Displaying publications 61 - 80 of 215 in total

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  1. Quantification and characterisation of Trichoderma spp. from different ecosystems
    Sariah M, Choo CW, Zakaria H, Norihan MS
    Mycopathologia, 2005 Jan;159(1):113-7.
    PMID: 15750742
    Basal stem rot of oil palm caused by Ganoderma boninense is of major economic importance. Observations of the low incidence of disease due to Ganoderma species in natural stands, suggest that the disease is kept under control by some biological means. Trichoderma spp. are saprophytic fungi with high antagonistic activities against soil-borne pathogens. However, their abundance and distribution are soil and crop specific. Trichoderma species have been found to be concentrated in the A1 (0-30 cm) and Be soil horizons (30-60 cm), although the abundance of Trichoderma was not significantly different between the oil palm and non-oil palm ecosystems. Characterisation of Trichoderma isolates based on cultural, morphological and DNA polymorphism showed that T. harzianum, T. virens, T. koningii and T. longibrachiatum made up 72, 14, 10 and 4% of the total Trichoderma isolates isolated. As Trichoderma species are present in the oil palm ecosystem, but at lower numbers and in locations different from those desired, soil augmentation with antagonistic Trichoderma spp. can be developed as a strategy towards integrated management of basal stem rot of oil palm.
    Matched MeSH terms: Soil Microbiology*
  2. Degradation of medium-chain-length polyhydroxyalkanoates in tropical forest and mangrove soils
    Lim SP, Gan SN, Tan IK
    Appl Biochem Biotechnol, 2005 Jul;126(1):23-33.
    PMID: 16014996
    Bacterial polyhydroxyalkanoates (PHAs) are perceived to be a suitable alternative to petrochemical plastics because they have similar material properties, are environmentally degradable, and are produced from renewable resources. In this study, the in situ degradation of medium-chain-length PHA (PHAMCL) films in tropical forest and mangrove soils was assessed. The PHAMCL was produced by Pseudomonas putida PGA1 using saponified palm kernel oil (SPKO) as the carbon source. After 112 d of burial, there was 16.7% reduction in gross weight of the films buried in acidic forest soil (FS), 3.0% in the ones buried in alkaline forest soil by the side of a stream (FSst) and 4.5% in those buried in mangrove soil (MS). There was a slight decrease in molecular weight for the films buried in FS but not for the films buried in FSst and in MS. However, no changes were observed for the melting temperature, glass transition temperature, monomer compositions, structure, and functional group analyses of the films from any of the burial sites during the test period. This means that the integral properties of the films were maintained during that period and degradation was by surface erosion. Scanning electron microscopy of the films from the three sites revealed holes on the film surfaces which could be attributed to attack by microorganisms and bigger organisms such as detritivores. For comparison purposes, films of polyhydroxybutyrate (PHB), a short-chain-length PHA, and polyethylene (PE) were buried together with the PHAMCL films in all three sites. The PHB films disintegrated completely in MS and lost 73.5% of their initial weight in FSst, but only 4.6% in FS suggesting that water movement played a major role in breaking up the brittle PHB films. The PE films did not register any weight loss in any of the test sites.
    Matched MeSH terms: Soil Microbiology*
  3. The impact of tropical forest logging and oil palm agriculture on the soil microbiome
    Tripathi BM, Edwards DP, Mendes LW, Kim M, Dong K, Kim H, et al.
    Mol Ecol, 2016 May;25(10):2244-57.
    PMID: 26994316 DOI: 10.1111/mec.13620
    Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.
    Matched MeSH terms: Soil Microbiology*
  4. Persistence and bioactivity of metsulfuron-methyl in three soils
    Ismail BS, Azlizan BA
    J Environ Sci Health B, 2002 Jul;37(4):345-53.
