Fire is one of the major issues facing Southeast Asian peatlands causing socio-economic, human health and climate crises. Many of these fires in the region are associated with land clearing or management practices for oil palm plantations. Here we study the direct post-fire impacts of slash-and-burn oil palm agriculture on greenhouse gas emissions, peat physico-chemical properties and nutrient concentrations. Greenhouse gas (GHG) emissions were measured using Los Gatos ultraportable greenhouse gas analyser one month after a fire in dry season and five months after the fire event, in wet season. Surface soil samples were collected from each individual GHG measurement points, along with 50 cm cores from both burnt and non-burnt control areas for lab analyses. As an immediate post-fire impact, carbon dioxide (CO2) and methane (CH4) emissions, pH, electrical conductivity, and all macronutrient concentrations except nitrogen (N) were increased multi-fold, while the redox potential, carbon (C) and N content were greatly reduced in the burnt region. While some of the properties such as CO2 emissions, and electrical conductivity reverted to normal after five months, other properties such as CH4 emissions, pH and nutrient concentrations remained high in the burnt region. This study also found very high loss of surface peat C content in the burnt region post fire, which is irreversible. The results also show that surface peat layers up to 20 cm depth were affected the most by slash-and-burn activity in oil palm agriculture, however the intensity of fire can vary widely between different oil palm management and needs further research to fully understand the long term and regional impacts of such slash-and-burn activity in tropical peatlands.
The oil palm industry, especially in Indonesia and Malaysia is being threatened by Basal Stem Rot (BSR) disease caused by Ganoderma boninense. There is no conclusive remedy in handling this disease effectively. In this study, metagenomics analysis of soil were analyzed for a better understanding of the microbial diversity in relation to BSR disease. Study was conducted in three plantation sites of Sabah, Malaysia which incorporated different disease management and agronomic practices. The estates are located at Sandakan (Kam Cheong Plantation), Lahad Datu (FGV Ladang Sahabat) and Tawau (Warisan Gagah). Soil samples were collected from disease free, high and low BSR incidence plots. Illumina MiSeq metagenomic analysis using V3-V4 region of 16S rRNA gene was employed to study the microbial diversity. Bacteria (97.4%) and Archaea (0.2%) were found majority in kingdom taxonomy level. The most abundant phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia. Higher alpha diversity of all species was observed among all tested soil from each estates. Beta analysis was analyzed using non phylogenetic UnifRac matrix and visualized using Principal Coordinates Analysis (PCoA). The tested soil samples in Kam Cheong Plantation were found to have similar bacterial communities. The data provided is useful as an indicator in developing biology controls against Ganoderma boninense.
In this study, the differences on the physico-chemical parameters, lignocellulose degradation, dynamic succession of microbial community, gene expression of carbohydrate-active enzymes and antibiotics resistance genes were compared during composting systems of bagasse pith/pig manure (BP) and manioc waste/pig manure (MW). The results revealed that biodegradation rates of organic matter, cellulose, hemicellulose and lignin (29.14%, 17.53%,45.36% and 36.48%) in BP were higher than those (15.59%, 16.74%, 41.23% and 29.77%) in MW. In addition, the relative abundance of Bacillus, Luteimonas, Clostridium, Pseudomonas, Streptomyces and expression of genes encoding carbohydrate- active enzymes in BP were higher than those in MW based on metagenomics sequencing. During composting, antibiotics and antibiotic resistance genes were substantially reduced, but the removal efficiency was divergent in the both samples. Taken together, metagenomics analysis was a potential method for evaluating lignocellulose's biodegradation process and determining the elimination of antibiotic and antibiotic resistance genes from different composting sources of biomass.
