Bacteria under the operational group Bacillus amyloliquefaciens (OGBa) are all Gram-positive, endospore-forming, and rod-shaped. Taxonomically, the OGBa belongs to the Bacillus subtilis species complex, family Bacillaceae, class Bacilli, and phylum Firmicutes. To date, the OGBa comprises four bacterial species: Bacillus amyloliquefaciens, Bacillus siamensis, Bacillus velezensis and Bacillus nakamurai. They are widely distributed in various niches including soil, plants, food, and water. A resurgence in genome mining has caused an increased focus on the biotechnological applications of bacterial species belonging to the OGBa. The members of OGBa are known as plant growth-promoting bacteria (PGPB) due to their abilities to fix nitrogen, solubilize phosphate, and produce siderophore and phytohormones, as well as antimicrobial compounds. Moreover, they are also reported to produce various enzymes including α-amylase, protease, lipase, cellulase, xylanase, pectinase, aminotransferase, barnase, peroxidase, and laccase. Antimicrobial compounds that able to inhibit the growth of pathogens including non-ribosomal peptides and polyketides are also produced by these bacteria. Within the OGBa, various B. velezensis strains are promising for use as probiotics for animals and fishes. Genome mining has revealed the potential applications of members of OGBa for removing organophosphorus (OPs) pesticides. Thus, this review focused on the applicability of members of OGBa as plant growth promoters, biocontrol agents, probiotics, bioremediation agents, as well as producers of commercial enzymes and antibiotics. Here, the bioformulations and commercial products available based on these bacteria are also highlighted. This review will better facilitate understandings of members of OGBa and their biotechnological applications.
Salinity is one of the major constraintsin the rice production worldwide. Rice plants have moderate tolerance towardssalinity. Salinitychangescell membrane permeability and fatty acid compositionsby releasing the free fatty acids. Nonetheless, the effect of exogenous fatty acid such as arachidonic acid (AA) on rice grown on saline soil is yetunknown. Theobjective of the current study isto determine the effectofAA onthe morphological traits and freefatty acidsofrice plantgrown under saline conditions.Rice plants grown on saline soil (EC=12 ds/m)were treated with 50 μMAAon day 45 after transplant. Leaves and panicleswere sampledafter two weeks of treatment and analysed for fatty acid profile using GC-MS. Themorphological traits were observedat the maturity stage. Results showed that AA treatment improved the grain fill-in of the saline stress riceand reduced the accumulation of free fatty acids in the cell. The AAtreatment also increased the linoleic acid (18:2), linolenic acid (18:3) in paniclesand, dihomo-γ-linolenic acid(20:3) and nervonic acid (24:1) in leaves. The finding suggests that exogenous AAregulates salinity stress in rice by reducing the accumulation offree fatty acids.
Termites are the major decomposers in tropical region but yet their occurrences in oil palm plantation especially in peat soil are generally treated as pest. Study of termite species in peat land was conducted in selected oil palm plantations in North Sarawak with 5-7 years old palms and South Sarawak with 13-15 years old palms with two sites in each area. Results of quadrate (25 x 25 x 30 cm) sampling showed termite was significantly higher in relative density with increasing depth of soil (0-10 = 21.23, 10-20 = 42.52 and 20-30 cm = 81.12%) which could be advantaged from being predated by ants (Hymenoptera: Formicidae) which were higher in density from soil surface to 10 cm soil depth with relative density of 31.84%. Modified transect sampling (50x6 m) had successfully sampled 18 species of termites from 2 families (Rhinotermitidae and Termitidae), 5 subfamilies (Rhinotermitinae, Coptotermitinae, Termitinae, Macrotermitinae and Nasutitermitinae) and 11 genera (Coptotermes, Schedorhinotermes, Termes, Macrotermes, Nasutitermes, Globitermes, Amitermes, Parrhinotermes, Pericapritermes, Havilanditermes and Prohamitermes). Both plantation sites have termite dominantly feeding on rotten wood as a result of abundant dead woods. However, Coptotermes curvignathus Holmgren was identified to feed on the living tissues of oil palm causing damage or death of the tree. Study showed higher encounter of soil-feeding termite in longer established plantation. It indicates the gradually shifting of soil condition towards a stabilized environment which favors the successful settlement of soil feeder termite species. Termite control should be more targets specific to avoid harming beneficial termites.