    PMID: 12081026
    The persistence of metsulfuron-methyl (methyl 2-[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)aminocarbonyl]aminosul fonyl]benzoate) in nonautoclaved and autoclaved Selangor, Lating, and Serdang series soils incubated at different temperatures and with different moisture contents was investigated under laboratory conditions using cucumber (Cucumis sativus L.) as the bioassay species. Significant degradation of metsulfuron-methyl was observed in nonautoclaved soil compared with the autoclaved soil sample, indicating the importance of microorganisms in the breakdown process. At higher temperatures the degradation rate in nonautoclaved soil improved with increasing soil moisture content. In nonautoclaved Selangor, Lating and Serdang series soils, the half-life was reduced from 4.79 to 2.78 days, 4.9 to 3.5, and from 3.3 to 1.9 days, respectively, when the temperature was increased from 20 degrees to 30 degrees C at 80% field capacity. Similarly, in nonautoclaved soil, the half-life decreased with an increasing soil moisture from 20% to 80% at 30 degrees C in the three soils studied. In the autoclaved soil, the half-life values were slightly higher than those obtained in the nonautoclaved soils, perhaps indicating that the compound may be broken down by nonbiological processes. The fresh weight of the bioassay species was reduced significantly in Serdang series soil treated with metsulfuron-methyl at 0.1 ppm. However, the reduction in fresh weight of the seedlings was least in Lating series soil, followed by Selangor series soil.
    Matched MeSH terms: Soil Microbiology*
  5. Fulltext Socio-environmental predictors of soil-transmitted helminthiasis in a rural community in Malaysia
    Hidayah NI, Teoh ST, Hillman E
    Southeast Asian J. Trop. Med. Public Health, 1997 Dec;28(4):811-5.
    PMID: 9656406
    Soil-transmitted helminthiasis is a common problem in communities with poor socio-environmental conditions. This study was undertaken to identify important socio-environmental predictors of soil-transmitted helminthiasis in Bachok, a rural community in Kelantan for the development and implementation of an effective prevention and control program. Of 363 children randomly sampled, 38.8% were infected with soil-transmitted helminthiasis. Risk predictors of soil-transmitted helminthiasis found to be significant after adjustment included poor household hygiene score and large household size. The probability of being infected was 0.58 amongst children with both of these risk factors.
    Matched MeSH terms: Soil Microbiology*
  6. Effects of two acetanilide herbicides on microbial populations and their cellulolytic activities
    Sahid IB, Yap MY
    Bull Environ Contam Toxicol, 1994 Jan;52(1):61-8.
    PMID: 8130418
    Matched MeSH terms: Soil Microbiology*
  7. Prevalence, distribution and intensity of soil-transmitted helminthiases among Malaysian children
    Kan SP, Poon GK
    Public Health, 1987 Jul;101(4):243-51.
    PMID: 3659238
    Matched MeSH terms: Soil Microbiology*
  8. Complete Genome Sequence of a Novel Polyhydroxyalkanoate (PHA) Producer, Jeongeupia sp. USM3 (JCM 19920) and Characterization of Its PHA Synthases
    Zain NA, Ng LM, Foong CP, Tai YT, Nanthini J, Sudesh K
    Curr Microbiol, 2020 Mar;77(3):500-508.
    PMID: 31893298 DOI: 10.1007/s00284-019-01852-z
    A novel polyhydroxyalkanoate (PHA)-producing bacterium, Jeongeupia sp. USM3 (JCM 19920) was isolated from the limestone soil at Gua Tempurung, Perak, Malaysia. This is the first report on the complete genome sequence for the genus Jeongeupia. This genome consists of a circular chromosome with a size of 3,788,814 bp and contains 3557 genes. Two PHA synthase (phaC) genes encoding for the key enzyme in the polymerization of PHA monomers and other PHA-associated genes were identified from the genome. Phylogenetic analysis of the PhaC protein sequences has revealed that both PhaC1 and PhaC2 of Jeongeupia sp. USM3 are categorized as Class I PHA synthases with 56% similarity to each other. Both of the PHA synthase genes of this isolate were cloned and heterologously expressed in a PHA mutant strain Cupriavidus necator PHB-4. The ability of the transformants to accumulate PHA showed that both PhaC1 and PhaC2 were functional.
    Matched MeSH terms: Soil Microbiology*
  9. Fulltext pH dominates variation in tropical soil archaeal diversity and community structure
    Tripathi BM, Kim M, Lai-Hoe A, Shukor NA, Rahim RA, Go R, et al.
    FEMS Microbiol Ecol, 2013 Nov;86(2):303-11.
