. Longer flow path provided by baffled wetland units allowed more contact of the wastewater with the rhizomes, microbes and micro-aerobic zones resulting in relatively higher oxidation reduction potential (ORP) and enhanced performance as kinetic studies revealed faster AO7 biodegradation rate under aerobic condition. In addition, complete mineralization of AO7 was achieved in planted baffled wetland unit due to the availability of a combination of aerobic, anoxic and anaerobic conditions.
This study investigated the optimum conditions for total petroleum hydrocarbon (TPH) removal from diesel-contaminated water using phytoremediation treatment with Scirpus grossus. In addition, TPH removal from sand was adopted as a second response. The optimum conditions for maximum TPH removal were determined through a Box-Behnken Design. Three operational variables, i.e. diesel concentration (0.1, 0.175, 0.25% Vdiesel/Vwater), aeration rate (0, 1 and 2 L/min) and retention time (14, 43 and 72 days), were investigated by setting TPH removal and diesel concentration as the maximum, retention time within the given range, and aeration rate as the minimum. The optimum conditions were found to be a diesel concentration of 0.25% (Vdiesel/Vwater), a retention time of 63 days and no aeration with an estimated maximum TPH removal from water and sand of 76.3 and 56.5%, respectively. From a validation test of the optimum conditions, it was found that the maximum TPH removal from contaminated water and sand was 72.5 and 59%, respectively, which was a 5 and 4.4% deviation from the values given by the Box-Behnken Design, providing evidence that S. grossus is a Malaysian native plant that can be used to remediate wastewater containing hydrocarbons.
Putrajaya Wetlands in Malaysia, a 200ha constructed wetland system consisting of 24 cells, was created in 1997-1998 to treat surface runoff caused by development and agricultural activities from an upstream catchment before entering Putrajaya Lake (400ha). It was designed for stormwater treatment, flood control and amenity use. The water quality improvement performance of a section of the wetland cells is described. The nutrient removal performance was 82.11% for total nitrogen, 70.73% for nitrate-nitrogen and 84.32% for phosphate, respectively, along six wetland cells from Upper North UN6 to UN1 from April to December 2004. Nutrient removal in pilot scale tank systems, simulating a constructed wetland and planted with examples of common species at Putrajaya, the Common Reed Phragmites karka and Tube Sedge Lepironia articulata, and the capacity of these species to retain nutrients in above and below-ground plant biomass and substrate is reported. The uptake of nutrients by the Common Reed and Tube Sedge from the pilot tank system was 42.1% TKN; 28.9% P and 17.4% TKN; 26.1% P, respectively. The nutrient uptake efficiency of the Common Reed was higher in above-ground than in below-ground tissue. The results have implications for plant species selection in the design of constructed wetlands in Malaysia and for optimizing the performance of these systems.