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.
Roseomonas sp. strain B5 was isolated from Malaysian tropical soil that showed N-acylhomoserine lactone degradation. This is the first genome announcement of a member from the genus of Roseomonas and the first report on the quorum-quenching activity of Roseomonas spp.
To clarify characteristics of carbon (C) allocation in a Bornean tropical rainforest without dry seasons, gross primary production (GPP) and C allocation, i.e., above-ground net primary production (ANPP), aboveground plant respiration (APR), and total below-ground carbon flux (TBCF) for the forest were examined and compared with those from Amazonian tropical rainforests with dry seasons. GPP (30.61 MgC ha(-1) year(-1), eddy covariance measurements; 34.40 MgC ha(-1) year(-1), biometric measurements) was comparable to those for Amazonian rainforests. ANPP (6.76 MgC ha(-1) year(-1)) was comparable to, and APR (8.01 MgC ha(-1) year(-1)) was slightly lower than, their respective values for Amazonian rainforests, even though aboveground biomass was greater at our site. TBCF (19.63 MgC ha(-1) year(-1)) was higher than those for Amazonian forests. The comparable ANPP and higher TBCF were unexpected, since higher water availability would suggest less fine root competition for water, giving higher ANPP and lower TBCF to GPP. Low nutrient availability may explain the comparable ANPP and higher TBCF. These data show that there are variations in C allocation patterns among mature tropical rainforests, and the variations cannot be explained solely by differences in soil water availability.
We analyzed the epidemiological data of all people who were involved in the search and rescue operation in Lubuk Yu, a natural recreational forest with waterfall and stream. The hospital admission records of the cases who fulfilled the case definition and the environmental samples result taken at Lubuk Yu recreational area were studied. 153 people were exposed to this outbreak, 85 (55.5%) were professional rescuers from various government agencies and 68 (44.5%) were villagers. 21 fulfilled the case definition. Ten cases were confirmed melioidosis, six melioidosis alone and four coinfected with leptospirosis. There were eight deaths in this outbreak, seven were villagers and one professional rescuer. Overall case fatality was 70%. All confirmed melioidosis cases and seven who died had diabetes mellitus. The morbidity rate were higher among the villagers, 23.5% compared to professional rescuers, 5.9%. The case fatality rate were also higher in this group which was 100% compared to 33.3% in professional rescuers. The soil and water samples in Lubuk Yu recreational area were positive for leptospira and Burkholderia pseudomallei. The presence of co-infection and co-morbidities especially diabetes mellitus among the exposed led to the high mortality in this outbreak hence a high index of suspicion is important among the healthcare professionals in the management of melioidosis cases. To avoid similar incident in future, search and rescue operation should be only conducted by professional rescuers with appropriate personal protective equipment. A register of rescuers should be maintained for surveillance and follow up if necessary.
The major limitation of direct application of tannery sludge compost in agriculture is the total heavy metal contents and their bioavailability to the soil-plant system. This study focused on the heavy metal characterization and the influence of changing the physicochemical properties of the medium throughout the composting on the concentrations, bioavailability or chemical forms of Cr, Cu, Zn, Pb and Cd in tannery sludge. The study shows that throughout the 60 days of composting, physicochemical analysis and Fourier-transformed infrared (FTIR) spectroscopic characterization show that all parameters elaborated and reached relatively stable levels reflecting the stability and maturity of the final product, and revealed the biodegradation of components that can be easily assimilated by microorganism. The C/N ratio reaches the optimal range of stable compost; inorganic nitrogen is transformed into stable organic forms. The total concentration of Cr, Zn, Cu, Pb and Cd is very low rendering final compost acceptable for agricultural use. The germination index for both Chinese cabbage and lettuce was 97% after 60 days of composting, showing that the final compost was not phytotoxic. Furthermore, in using a sequential extraction method in sludge compost at different phases of treatment, a less than 2% of metals bound to bioavailable fractions X-(KNO(3)+H(2)O). A large proportion of the heavy metals were associated to the residual fraction (75-85%) and more resistant fractions to extraction X-NaOH, X-EDTA, X-HNO(3) (15-25%). Mobile fractions of metals are poorly predictable from the total content. Bioavailability of all fractions of elements tends to decrease.