A comprehensive study of the chemical composition of rainwater was carried out from October 2016 to September 2017 in the equatorial tropical rainforest region of northwestern Borneo. Monthly cumulative rainwater samples were collected from different locations in the Limbang River Basin (LRB) and were later categorized into seasonal samples representing northeast monsoon (NEM), southwest monsoon (SWM), and inter-monsoon (IM) periods. Physical parameters (pH, EC, TDS, DO, and turbidity), major ions (HCO3-, Cl-, Ca2+, Mg2+, Na+, and K+) and trace metals (Co, Ni, Cd, Fe, Mn, Pb, Zn, and Cu) were analyzed from collected rainwater samples. Rainwater is slightly alkaline with mean pH higher than 5.8. Chloride and bicarbonate are the most abundant ions, and the concentration of major ions in seasonal rainwater has shown slight variation which follows a descending order of HCO3-> Cl-> Na+ > Ca2+ > Mg2+ > K+ in NEM and Cl- > HCO3- > Na+ > Ca2+ > K+ > Mg2+ in SWM and Cl- > HCO3- > Na+ > Ca2+ > Mg2+ > K+ in IM period. Trace metals such as Fe and Ni have shown dominance in seasonal rainwater samples, and all the metals have shown variation in concentration in different seasons. Variation in chemical characteristic of seasonal rainwater samples identified through piper diagram indicates dominance of Ca2+-Mg2+-HCO3- and mixed Ca2+-Mg2+-Cl- facies during NEM, SWM, and IM periods. Statistical analysis of the results through two-way ANOVA and Pearson's correlation also indicates significant variation in physico-chemical characteristics. This suggests a variation in contributing sources during the monsoon seasons. Factor analysis confirmed the source variation by explaining the total variance of 79.80%, 90.72%, and 90.52% with three factor components in NEM, SWM, and IM rainwater samples with different loading of parameters. Enrichment factor analysis revealed a combined contribution of marine and crustal sources except K+ which was solely from crustal sources. Sample analysis of backward air mass trajectory supports all these findings by explaining seasonal variation in the source of pollutants reaching the study area. Overall, the results show that the chemical composition of seasonal rainwater samples in LRB was significantly influenced by natural as well as anthropogenic processes. These include (long-range and local) industrial activities, fossil fuel combustion, forest burning, transportation activities including road transport and shipping activities, and land-derived soil dust along with chemical constituents carried by seasonal wind.
Extensive use of carbofuran insecticide harms the environment and human health. Carbofuran is an endocrine disruptor and has the highest acute toxicity to humans than all groups of carbamate pesticides used. Carbofuran is highly mobile in soil and soluble in water with a lengthy half-life (50 days). Therefore, it has the potential to contaminate groundwater and nearby water bodies after rainfall events. A bacterial strain BRC05 was isolated from agricultural soil characterized and presumptively identified as Enterobacter sp. The strain was immobilized using gellan gum as an entrapment material. The effect of different heavy metals and the ability of the immobilized cells to degrade carbofuran were compared with their free cell counterparts. The results showed a significant increase in the degradation of carbofuran by immobilized cells compared with freely suspended cells. Carbofuran was completely degraded within 9 h by immobilized cells at 50 mg/L, while it took 12 h for free cells to degrade carbofuran at the same concentration. Besides, the immobilized cells completely degraded carbofuran within 38 h at 100 mg/L. On the other hand, free cells degraded the compound in 68 h. The viability of the freely suspended cell and degradation efficiency was inhibited at a concentration greater than 100 mg/L. Whereas, the immobilized cells almost completely degraded carbofuran at 100 mg/L. At 250 mg/L concentration, the rate of degradation decreased significantly in free cells. The immobilized cells could also be reused for about nine cycles without losing their degradation activity. Hence, the gellan gum-immobilized cells of Enterobacter sp. could be potentially used in the bioremediation of carbofuran in contaminated soil.
Meghna River Estuary, the largest estuarine system (GBM, Ganges-Brahmaputra-Meghna) in Bangladesh, is a major spawning ground of national fish, Hilsha shad. In this study, we collected 24 surface sediment and 24 water samples from the entire lower estuary (4 sites, 3 sampling points from each site, 2 replicas from each sampling point) to detect trace/heavy metals. Sediment samples were collected from the top surface soil (0-5 cm) using Ekman grab sampler and water samples from 5 cm below the surface layer using plastic water bottles. After collection, sediment and water samples were preserved as necessary using HNO3 (for water). Immediately after reaching the laboratory, sediment samples were dried in an oven at 70°C until the constant weight gained. The metals were then analyzed using energy-dispersive X-ray fluorescence method (EDXRF) and calculated the metal concentrations. In total, 12 metals were detected and the average value (mg/Kg) of all metals for sediment samples followed the descending order of Fe > Ca > K >Ti >Sr >Zr >Rb> Cu > Zn >Pb >As > Ni, and for water the order (µg/mL) of Fe >Ti > Ca > Co >Mn > Ni > Zn >Sr > Cu > As > Se . Besides, several physicochemical parameters i.e. water pH, soil pH, temperature, salinity, dissolved oxygen, hardness, and alkalinity of the 12 sampling points were also measured in-situ using handheld instruments.
