Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes.
This study discusses the isolation and identification of a new Streptomycetes highly active chitinase producer. Fifteen strains were isolated from Malaysian soil samples. The isolate WICC-A03 was found to be the most active chitinase producer. Its antifungal activity was evaluated against many phytopathogens. The identification of WICC-A03 using phenotypic and genotypic methods strongly indicated that strain WICC-A03 belonged to the genus Streptomyces and displayed similarity (91%) with Streptomyces glauciniger. Thus, it was given the suggested name S. glauciniger WICC-A03 with accession number: JX139754. WICC-A03 produces extracellular chitinase in a medium containing 1.5% colloidal chitin in submerged culture on 144 h. The produced enzyme was partially characterised and its molecular weight of 50 kDa was determined by using SDS-PAGE. This study indicates that WICC-A03 is a potential chitinase producer for biocontrol of plant pathogens. Further experiments are being carried out to optimise medium composition and cultivation conditions under lab and bioreactor scale.
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.
Twenty seven filamentous fungal strains representing five genera; Aspergillus, Penicillium, Trichoderma, Myriodontium and Pleurotus were isolated from four sources; domestic wastewater sludge cake (SC) from IWK (Indah Water Konsortium) wastewater treatment plant, palm oil mill effluent compost from Sri Ulu palm Oil Processing Mill, compost of plant debris, and fungal fruiting bodies from a rotten wood stump. Thirty-three strains/isolates were tested for their ability to convert domestic wastewater sludge into compost by assessing biomass production and growth rate on sludge enriched media. The strains/isolates Aspergillus niger, SS-T2008, WW-P1003 and RW-P1 512 produced the highest dry biomass at higher sludge supplemented culture media from their respective group (Aspergillus, Trichoderma, Penicillium and Basidiomycetes, respectively). This implied these strains are better adapted for growth at higher sludge rich substances, and subsequently may be efficient in bioconversion/biodegradation of sludge. The fungi isolated from ecological closely related sources were more amendable to adaptation in a sludge rich culture media.
This paper reviews the literature on leptospirosis in Malaysia from its first description in 1928 until the present day. Most of the early reports were on investigations of leptospirosis in wildlife and man and up-to-date, thirty-seven leptospiral serovars from thirteen serogroups have been bacteriologically identified. The thirteen serogroups are: Australis, Autumnalis Bataviae, Canicola, Celledoni, Grippotyphosa, Hebdomadis, Icterohaemorrhagiae, Javanica, Pomona, Pyrogenes, Sejroe and Tarassovi. Rats have been ascribed as the principal maintenance host of leptospires in Malaysia. However, serovars from the Pomona, Pyrogenes and Sejroe serogroups have yet to be isolated from rats. It is considered that the majority of leptospirosis cases in man were due to association of man with an environment where rats were plentiful. Recent investigations on domestic animals disclosed a high prevalence of infection in cattle and pigs and they were suspected as being the maintenance host for serovar hardjo and pomona respectively. There is ample scope for research in leptospirosis, particularly in the epidemiology and control of the disease in domestic animals. The strategy to control the infection in domestic animals and man in Malaysia is bound to be different from that of the temperate countries, basically due to the presence of a large number of leptospiral serovars in wildlife, further confounded by geographical and financial constraints.
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.
A stab-culture method was adapted to screen for azo dyes-decolorizing bacteria from soil and water samples. Decolorized azo dye in the lower portion of the solid media indicates the presence of anaerobic azo dyes-decolorizing bacteria, while aerobic decolorizing bacteria decolorizes the surface portion of the solid media. Of twenty soil samples tested, one soil sample shows positive results for the decolourisation of two azo dyes; Biebrich scarlet (BS) and Direct blue 71 (DB) under anaerobic conditions. A gram negative and oxidase negative bacterial isolate was found to be the principal azo dyes degrader The isolate was identified by using the Biolog identification system as Serratia marcescens.
Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202(T) and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter. Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838(T) (97.9-98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963(T) and Acinetobacter bouvetii 4B02(T) (85.4-87.6 and 78.1-82.7 %, respectively). Strain 11-0202(T) displayed low DNA-DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter. The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter: summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3-27.2 %), C18 : 1ω9c (19.9-22.1 %), C16 : 0 (15.2-22.0 %) and C12 : 0 (9.2-14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202(T) ( = KCTC 32033(T) = JCM 18512(T)).
Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.
The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis. 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307(T) = NCIMB 14709(T) = NRRL B-24844(T)), Amycolatopsis ruanii sp. nov. (type strain NMG112(T) = NCIMB 14711(T) = NRRL B-24848(T)) and Amycolatopsis thermalba sp. nov. (type strain SF45(T) = NCIMB 14705(T) = NRRL B-24845(T)).