Concern about environmental protection has increased over the years from a global viewpoint. To date, the percolation of pesticide waste into the groundwater tables and aquifer systems remains an aesthetic issue towards the public health and food chain interference. With the renaissance of activated carbon, there has been a consistent growing interest in this research field. Confirming the assertion, this paper presents a state of art review of pesticide agrochemical practice, its fundamental characteristics, background studies and environmental implications. Moreover, the key advance of activated carbon adsorption, its major challenges together with the future expectation are summarized and discussed. Conclusively, the expanding of activated carbon adsorption represents a plausible and powerful circumstance, leading to the superior improvement of environmental preservation.
The contamination of groundwater by heavy metal, originating either from natural soil sources or from anthropogenic sources is a matter of utmost concern to the public health. Remediation of contaminated groundwater is of highest priority since billions of people all over the world use it for drinking purpose. In this paper, thirty five approaches for groundwater treatment have been reviewed and classified under three large categories viz chemical, biochemical/biological/biosorption and physico-chemical treatment processes. Comparison tables have been provided at the end of each process for a better understanding of each category. Selection of a suitable technology for contamination remediation at a particular site is one of the most challenging job due to extremely complex soil chemistry and aquifer characteristics and no thumb-rule can be suggested regarding this issue. In the past decade, iron based technologies, microbial remediation, biological sulphate reduction and various adsorbents played versatile and efficient remediation roles. Keeping the sustainability issues and environmental ethics in mind, the technologies encompassing natural chemistry, bioremediation and biosorption are recommended to be adopted in appropriate cases. In many places, two or more techniques can work synergistically for better results. Processes such as chelate extraction and chemical soil washings are advisable only for recovery of valuable metals in highly contaminated industrial sites depending on economical feasibility.
Nitrification of mature sanitary landfill leachate with high-strength of N-NH(4) + (1080-2350 mg L(-1)) was performed in a 10 L continuous nitrification activated sludge reactor. The nitrification system was acclimatized with synthetic leachate during feed batch operation to avoid substrate inhibition before being fed with actual mature leachate. Successful nitrification was achieved with an approximately complete ammonium removal (99%) and 96% of N-NH(4) + conversion to N-NO(-) (3) . The maximum volumetric and specific nitrification rates obtained were 2.56 kg N-NH(4) (+) m(-3) day(-1) and 0.23 g N-NH(4) ( +) g(-1) volatile suspended solid (VSS) day(-1), respectively, at hydraulic retention time (HRT) of 12.7 h and solid retention time of 50 days. Incomplete nitrification was encountered when operating at a higher nitrogen loading rate of 3.14 kg N-NH(4) (+) m(-3) day(-1). The substrate overloading and nitrifiers competition with heterotrophs were believed to trigger the incomplete nitrification. Fluorescence in situ hybridization (FISH) results supported the syntrophic association between the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria. FISH results also revealed the heterotrophs as the dominant and disintegration of some AOB cell aggregates into single cells which further supported the incomplete nitrification phenomenon.