    PMID: 23773164 DOI: 10.1111/1574-6941.12163
    Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.
    Matched MeSH terms: Soil Microbiology*
  10. Bacterial diversity associated with empty oil palm fruit bunch compost as revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes
    Liew PW, Jong BC, Goh CM, Ahmad M
    J Gen Appl Microbiol, 2009 Jun;55(3):233-40.
    PMID: 19590151
    Matched MeSH terms: Soil Microbiology*
  11. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests
    Tripathi BM, Lee-Cruz L, Kim M, Singh D, Go R, Shukor NA, et al.
    Microb Ecol, 2014 Aug;68(2):247-58.
    PMID: 24658414
    Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.
    Matched MeSH terms: Soil Microbiology*
  12. Reduction of molybdate to molybdenum blue by Enterobacter sp. strain Dr.Y13
    Shukor MY, Rahman MF, Shamaan NA, Syed MA
    J Basic Microbiol, 2009 Sep;49 Suppl 1:S43-54.
    PMID: 19455513 DOI: 10.1002/jobm.200800312
    Extensive use of metals in various industrial applications has caused substantial environmental pollution. Molybdenum-reducing bacteria isolated from soils can be used to remove molybdenum from contaminated environments. In this work we have isolated a local bacterium with the capability to reduce soluble molybdate to the insoluble molybdenum blue. We studied several factors that would optimize molybdate reduction. Electron donor sources such as glucose, sucrose, lactose, maltose and fructose (in decreasing efficiency) supported molybdate reduction after 24 h of incubation with optimum glucose concentration for molybdate reduction at 1.5% (w/v). The optimum pH, phosphate and molybdate concentrations, and temperature for molybdate reduction were pH 6.5, 5.0, 25 to 50 mM and 37 degrees C, respectively. The Mo-blue produced by cellular reduction exhibited a unique absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. Metal ions such as chromium, cadmium, copper, silver and mercury caused approximately 73, 71, 81, 77 and 78% inhibition of the molybdenum-reducing activity, respectively. All of the respiratory inhibitors tested namely rotenone, azide, cyanide and antimycin A did not show any inhibition to the molybdenum-reducing activity suggesting components of the electron transport system are not responsible for the reducing activity. The isolate was tentatively identified as Enterobacter sp. strain Dr.Y13 based on carbon utilization profiles using Biolog GN plates and partial 16S rDNA molecular phylogeny.
    Matched MeSH terms: Soil Microbiology*
  13. Effects of simulated warming on bacterial diversity and abundance in tropical soils from East Malaysia using open top chambers
    Chua CY, Wong CMVL
    Can J Microbiol, 2021 Jan;67(1):64-74.
    PMID: 33084348 DOI: 10.1139/cjm-2019-0461
    The effects of global warming are increasingly evident, where global surface temperatures and atmospheric concentration of carbon dioxide have increased in past decades. Given the role of terrestrial bacteria in various ecological functions, it is important to understand how terrestrial bacteria would respond towards higher environmental temperatures. This study aims to determine soil bacterial diversity in the tropics and their response towards in situ warming using an open-top chamber (OTC). OTCs were set up in areas exposed to sunlight throughout the year in the tropical region in Malaysia. Soil samples were collected every 3 months to monitor changes in bacterial diversity using V3-V4 16S rDNA amplicon sequencing inside the OTCs (treatment plots) and outside the OTCs (control plots). After 12 months of simulated warming, an average increase of 0.81 to 1.15 °C was recorded in treatment plots. Significant changes in the relative abundance of bacterial phyla such as Bacteroidetes and Chloroflexi were reported. Increases in the relative abundance of Actinobacteria were also observed in treatment plots after 12 months. Substantial changes were observed at the genus level, where most bacterial genera decreased in relative abundance after 12 months. This study demonstrated that warming can alter soil bacteria in tropical soils from Kota Kinabalu.
    Matched MeSH terms: Soil Microbiology*
  14. Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T)
    Ee R, Yong D, Lim YL, Yin WF, Chan KG
    J Biotechnol, 2015 Jun 20;204:5-6.
