Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its' potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.
Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.
The aim of the present study was to examine the prevalence of thermophilic Campylobacter spp. (Campylobacter jejuni and Campylobacter coli) in soil, poultry manure, irrigation water, and freshly harvested vegetables from vegetable farms in Malaysia. C. jejuni was detected in 30.4% and 2.7% of the soil samples, 57.1% and 0% of the manure samples, and 18.8% and 3% of the vegetable samples from farm A and farm B, respectively, when using the MPNPCR method. Campylobacter spp. was not found in any of the irrigation water samples tested. Therefore, the present results indicate that the aged manure used by farm A was more contaminated than the composted manure used by farm B. Mostly, the leafy and root vegetables were contaminated. C. coli was not detected in any of the samples tested in the current study. Both farms tested in this study were found to be contaminated by campylobacters, thereby posing a potential risk for raw vegetable consumption in Malaysia. The present results also provide baseline data on Campylobacter contamination at the farm level.
Epidemiology of melioidosis is poorly understood because its occurrence is influenced by complex interaction of environmental, climatic, physicochemical and host factors. We investigated the potential risk factors for the exposure to Burkholderia pseudomallei in small ruminants' farms in Peninsular Malaysia.
In this study we analysed three bacterial strains coded L10.10T, A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993T. Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4-30°C, and at pH 4.0-10. The DNA G+C content is 58.2-58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10T, A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10T (LMG 29628T, DSM 101070T).
Enhancing crop yield to accommodate the ever-increasing world population has become critical, and diminishing arable land has pressured current agricultural practices. Intensive farming methods have been using more pesticides and insecticides (biocides), culminating in soil deposition, negatively impacting the microbiome. Hence, a deeper understanding of the interaction and impact of pesticides and insecticides on microbial communities is required for the scientific community. This review highlights the recent findings concerning the possible impacts of biocides on various soil microorganisms and their diversity. This review's bibliometric analysis emphasised the recent developments' statistics based on the Scopus document search. Pesticides and insecticides are reported to degrade microbes' structure, cellular processes, and distinct biochemical reactions at cellular and biochemical levels. Several biocides disrupt the relationship between plants and their microbial symbionts, hindering beneficial biological activities that are widely discussed. Most microbial target sites of or receptors are biomolecules, and biocides bind with the receptor through a ligand-based mechanism. The biomarker action mechanism in response to biocides relies on activating the receptor site by specific biochemical interactions. The production of electrophilic or nucleophilic species, free radicals, and redox-reactive agents are the significant factors of biocide's metabolic reaction. Most studies considered for the review reported the negative impact of biocides on the soil microbial community; hence, technological development is required regarding eco-friendly pesticide and insecticide, which has less or no impact on the soil microbial community.
Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.
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.
A white-rot fungus of Polyporus sp. S133 was isolated from an oil-polluted soil. The metabolism of pyrene by this fungus was investigated in liquid medium with 5 mg of the compound. Depletion of pyrene was evident during the 30-day growth period and was 21% and 90%, respectively, in cometabolism and metabolism of pyrene alone. Pyrene was absorbed to fungal cells or biodegraded to form simpler structural compounds. Seventy-one percent of eliminated pyrene was transformed by Polyporus sp. S133 into other compounds, whereas only 18% was absorbed in the fungal cell. The effects of pH and temperature on biomass production of Polyporus sp. S133 for pyrene were examined; the properties of laccase and 1,2-dioxygenase produced by Polyporus sp. S133 during pyrene degradation were investigated. The optimal values of pH were 3, 5, and 4 for laccase, 1,2-dioxygenase, and biomass production, respectively, whereas the optimal values of temperature were 25 °C for laccase and 50 °C for 1,2-dioxygenase and biomass production. Under optimal conditions, pyrene was mainly metabolized to 1-hydroxypyrene and gentisic acid. The structure of 1-hydroxypyrene and gentisic acid was determined by gas chromatography-mass spectrometry after identification using thin-layer chromatography.
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.