Plastic waste constitutes the third largest waste volume in Malaysian municipal solid waste (MSW), next to putrescible waste and paper. The plastic component in MSW from Kuala Lumpur averages 24% (by weight), whereas the national mean is about 15%. The 144 waste dumps in the country receive about 95% of the MSW, including plastic waste. The useful life of the landfills is fast diminishing as the plastic waste stays un-degraded for more than 50 years. In this study the compostability of polyethylene and pro-oxidant additive-based environmentally degradable plastics (EDP) was investigated. Linear low-density polyethylene (LLDPE) samples exposed hydrolytically or oxidatively at 60 degrees C showed that the abiotic degradation path was oxidative rather than hydrolytic. There was a weight loss of 8% and the plastic has been oxidized as shown by the additional carbonyl group exhibited in the Fourier transform infra red (FTIR) Spectrum. Oxidation rate seemed to be influenced by the amount of pro-oxidant additive, the chemical structure and morphology of the plastic samples, and the surface area. Composting studies during a 45-day experiment showed that the percentage elongation (reduction) was 20% for McD samples [high-density polyethylene, (HDPE) with 3% additive] and LL samples (LLDPE with 7% additive) and 18% reduction for totally degradable plastic (TDP) samples (HDPE with 3% additive). Lastly, microbial experiments using Pseudomonas aeroginosa on carbon-free media with degradable plastic samples as the sole carbon source, showed confirmatory results. A positive bacterial growth and a weight loss of 2.2% for degraded polyethylene samples were evident to show that the degradable plastic is biodegradable.
The presence of acrylamide in the environment poses a threat due to its well known neurotoxic, carcinogenic and teratogenic properties. Human activities in various geographical areas are the main anthropogenic source of acrylamide pollution. In this work, an acrylamide-degrading bacterium was isolated from Antarctic soil. The physiological characteristics and optimum growth conditions of the acrylamide-degrading bacteria were investigated. The isolate was tentatively identified as Pseudomonas sp. strain DRYJ7 based on carbon utilization profiles using Biolog GN plates and partial 16S rDNA molecular phylogeny. The results showed that the best carbon sources for growth was glucose and sucrose with no significant difference in terms of cellular growth between the two carbon sources (p>0.05). This was followed by fructose and maltose with fructose giving significantly higher cellular growth compared to maltose (p<0.05). Lactose and citric acid did not support growth. The optimum acrylamide concentration as a nitrogen source for cellular growth was at 500 mgl(-1). At this concentration, bacterial growth showed a 2-day lag phase before degradation took place concomitant with an increase in cellular growth. The isolate exhibited optimum growth in between pH 7.5 and 8.5. The effect of incubation temperature on the growth of this isolate showed an optimum growth at 15 degrees C. The characteristics of this isolate suggest that it would be useful in the bioremediation of acrylamide.
Phosphate solubilizing bacteria (PSB) can convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the field. In this study, isolation and precise identification of PSB were carried out in Malaysian (Serdang) oil palm field (University Putra Malaysia). Identification and phylogenetic analysis of 8 better isolates were carried out by 16S rRNA gene sequencing in which as a result five isolates belong to the Beta subdivision of Proteobacteria, one isolate was related to the Gama subdivision of Proteobacteria, and two isolates were related to the Firmicutes. Bacterial isolates of 6upmr, 2upmr, 19upmnr, 10upmr, and 24upmr were identified as Alcaligenes faecalis. Also, bacterial isolates of 20upmnr and 17upmnr were identified as Bacillus cereus and Vagococcus carniphilus, respectively, and bacterial isolates of 31upmr were identified as Serratia plymuthica. Molecular identification and characterization of oil palm strains as the specific phosphate solubilizer can reduce the time and cost of producing effective inoculate (biofertilizer) in an oil palm field.
The study was conducted based on two objectives as framework. The first objective is to determine the point of microwave signal reflection while penetrating into the simulation models and, the second objective is to analyze the reflection pattern when the signal penetrate into the layers with different relative permittivity, εr. Thus, several microwave models were developed to make a close proximity of the in vivo human brain. The study proposed two different layers on two different characteristics models. The radii on the second layer and the corresponding antenna positions are the factors for both models. The radii for model 1 is 60 mm with an antenna position of 10 mm away, in contrast, model 2 is 10 mm larger in size with a closely adapted antenna without any gap. The layers of the models were developed with different combination of materials such as Oil, Sandy Soil, Brain, Glycerin and Water. Results show the combination of Glycerin + Brain and Brain + Sandy Soil are the best proximity of the in vivo human brain grey and white matter. The results could benefit subsequent studies for further enhancement and development of the models.