    PMID: 25848988 DOI: 10.1016/j.jbiotec.2015.03.020
    Pandoraea vervacti DSM 23571(T) is an oxalate metabolizing bacterium isolated from an uncultivated field soil in Mugla, Turkey. Here, we present the first complete genome sequence of P. vervacti DSM 23571(T). A complete pathway for degradation of oxalate was revealed from the genome analysis. These data are important to path new opportunities for genetic engineering in the field of biotechnology.
    Matched MeSH terms: Soil Microbiology*
  15. A new peptaibol, RK-026A, from the soil fungus Trichoderma sp. RK10-F026 by culture condition-dependent screening
    Rawa MSA, Nogawa T, Okano A, Futamura Y, Nakamura T, Wahab HA, et al.
    Biosci Biotechnol Biochem, 2021 Jan 07;85(1):69-76.
    PMID: 33577647 DOI: 10.1093/bbb/zbaa051
    A new peptaibol, RK-026A (1) was isolated from a fungus, Trichoderma sp. RK10-F026, along with atroviridin B (2), alamethicin II (3), and polysporin B (4) as a cytotoxic compound, which was selected by principal component analysis of the MS data from 5 different culture conditions. The structure of 1 was determined as a new atroviridin B derivative containing Glu at the 18th residue instead of Gln by NMR and HR-MS analyses including the investigation of detailed MS/MS fragmentations. 1 showed cytotoxicity toward K562 leukemia cells at an IC50 value of 4.1 µm.
    Matched MeSH terms: Soil Microbiology*
  16. Fulltext Detection of pathogenic Leptospira from selected environment in Kelantan and Terengganu, Malaysia
    Ridzlan FR, Bahaman AR, Khairani-Bejo S, Mutalib AR
    Trop Biomed, 2010 Dec;27(3):632-8.
    PMID: 21399605 MyJurnal
    Leptospirosis is recognized as one of the important zoonotic diseases in the world including Malaysia. A total of 145 soil and water samples were collected from selected National Service Training Centres (NSTC) in Kelantan and Terengganu. The samples were inoculated into modified semisolid Ellinghausen McCullough Johnson Harris (EMJH) medium, incubated at room temperature for 1 month and examined under the dark-field microscope. Positive growth of the leptospiral isolates were then confirmed with 8-Azaguanine Test, Polymerase Chain Reaction (PCR) assay and Microscopic Agglutination Test (MAT). Fifteen cultures (10.34%) exhibited positive growths which were seen under dark field microscope whilst only 20% (3/15) were confirmed as pathogenic species. based on 8-Azaguanine Test and PCR. Serological identification of the isolates with MAT showed that hebdomadis was the dominant serovar in Terengganu. Pathogenic leptospires can be detected in Malaysian environment and this has the potential to cause an outbreak. Therefore, precautionary steps against leptospirosis should be taken by camp authorities to ensure the safety of trainees.
    Matched MeSH terms: Soil Microbiology*
  17. Screening of nematophagous-fungi from fresh faeces of grazing animals and soils
    Farah Haziqah MT, Nur Hikmah AM, Mat Hasan H, Hamdan A, Nik Him NAII
    Trop Biomed, 2019 Sep 01;36(3):687-693.
    PMID: 33597490
    An investigation was undertaken for screening and isolating nematophagous-fungi from the faecal samples of various grazing animals and soils in Malaysia. Total of 111 faeces and 50 soil samples were collected and the samples were cultured on 2% water agar plates. The growth of nematophagous-fungi was stimulated by sprinkling-baiting technique. The conidia of suspected nematophagous-fungi were inoculated on 2% water agar plates. All isolated were maintained on 2% cornmeal agar plates. Verticillium spp., Fusarium spp. and Arthrobotrys spp. were identified from the faecal and soil samples. 62.5% of the faecal samples and 100% of the soil samples were shown to be positive with nematophagous-fungi. This study highlights the present of nematophagous-fungi population in faecal and soil samples. Much study remains to be done to better understanding some fungi especially their mode of action and their predatory behaviour against parasitic nematodes.
    Matched MeSH terms: Soil Microbiology*
  18. Isolation and Quantification of Mimivirus-Like and Marseillevirus-Like Viruses from Soil Samples in An Aboriginal (Orang asli) Village in Peninsular Malaysia
    Tan YF, Lim CY, Chong CW, Lim PKC, Yap IKS, Leong PP, et al.