Three actinomycetes isolated from the surfaces of rocks in a medieval slate mine were examined in a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics of the isolates were typical of strains of the genus Amycolatopsis. The isolates had identical 16S rRNA gene sequences and formed a distinct phyletic line towards the periphery of the Amycolatopsis mediterranei clade, being most closely related to Amycolatopsis rifamycinica. The organisms shared a wide range of genotypic and phenotypic markers that distinguished them from their closest phylogenetic neighbours. On the basis of these results, a novel species, Amycolatopsis saalfeldensis sp. nov., is proposed. The type strain is HKI 0457(T) (=DSM 44993(T)=NRRL B-24474(T)).
The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)=NRRL B-24837(T)).
The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H4) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5T (= NCIMB 14970T = NRRL B-65279T).
Despite great development in socioeconomic status throughout 50 years of independence, Malaysia is still plagued with soil-transmitted helminthiases (STH). STH continue to have a significant impact on public health particularly in rural communities. In order to determine the prevalence of STH among rural Orang Asli children and to investigate the possible risk factors affecting the pattern of this prevalence, fecal samples were collected from 292 Orang Asli primary schoolchildren (145 males and 147 females) age 7-12 years, from Pos Betau, Kuala Lipis, Pahang. The samples were examined by Kato-Katz and Harada Mori techniques. Socioeconomic data were collected using pre-tested questionnaires. The overall prevalence of ascariasis, trichuriasis, and hookworm infections were 67.8, 95.5 and 13.4%, respectively. Twenty-nine point eight percent of the children had heavy trichuriasis, while 22.3% had heavy ascariasis. Sixty-seven point seven percent of the children had mixed infections. Age > 10 years (p = 0.016), no toilet in the house (p = 0.012), working mother (p = 0.040), low household income (p = 0.033), and large family size (p = 0.028) were identified as risk factors for ascariasis. Logistic regression confirmed low income, no toilet in the house and working mother as significant risk factors for ascariasis. The prevalence of STH is still very high in rural Malaysian communities. STH may also contribute to other health problems such as micronutrient deficiencies, protein-energy malnutrition and poor educational achievement. Public health personnel need to reassess current control measures and identify innovative and integrated ways in order to reduce STH significantly in rural communities.
Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4) is a soil-borne disease that infects bananas, causing severe economic losses worldwide. To reveal the relationship between bacterial populations and FW, the bacterial communities of healthy and TR4-infected rhizosphere and bulk soils were compared using 16S rRNA gene sequencing. Soil physicochemical properties associated with FW were also analyzed. We found the community structure of bacteria in the healthy and TR4 infected rhizosphere was significantly different compared to bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity than healthy plant with significant abundance of Proteobacteria. In the healthy rhizosphere soil, beneficial bacteria such as Burkholderia and Streptomyces spp. were more abundant. Compared to the infected rhizosphere soil, healthy rhizosphere soil was associated with RNA metabolism and transporters pathways and a high level of magnesium and cation exchange capacity. Overall, we reported changes in the key taxa of rhizospheric bacterial communities and soil physicochemical properties of healthy and FW-infected plants, suggesting their potential role as indicators for plant health.
The mangrove ecosystem of Malaysia remains yet to be fully explored for potential microbes that produce biologically active metabolites. In the present study, a mangrove-derived Streptomyces sp. strain MUSC 14 previously isolated from the state of Pahang, Malaysia Peninsula, was studied for its potential in producing antioxidant metabolites. The identity of Streptomyces sp. strain MUSC14 was consistent with the genotypic and phenotypic characteristics of the Streptomyces genus. The antioxidant potential of Streptomyces sp. strain MUSC 14 was determined through screening of its methanolic extract against sets of antioxidant assays. The results were indicative of Streptomyces sp. strain MUSC 14 displaying strong antioxidant activity against ABTS, DPPH free radicals and metal chelating activity of 62.71 ± 3.30%, 24.71 ± 2.22%, and 55.82 ± 2.35%, respectively. The result of ferric reducing activity measured in terms of dose was equivalent to 2.35-2.45 μg of positive control ascorbic acid. Furthermore, there was a high correlation between the total phenolic content and the antioxidant activities with r = 0.979, r = 0.858, and r = 0.983 representing ABTS, DPPH, and metal chelation, respectively. Overall, the present study suggests that Streptomyces sp. strain MUSC 14 from mangrove forest soil has potential to produce antioxidant metabolites that can be further exploited for therapeutic application.