Background. Central intermediary metabolism (CIM) in bacteria is defined as a set of metabolic biochemical reactions within a cell, which is essential for the cell to survive in response to environmental perturbations. The genes associated with CIM are commonly found in both pathogenic and non-pathogenic strains. As these genes are involved in vital metabolic processes of bacteria, we explored the efficiency of the genes in genotypic characterization of Burkholderia pseudomallei isolates, compared with the established pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) schemes. Methods. Nine previously sequenced B. pseudomallei isolates from Malaysia were characterized by PFGE, MLST and CIM genes. The isolates were later compared to the other 39 B. pseudomallei strains, retrieved from GenBank using both MLST and sequence analysis of CIM genes. UniFrac and hierachical clustering analyses were performed using the results generated by both MLST and sequence analysis of CIM genes. Results. Genetic relatedness of nine Malaysian B. pseudomallei isolates and the other 39 strains was investigated. The nine Malaysian isolates were subtyped into six PFGE profiles, four MLST profiles and five sequence types based on CIM genes alignment. All methods demonstrated the clonality of OB and CB as well as CMS and THE. However, PFGE showed less than 70% similarity between a pair of morphology variants, OS and OB. In contrast, OS was identical to the soil isolate, MARAN. To have a better understanding of the genetic diversity of B. pseudomallei worldwide, we further aligned the sequences of genes used in MLST and genes associated with CIM for the nine Malaysian isolates and 39 B. pseudomallei strains from NCBI database. Overall, based on the CIM genes, the strains were subtyped into 33 profiles where majority of the strains from Asian countries were clustered together. On the other hand, MLST resolved the isolates into 31 profiles which formed three clusters. Hierarchical clustering using UniFrac distance suggested that the isolates from Australia were genetically distinct from the Asian isolates. Nevertheless, statistical significant differences were detected between isolates from Malaysia, Thailand and Australia. Discussion. Overall, PFGE showed higher discriminative power in clustering the nine Malaysian B. pseudomallei isolates and indicated its suitability for localized epidemiological study. Compared to MLST, CIM genes showed higher resolution in distinguishing those non-related strains and better clustering of strains from different geographical regions. A closer genetic relatedness of Malaysian isolates with all Asian strains in comparison to Australian strains was observed. This finding was supported by UniFrac analysis which resulted in geographical segregation between Australia and the Asian countries.
Emergence of antimicrobial resistance coupled with the slowdown in discovery of new antimicrobial compounds points to serious consequences for human health. Therefore, scientists are looking for new antimicrobial compounds from unique and understudied ecosystems such as tropical peat swamp forests. Over the course of isolating antimicrobial producing bacteria from North Selangor tropical peat swamp forest, Malaysia, a Gram variable, rod shaped, endospore forming, facultative anaerobic novel strain MSt1(T) that exerts potent and broad spectrum antimicrobial activity was isolated. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MSt1(T) belonged to the genus Paenibacillus with the highest similarity to Paenibacillus elgii SD17(T) (99.5%). Whole genome comparison between strain MSt1(T) with its closely related species using average nucleotide identity (ANI) revealed that similarity between strain MSt1(T) with P. elgii B69 (93.45%) and Paenibacillus ehimensis A2 (90.42%) was below the recommended threshold of 95%. Further analysis using in silico pairwise DDH also showed that similarity between strain MSt1(T) with P. elgii B69 (55.4%) and P. ehimensis A2 (43.7%) was below the recommended threshold of 70%. Strain MSt1(T) contained meso-diaminopilemic acid in the cell wall and MK-7 as the major menaquinone. The major fatty acids of strain MSt1(T) were anteiso-C15:0 (48.2%) and C16:0 (29.0%) whereas the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unknown lipid, two unknown glycolipids, and one unknown phospholipid. Total DNA G+C content of strain MSt1(T) was 51.5 mol%. The extract from strain MSt1(T) exerted strong antimicrobial activity against Escherichia coli ATCC 25922 (MIC = 1.5 μg/mL), MRSA ATCC 700699 (MIC = 25 μg/mL) and Candida albicans IMR (MIC = 12.5 μg/mL). Partially purified active fraction exerted a strong effect against E. coli ATCC 25922 resulting in cell rupture when viewed with SEM. Based on distinctive taxonomic differences between strain MSt1(T) when compared to its closely related type species, we propose that strain MSt1(T) represents a novel species within the genus of Paenibacillus, for which the name Paenibacillus tyrfis sp. nov. (= DSM 100708(T) = MCCC 1K01247(T)) is proposed.