    Intervirology, 2018;61(2):92-95.
    PMID: 30121676 DOI: 10.1159/000491602
    BACKGROUND: The giant amoebal viruses of Mimivirus and Marseillevirus are large DNA viruses and have been documented in water, soil, and sewage samples. The trend of discovering these giant amoebal viruses has been increasing throughout Asia with Japan, India, and Saudi Arabia being the latest countries to document the presence of these viruses. To date, there have been no reports of large amoebal viruses being isolated in South East Asia.

    OBJECTIVE: In this study, we aim to discover these viruses from soil samples in an aboriginal village (Serendah village) in Peninsular -Malaysia.

    METHOD AND RESULTS: We successfully detected and isolated both Mimivirus-like and Marseillevirus-like viruses using Acanthamoeba castellanii. Phylogeny analysis identified them as Mimivirus and Marseillevirus, respectively.

    CONCLUSION: The ubiquitous nature of both Mimivirus and Marseillevirus is further confirmed in our study as they are detected in higher quantity in soil that is near to water vicinities in an aboriginal village in Peninsular Malaysia. However, this study is limited by our inability to investigate the impact of Mimivirus and Marseillevirus on the aboriginal villagers. More studies on the potential impact of these viruses on human health, especially on the aborigines, are warranted.

    Matched MeSH terms: Soil Microbiology*
  19. Effects of Soil Amendments on Microbial Activities in a Typical Cd-Contaminated Purple Field Soil, Southwestern China
    Wang W, Zhou F, Chang Y, Cui J, He D, Du J, et al.
    Bull Environ Contam Toxicol, 2020 Mar;104(3):380-385.
    PMID: 31932904 DOI: 10.1007/s00128-020-02786-0
    In this study, three soil amendments (inorganic, liming, or organic-inorganic materials) were used in a Cd-contaminated purple field soil to investigate their impacts on soil Cd availability, enzyme (urease, catalase, sucrase, and acid phosphatase) activities, microbial biomass (carbon/nitrogen) and type (bacteria, fungi, and actinomycetes) in mustard and corn trials. Results showed that soil amendments generally decreased soil exchangeable Cd, fungi and bacterial populations while increasing the activities of all the four soil enzymes tested, microbial biomass carbon and populations of actinomycetes (p Soil pH and microbial biomass nitrogen did not exhibit any significant response (p > 0.05) whereas stronger effects appeared in soil organic matter and available nutrients (nitrogen, phosphorous and potassium; p soil available phosphorous significantly correlated with soil microbial activity in both mustard and corn trails (p soil health in the remediation of the Cd-contaminated purple soils.
    Matched MeSH terms: Soil Microbiology*
  20. Occurrence and contamination profiles of antibiotic resistance genes from swine manure to receiving environments in Guangdong Province southern China
    Wen X, Mi J, Wang Y, Ma B, Zou Y, Liao X, et al.
    Ecotoxicol Environ Saf, 2019 May 30;173:96-102.
    PMID: 30769208 DOI: 10.1016/j.ecoenv.2019.02.023
    Livestock farms are commonly regarded as the main sources of antibiotic resistance genes (ARGs), emerging pollutants with potential implications for human health, in the environment. This study investigated the occurrence and contamination profiles of nine ARGs of three types from swine manure to receiving environments (soil and water) in Guangdong Province, southern China. All ARGs occurred in 100% of swine manure samples. Moreover, the absolute concentration of total ARGs varied from 3.01 × 108 to 7.18 × 1014 copies/g, which was significantly higher than that in wastewater and manured soil (p soil, the tetracycline resistance gene tetO was predominant. ARGs in swine manure were relatively stable among swine growth periods after the nursery period. The ARG concentration did not differ significantly between manured and unmanured soil (p > 0.05). However, the number of ARGs (ermB, qnrS, acc(6')-Ib, tetM, tetO and tetQ) decreased but were not eliminated by wastewater treatment components (p soil when the substances were applied as fertilizers. Therefore, effective removal and a standard permissible environmental level of ARGs should be established to control the risk of spreading ARGs in the environment.
    Matched MeSH terms: Soil Microbiology*
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