Herbicides are inevitable inputs to control excessive weed in crop land, particularly where modern agricultural practices such as conservation tillage, are opted. Intensive farming has increased the market value of herbicides among the other pesticides. Although herbicides are effective in controlling weed population, administration of this synthetic chemicals may alter the soil microbial community causing potential increase of plant pathogens. Moreover, herbicides may also have nontarget effects on the cultivated crops making them more susceptible to diseases. Actions of herbicides in soil that either stimulate microbial growth or wipe out some microbial population may create space for the thrivial of opportunistic fungi. Previous studies showed that white rot fungi are more tolerant to herbicides as they produce lignin degrading enzymes that are highly oxidative, non-specific and are able to transform a wide range of herbicides. Besides that, this group of fungi can grow on agricultural waste substrates. Influence of these herbicides on soil microbial ecosystem and interactions of plants and pathogenic white rot fungi modulate disease development in plant hosts.
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.
Extensive contamination of soils by highly recalcitrant contaminants such as polycyclic aromatic hydrocarbons (PAHs) is an environmental problem arising from rapid industrialisation. This work focusses on the remediation of soil contaminated with 3- and 4-aromatic ring PAHs (phenanthrene (PHE) and fluoranthene (FLUT)) through catalysed hydrogen peroxide propagation (CHP). In the present work, the operating parameters of the CHP treatment in packed soil column was optimised with central composite design (H2O2/soil 0.081, Fe(3+)/soil 0.024, sodium pyrophosphate (SP)/soil 0.024, pH of SP solution 7.73). The effect of contaminant aging on PAH removals was also investigated. Remarkable oxidative PAH removals were observed for the short aging and extended aging period (up to 86.73 and 70.61 % for PHE and FLUT, respectively). The impacts of CHP on soil biological, chemical and physical properties were studied for both spiked and aged soils. Overall, the soil functionality analyses after the proposed operating condition demonstrated that the values for soil respiration, electrical conductivity, pH and iron precipitation fell within acceptable limits, indicating the compatibility of the CHP process with land restoration.
Leptospirosis is an emerging zoonotic disease endemic in tropical regions. Aiming at assessing the potential infection risks via recreational exposure, the molecular prevalence of pathogenic Leptospira in 14 amenity forests in five selected districts of the state of Perak was determined. Water and soil samples along streams and waterfalls were subjected to culture of leptospires and the pathogenic Leptospira spp. was detected by lipL32-based polymerase chain reaction (PCR). Twenty out of 154 samples (13%) that tested positive for leptospires were mostly soils and still water recorded with tolerable temperatures (22.2- 26.5°C) and pHs (5.73-6.70). The localised prevalence was highly varied among eight positive forests (6.7-41.7%), particularly higher in Kampar and Kinta districts which are the more populated urban areas. The importance of public health surveillance should not be underrated given the high prevalence of Leptospira spp. in forests in close proximity to indigenous settlements, even where the places are clean. Overall, this study discovered a wide distribution of pathogenic Leptospira spp. in recreational areas.
Plant growth promoting rhizobacteria (PGPR) shows an important role in the sustainable agriculture industry. The increasing demand for crop production with a significant reduction of synthetic chemical fertilizers and pesticides use is a big challenge nowadays. The use of PGPR has been proven to be an environmentally sound way of increasing crop yields by facilitating plant growth through either a direct or indirect mechanism. The mechanisms of PGPR include regulating hormonal and nutritional balance, inducing resistance against plant pathogens, and solubilizing nutrients for easy uptake by plants. In addition, PGPR show synergistic and antagonistic interactions with microorganisms within the rhizosphere and beyond in bulk soil, which indirectly boosts plant growth rate. There are many bacteria species that act as PGPR, described in the literature as successful for improving plant growth. However, there is a gap between the mode of action (mechanism) of the PGPR for plant growth and the role of the PGPR as biofertilizer-thus the importance of nano-encapsulation technology in improving the efficacy of PGPR. Hence, this review bridges the gap mentioned and summarizes the mechanism of PGPR as a biofertilizer for agricultural sustainability.
The spatial distribution of basidiocarps provides much information on the dispersal abilities, habitat preferences, and inter- and intraspecific interactions of aphyllophoraceous fungi. To reveal the spatial distribution and resource utilization patterns of aphyllophoraceous fungi in Malaysia, we conducted field observations in a primary forest in 2006 and analyzed the relationships between the abundance of eight dominant fungal species and various environmental factors. The topographical characteristics were significantly patchily distributed at the 100-m scale, whereas woody debris and most fungal species were distributed randomly. Although the dominant fungal species differed among the decay classes and diameters of the woody debris, the abundance of a few dominant species was significantly correlated with environmental factors. Although the latter factors might affect the spatial distribution of these fungi, the effects appear to be so small that they would not create an aggregated distribution at a few 100-m scales.