Mangrove derived microorganisms constitute a rich bioresource for bioprospecting of bioactive natural products. This study explored the antioxidant potentials of Streptomyces bacteria derived from mangrove soil. Based on 16S rRNA phylogenetic analysis, strain MUM292 was identified as the genus Streptomyces. Strain MUM292 showed the highest 16S rRNA gene sequence similarity of 99.54% with S. griseoruber NBRC12873T. Furthermore, strain MUM292 was also characterized and showed phenotypic characteristics consistent with Streptomyces bacteria. Fermentation and extraction were performed to obtain the MUM292 extract containing the secondary metabolites of strain MUM292. The extract displayed promising antioxidant activities, including DPPH, ABTS, and superoxide radical scavenging and also metal-chelating activities. The process of lipid peroxidation in lipid-rich product was also retarded by MUM292 extract and resulted in reduced MDA production. The potential bioactive constituents of MUM292 extract were investigated using GC-MS and preliminary detection showed the presence of pyrazine, pyrrole, cyclic dipeptides, and phenolic compound in MUM292 extract. This work demonstrates that Streptomyces MUM292 can be a potential antioxidant resource for food and pharmaceutical industries.
Arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) associations are critical for host-tree performance. However, how mycorrhizal associations correlate with the latitudinal tree beta-diversity remains untested. Using a global dataset of 45 forest plots representing 2,804,270 trees across 3840 species, we test how AM and EcM trees contribute to total beta-diversity and its components (turnover and nestedness) of all trees. We find AM rather than EcM trees predominantly contribute to decreasing total beta-diversity and turnover and increasing nestedness with increasing latitude, probably because wide distributions of EcM trees do not generate strong compositional differences among localities. Environmental variables, especially temperature and precipitation, are strongly correlated with beta-diversity patterns for both AM trees and all trees rather than EcM trees. Results support our hypotheses that latitudinal beta-diversity patterns and environmental effects on these patterns are highly dependent on mycorrhizal types. Our findings highlight the importance of AM-dominated forests for conserving global forest biodiversity.
Tropical peatlands are globally important ecosystems with high C storage and are endangered by anthropogenic disturbances. Microbes in peatlands play an important role in sustaining the functions of peatlands as a C sink, yet their characteristics in these habitats are poorly understood. This research aimed to elucidate the responses of these complex ecosystems to disturbance by exploring greenhouse gas (GHG) emissions, nutrient contents, soil microbial communities and the functional interactions between these components in a primary and secondary peat swamp forest in Peninsular Malaysia. GHG measurements using closed chambers, and peat sampling were carried out in both wet and dry seasons. Microbial community phenotypes and nutrient content were determined using phospholipid fatty acid (PLFA) and inductively-coupled plasma mass spectrometry (ICP-MS) analyses respectively. CO2 emissions in the secondary peat swamp forest were > 50% higher than in the primary forest. CH4 emission rates were ca. 2 mg m-2 h-1 in the primary forest but the secondary forest was a CH4 sink, showing no seasonal variations in GHG emissions. Almost all the nutrient concentrations were significantly lower in the secondary forest, postulated to be due to nutrient leaching via drainage and higher rates of decomposition. Cu and Mo concentrations were negatively correlated with CO2 and CH4 emissions respectively. Microbial community structure was overwhelmingly dominated by bacteria in both forest types, however it was highly sensitive to land-use change and season. Gram-positive and Gram-negative relative abundance were positively correlated with CO2 and CH4 emissions respectively. Drainage related disturbances increased CO2 emissions, by reducing the nutrient content including some with known antimicrobial properties (Cu & Na) and by favouring Gram-positive bacteria over Gram-negative bacteria. These results suggest that the biogeochemistry of secondary peat swamp forest is fundamentally different from that of primary peat swamp forest, and these differences have significant functional impacts on their respective environments.
For decades Malaysia was the world's largest producer of Sn, but now the vast open cast mining operations have left a legacy of some 100,000 ha of what is effectively wasteland, covered with a mosaic of tailings and lagoons. Few plants naturally recolonise these areas. The demand for such land for both urban expansion and agricultural use has presented an urgent need for better characterisation. This study reports on the formation of artificial soils from alluvial Sn mining waste with a focus on the effects of experimental treatments on soil chemistry. Soil organic matter, clay, and pH were manipulated in a controlled environment. Adding both clay tailings and peat enhanced the cation exchange capacity of sand tailings but also reduced the pH. The addition of peat reduced the extractable levels of some elements but increased the availability of Ca and Mg, thus proving beneficial. The use of clay tailings increased the levels of macro and micronutrients but also released Al, As, La, Pb and U. Additionally, the effects of soil mix and mycorrhizal treatments on growth and foliar chemistry were studied. Two plant species were selected: Panicum milicaeum and Pueraria phaseoloides. Different growth patterns were observed with respect to the additions of peat and clay. The results for mycorrhizal treatment (live inoculum or sterile carrier medium) are more complex, but both resulted in improved growth. The use of mycorrhizal fungi could greatly enhance rehabilitation efforts on sand tailings.