It is important to provide a baseline of fungal composition in the captive wildlife environment to better understand their role in overall wildlife health. The objectives were to identify species of fungi existing within wildlife animal enclosures and their environment at the National Wildlife Rescue Centre (NWRC) and the National Zoo, Malaysia and to describe their medical and veterinary importance. Samples of air, wall or floor swab, enrichment swab and soil were taken from the animal enclosures, exercise yard and enrichments at NWRC and National Zoo respectively. All samples including those pre-treated samples were plated onto Sabouraud's Dextrose Agar (SDA). Numerous fungi were grown on all sampling SDA plates regardless by either single or multiple growth. Samples of air in both NWRC and National Zoo had the highest growth of Penicillium spp. with a prevalence of 31.2% and 83.7% respectively. Samples of swab from the wall, floor and enrichments were predominantly by Candida spp. (42.6%) in NWRC and Penicillium spp. (41.6%) in the National Zoo. Prevalence of multiple fungi isolated from the soil samples in NWRC were 57.9% and yeast species was the most common in National Zoo with a prevalence of 88.9%. Overall, 29 and 8 isolates were found in both samples from the NWRC and National Zoo with a predominant species of potential zoonotic fungi have been identified in both premises. The expected fungus Aspergillus spp. was not isolated in all samples in NWRC. Prevalent fungal species found in this study are known to cause disease in animals and humans as primary pathogen and also as opportunistic pathogens that may also cause infection. Thus, health safety precautions should be considered particularly in dealing with conservation of endangered wildlife species, along with personnel and public involvements.
Limited information is available that seed biopriming with plant growth-promoting Enterobacter spp. play a prominent role to enhance vegetative growth of plants. Contrary to Enterobacter cloacae, Enterobacter hormaechei is a less-studied counterpart despite its vast potential in plant growth-promotion mainly through the inorganic phosphorus (P) and potassium (K) solubilization abilities. To this end, 18 locally isolated bacterial pure cultures were screened and three strains showed high P- and K-solubilizing capabilities. Light microscopy, biochemical tests and 16S rRNA gene sequencing revealed that strains 15a1 and 40a were closely related to Enterobacter hormaechei while strain 38 was closely related to Enterobacter cloacae (Accession number: MN294583; MN294585; MN294584). All Enterobacter spp. shared common plant growth-promoting traits, namely nitrogen (N2) fixation, indole-3-acetic acid production and siderophore production. The strains 38 and 40a were able to produce gibberellic acid, while only strain 38 was able to secrete exopolysaccharide on agar. Under in vitro germination assay of okra (Abelmoschus esculentus) seeds, Enterobacter spp. significantly improved overall germination parameters and vigor index (19.6%) of seedlings. The efficacy of root colonization of Enterobacter spp. on the pre-treated seedling root tips was confirmed using Scanning Electron Microscopy (SEM). The pot experiment of bioprimed seeds of okra seedling showed significant improvement of the plant growth (> 28%) which corresponded to the increase of P and K uptakes (> 89%) as compared to the uninoculated control plants. The leaf surface area and the SPAD chlorophyll index of bioprimed plants were increased by up to 29% and 9% respectively. This report revealed that the under-explored species of P- and K-solubilizing Enterobacter hormaechei sp. with multiple plant beneficial traits presents a great potential sustainable approach for enhancement of soil fertility and P and K uptakes of plants.
Actinobacteria from underexplored and unusual environments have gained significant attention for their capability in producing novel bioactive molecules of diverse chemical entities. Streptomyces is the most prolific Actinobacteria in producing useful molecules. Rapid decline effectiveness of existing antibiotics in the treatment of infections are caused by the emergence of multidrug-resistant pathogens. Intensive efforts are urgently required in isolating non-Streptomyces or rare Actinobacteria and understanding of their distribution in the harsh environment for new drug discovery. In this study, pretreatment of soil samples with 1.5% phenol was used for the selective isolation of Actinobacteria from Dee Island and Greenwich Island. A high number of non-Streptomyces (69.4%) or rare Actinobacteria was significantly recovered despite the Streptomyces (30.6%), including the genera Micromonospora, Micrococcus, Kocuria, Dermacoccus, Brachybacterium, Brevibacterium, Rhodococcus, Microbacterium and Rothia. Reduced diversity and shift of distribution were observed at the elevated level of soil pH. The members of genera Streptomyces, Micromonospora and Micrococcus were found to distribute and tolerate to a relatively high pH level of soil (pH 9.4-9.5), and could potentially be alkaliphilic Actinobacteria. The phylogenetic analysis had revealed some potentially new taxa members of the genera Micromonospora, Micrococcus and Rhodococcus. Principal Component Analysis of soil samples was used to uncover the factors that underlie the diversity of culturable Actinobacteria. Water availability in soil was examined as the principal factor that shaped the diversity of the Actinobacteria, by providing a dynamic source for microbial interactions and elevated diversity of Actinobacteria.
Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment-calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept-non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3-V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.
Fusarium wilt disease is one of the most problematic and destructive disease in cucumber production. The causative agents are Fusarium oxysporum and F. solani. These pathogens are soil borne and transmitted through infested soil and water. A field survey was conducted to study the disease prevalence in the major growing areas of cucumber in Peninsular Malaysia. Field study revealed that the disease was highly prevalence in the field with the disease incidence was in the range of 10%-60%. The morphological properties of F. oxysporum are microconidia (3.8-15.7 μm × 2.9-4.9 μm), macroconidia (14.8-38.5 μm × 2.4-5.7 μm) and number of septate was 1-4. While for F. solani are microconidia (3.39-14.63 μm × 2.36-4.44 μm), macroconidia (7.22-50.46 μm × 2.43-6.14 μm) and number of septate was 1-5. Based on molecular identification had confirmed that the disease is caused by F. oxysporum and F. solani with similarity index of 99%-100% based on internal transcribed spacer (ITS) gene sequences. The pathogenicity test showed that the symptoms of Fusarium wilt disease was firstly appeared as yellowing of old leaves. Progressively, the infected plant will be wilted and finally died. The outputs of this study are highly important to establish an effective disease management programme to reduce disease prevalence and yield loss in the field.
Conventional hydrogeologic framework models used to compute ocean island sustainable yields and aquifer storage neglect the complexity of the nearshore and offshore submarine environment. However, the onshore aquifer at the island of Hawai'i exhibits a notable volumetric discrepancy between high-elevation freshwater recharge and coastal discharge. In this study, we present a novel transport mechanism of freshwater moving from onshore to offshore through a multilayer formation of water-saturated layered basalts with interbedded low-permeability layers of ash/soil. Marine electromagnetic imaging reveals ∼35 km of laterally continuous resistive layers that extend to at least 4 km from west of Hawai'i's coastline, containing about 3.5 km3 of freshened water. We propose that this newly found transport mechanism of fresh groundwater may be the governing mechanism in other volcanic islands. In such a scenario, volcanic islands worldwide can use these renewable offshore reservoirs, considered more resilient to climate change-driven droughts, as new water resources.
Co-application of biochar and biosolids to soil has potential to mitigate N leaching due to physical and chemical properties of biochar. Changes in N cycling pathways in soil induced by co-application of biological amendments could further mitigate N loss, but this is largely unexplored. The aim of this study was to determine whether co-application of a biochar and a modified biosolids product to three pasture soils differing in texture could alter the relative abundance of N cycling genes in soil sown with subterranean clover. The biosolids product contained lime and clay and increased subterranean clover shoot biomass in parallel with increases in soil pH and soil nitrate. Its co-application with biochar similarly increased plant growth and soil pH with a marked reduction in nitrate in two coarse textured soils but not in a clayey soil. While application of the biosolids product altered in silico predicted N cycling functional genes, there was no additional change when applied to soil in combination with biochar. This supports the conclusion that co-application of the biochar and biosolids product used here has potential to mitigate loss of N in coarse textured soils due to N adsoption by the biochar and independently of microbial N pathways.
Effects of metsulphuron-methyl on the activities of amylase, invertase and xylanase in loamy sand and clay were evaluated for up to 28 days under laboratory conditions. Metsulphuron-methyl at 1.0 microg/g caused a significant reduction in amylase, invertase and xylanase activities for the entire period of study, especially at 28 days incubation in both soils. The lowest activities of the three enzymes were observed in the presence of 5.0 microg/g at 28 days incubation.
Multi-year instrumental records for input, throughflow and output waters of the Lilburn Cave system provide control on denudation rates as they respond to seasonal and spatial variability. Data suggest that maximum denudation is in the late fall and early winter. This is when non-snowmelt discharge is at its maximum. At lower discharge rates the volume of water moving through the cave system is the limiting control on the volume of denudation. During periods of snowmelt the limiting control is the rate at which the calcite dissolves. This is probably the result of water flowing through wider channels during these times. Based on instrumental measurements, there is considerable variation in terms of where denudation occurs inside the cave. The loci of dissolution change from year to year. This is to be expected in the dynamic environment of the cave where materials shift routinely. This variability should be studied over longer periods of time in order to more fully understand its extent. The relatively small area of carbonate exposure relative to the area of the drainage basin gives rise to relatively high denudation rates. The carbonate is being removed at a rate of about 5000 metric tons per year, or at about 830 mm/y. This is about five times the rate reported in the humid karst regions of Malaysia. This information indicates that the relative proportion of carbonate in the drainage basin needs to be considered when trying to estimate denudation in other areas.