Streptomyces pluripotens MUSC 137 was isolated from mangrove soil obtained from Tanjung Lumpur, Pahang, Malaysia. We investigated the phylogenetic, genomic, biochemical, and phenotypic characteristics of this strain. Uniquely adapted microorganisms from mangrove habitats have previously yielded compounds of biopharmaceutical interest. In order to examine the bioactivities possessed by the strain, fermentation extract was prepared through solvent extraction method prior to bioactivities screenings. Antioxidant activity was examined via DPPH assay while the cytotoxic effect was assessed by means of examining the activity of the extract against selected human cancer cell lines, namely colon cancer cells (HCT-116, Caco-2, SW480, and HT-29), breast cancer cell (MCF-7), lung cancer cell (A549), prostate cancer cell (DU145), and cervical cancer cell (Ca Ski). The results revealed MUSC 137 possesses significant antioxidant activity and demonstrates cytotoxic effect against several cancer cell lines tested. The results indicated MCF-7 cells were most susceptible to the extract with the lowest IC50 (61.33 ± 17.10 μg/mL), followed by HCT-116 and A549. Additionally, selective index (SI) showed that MUSC 137 extract was less toxic against normal cell lines when compared to MCF-7 and HCT-116 cells. The extract was further subjected to chemical analysis using GC-MS and revealed the presence of deferoxamine and pyrrolizidines related compounds which may account for the antioxidant and cytotoxic properties observed.
Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.
Quorum-sensing regulates bacterial biofilm formation and virulence factors, thereby making it an interesting target for attenuating pathogens. In this study, we investigated anti-biofilm and anti-quorum-sensing compounds from secondary metabolites of halophiles marine streptomyces against urinary catheter biofilm forming Proteus mirabilis without effect on growth viability. A total of 40 actinomycetes were isolated from samples collected from different places in Iraq including marine sediments and soil samples. Fifteen isolates identified as streptomyces and their supernatant screened as anti-quorum-sensing by inhibiting quorum-sensing regulated prodigiosin biosynthesis of Serratia marcescens strain Smj-11 as a reporter strain. Isolate Sediment Lake Iraq (sdLi) showed potential anti-quorum-sensing activity. Out of 35 clinical isolates obtained from Urinary catheter used by patient at the Universiti Kebangsaan Malaysia Medical Center, 22 isolates were characterized and identified as Proteus mirabilis. Isolate Urinary Catheter B4 (UCB4) showed the highest biofilm formation with highest resistance to used antibiotic and was chosen for further studies. Ethyl acetate secondary metabolites extract was produced from sdLi isolate. First, we determined the Minimum Inhibitory Concentration (MIC) of sdLi crude extract against UCB4 isolate, and all further experiments used concentrations below the MIC. Tests of subinhibitory concentrations of sdLi crude extract showed good inhibition against UCB4 isolate biofilm formation on urinary catheter and cover glass using Scanning electron microscopy and light microscopy respectively. The influence of sub-MIC of sdLi crude extract was also found to attenuate the quorum sensing (QS)-dependent factors such as hemolysin activity, urease activity, pH value, and motility of UCB4 isolate. Evidence is presented that these nontoxic secondary metabolites may act as antagonists of bacterial quorum sensing by competing with quorum-sensing signals for receptor binding.