This paper covers studies on the molecular and ecological aspects of G. glabra var. glandulifera, G. flavescens ssp. flavescens and G. echinata collected from Hatay (Turkey); with the aim to better understand their genetic variation and ecological requirements for possible conservation programs. The material including total genomic DNA was extracted by the CTAB, and for PCR reaction, a total of 14 SSR primers developed for Medicago truncatula were used. PCR amplifications were performed in a Multigen(®) Thermal Cycler. Soil samples were analysed for their texture, pH, total soluble salts, calcium carbonate, total N content, total phosphorus and organic matter content. In order to see the association between genetic, ecological and geographical data, a similarity matrix was generated. Genetic similarity distances between genotypes were correlated with those of Eucledian distances obtained from ecological and geographical data. Analysis of molecular variance (AMOVA) was performed using GenAlEx 6.5 software to determine variation among and within genetic variations. The genetic analysis showed that the highest expected heterozygosity values were obtained from G. glabra while the lowest were obtained from G. echinata. In general heterozygosity values were low, especially for G. echinata. Therefore, variation appears to be lower within each species than among three species. The physical and chemical analysis of soil and plant samples indicates that mineral accumulation in plants is substantially affected by the soil characteristics. There is a need for identification of better strategies for the improvement of varieties, especially for small farmers managing marginal soils. More studies should be conducted in order to safeguard these taxa, especially G. glabra var. glandulifera which is collected intensively due to its economic value, the same is true for endemic taxon G. flavescens ssp. flavescens.
Mycelium-bound lipase (MBL) was prepared using a strain of Geotrichum candidum isolated from local soil. At the time of maximum lipase activity (54 h), the mycelia to which the lipase was bound were harvested by filtration and centrifugation. Dry MBL was prepared by lyophilizing the mycelia obtained. The yield of MBL was 3.66 g/l with a protein content of 44.11 mg/g. The lipase activity and specific lipase activity were 22.59 and 510 U/g protein, respectively. The moisture content of the MBL was 3.85%. The activity of free (extracellular) lipase in the culture supernatant (after removal of mycelia) was less than 0.2 U/ml. The MBL showed selectivity for oleic acid over palmitic acid during hydrolysis of palm olein, indicating that the lipase from G. candidum displayed high substrate selectivity for unsaturated fatty acid containing a cis-9 double bond, even in crude form. This unique specificity of MBL could be a direct, simple and inexpensive way in the fats and oil industry for the selective hydrolysis or transesterification of cis-9 fatty acid residues in natural triacylglycerols.
Once-yearly, mass deworming with broad spectrum anthelmintics over a period of five years among four types of communities in Malaysia resulted in an overall education in the prevalence of soil-transmitted helminthiases by one-third to two-thirds. The reduction in prevalence of infection was highest among inhabitants in semi-urban settlements (65.5%), followed by those in the rural estates (53.0%) and high-rise flats (43.9%). Soil-transmitted helminthiases were only reduced by 35.5% in the urban slums. Reduction in infection with Trichuris trichiura was better than that with Ascaris lumbricoides whereas hook-infection was completely eliminated in some of the communities surveyed. The reduction in prevalence ofsoil-transmitted helminthiases by long-term, once-yearly deworming alone, without other supplementary interventions, reinforces the potential and feasibility of regular mass-deworming as an immediate and effective measure for the control ofsoil-transmitted helminthiases. This is of great public health significance especially in highly endemic communities where some form of intervention is urgently needed and facilities for other control measures such as the improvement of environmental sanitation and nutritional status and health education are neither feasible nor possible nor immediately available.
In this study, a total of 147 soil actinobacterial strains were screened for their ability to inhibit response of Chromobacterium violaceum CV026 to short chain N-acyl homoserine lactone (AHL) which is a quorum sensing molecule. Of these, three actinobacterial strains showed positive for violacein inhibition. We further tested these strains for the inhibition of Pseudomonas aeruginosa PAO1 quorum sensing-regulated phenotypes, namely, swarming and pyocyanin production. The three strains were found to inhibit at least one of the quorum sensing-regulated phenotypes of PAO1. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these strains belong to the genera Micromonospora, Rhodococcus and Streptomyces. This is the first report presenting quorum quenching activity by a species of the genus Micromonospora. Our data suggest that Actinobacteria may be a rich source of active compounds that can act against bacterial quorum sensing system.