The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×107 and 1.50×107, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.
Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.
Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests. In contrast, species diversity (α-diversity) differed to a much greater extent, being nearly six-fold higher in the mangrove forest (Chao1 index = 6,862) than in forests in Singapore and Sarawak (~1,250). In addition, natural mixed dipterocarp forests had lower species diversity than acacia and oil palm plantations, indicating that aboveground tree composition does not influence soil bacterial diversity. Shannon and Chao1 indices were correlated positively, implying that skewed operational taxonomic unit (OTU) distribution was associated with the abundance of overall and rare (singleton) OTUs. No OTUs were represented in all 28 forests, and forest-specific OTUs accounted for over 70% of all detected OTUs. Forests that were geographically adjacent and/or of the same forest type had similar bacterial species composition, and a positive correlation was detected between species divergence (β-diversity) and direct distance between forests. Both α- and β-diversities were correlated with soil pH. These results suggest that soil bacterial communities in different forests evolve largely independently of each other and that soil bacterial communities adapt to their local environment, modulated by bacterial dispersal (distance effect) and forest type. Therefore, we conclude that the biogeography of soil bacteria communities described here is non-random, reflecting the influences of contemporary environmental factors and evolutionary history.
Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.
Here we present the draft genome of Pseudomonas mendocina strain S5.2, possessing tolerance to a high concentration of copper. In addition to being copper resistant, the genome of P. mendocina strain S5.2 contains a number of heavy-metal-resistant genes known to confer resistance to multiple heavy-metal ions.
Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.
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.
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.
A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures. A model temperate crop, loose leaf lettuce, was grown on eutrophic soil under soil cooling and a number of parameters, such as fresh weight, height, the number of leaves, and root length, were evaluated upon harvest. Under soil cooling, significant differences were observed in the average fresh weight (P<0.05) and positive development of the roots, shoots, and leaves of lettuce. Janthinobacterium (8.142%), Rhodoplanes (1.991%), Arthrospira (1.138%), Flavobacterium (0.857%), Sphingomonas (0.790%), Mycoplana (0.726%), and Pseudomonas (0.688%) were the dominant bacterial genera present in cooled soil. Key soil fungal communities, including Pseudaleuria (18.307%), Phoma (9.968%), Eocronartium (3.527%), Trichosporon (1.791%), and Pyrenochaeta (0.171%), were also recovered from cooled soil. The present results demonstrate that the growth of temperate crops is dependent on soil temperature, which subsequently affects the abundance and diversity of soil microbial communities that maintain the growth of temperate crops at low soil temperatures.
The globally vital oil palm, a major oil producer, confronts productivity challenges due to Ganoderma boninense (Gb), causing output decline. Chemical control efforts have proven ineffective, prompting exploration of microbial-based biocontrol. While single fungal biocontrol research exists, the impact of employing multiple biocontrols concurrently to combat Ganoderma and enhance oil palm growth remains uncharted. This study examined four soil-derived fungal isolates for their ability to antagonize Gb PER71 in vitro. Molecular identification categorized them as Talaromyces spp. and Penicillium sp. Moreover, all isolates were revealed to have at least three plant growth-promoting (PGP) traits and were shown to have phosphoric hydrolase, ester hydrolase, peptide hydrolase, and glycosidase activities which are essential for plant growth. Furthermore, the synergistic evaluation of fungal isolates was tested against Gb PER71. One out of six combinations of fungal isolates showed a synergistic effect in vitro, and two showed a synergistic effect in planta. The application of single and combined fungal isolates tested in planta also suppressed Gb PER71 and enhanced oil palm growth compared to control groups. The findings indicate the promising potential of these isolates as biocontrol agents (BCAs) and bioformulations against Gb in oil palm cultivation.
Following gas generation in a Geological Disposal Facility (GDF), (14)C-containing gases could migrate through the geosphere, eventually diffusing into soils at the Earth's surface. This paper reports summary results from laboratory and field experiments to obtain information on the probable rates of a) diffusive transport and b) oxidation of (12/13)CH(4) (as a surrogate for (14)CH4) in a typical agricultural soil in the UK. Rates of CH(4) oxidation were generally low in the field and undisturbed soil columns, though a re-packed column of homogenised topsoil oxidised ambient atmospheric CH(4) 20× faster than an undisturbed soil column. In contrast to low observed rates of CH(4) oxidation, the effective diffusion of CH(4) through the soil was rapid. Isotopically labelled CH(4) injected at a depth of 45 cm in the field diffused to the surface and exited the soil over a time period ranging from 8 to 24 h. The rate of CH(4) diffusion through the soil was increased by the presence of ryegrass roots which increased soil porosity and decreased water content. δ(13)C values for laboratory column soils after labelled CH(4) injection experiments showed no sign of residual (13)C, despite the extremely high δ(13)C values of the injected (12/13)CH(4). If laboratory observations are confirmed by measurements in field samples it can be concluded that the majority of (14)CH(4) from a GDF which enters a soil with low methanotrophic activity will be lost to the free atmosphere after diffusing rapidly through the soil column.
Ergosterol is the main component of the fungal membrane and is not found in plants or other microbial cells. Therefore, it can be a useful biomarker for the quantification of fungal biomass. We are now reporting the first isolation and characterisation of ergosterol from the mycelium of G. boninense. The ergosterol structure was detected by Thin Liquid Chromatography (TLC) and Ultra Performance Liquid Chromatography (UPLC) and confirmed with Gas Chromatography coupled with Mass Spectrometry (GCMS) and Nuclear Magnetic Resonance (NMR) analysis.
Pathogenic leptospiras (1,424) isolated from natural waters and wet soils in Malaysia comprised 29 different serovars (synonym serotypes). All except two of the serovars had been found previously in Malaysia. The exceptional serovars were werrasingha, an Autumnalis serogroup member originally isolated in Ceylon, and a new serovar designated evansi. Serovar evansi had serological affinities with serovar ranarum which was isolated from the kidney of a frog in Iowa. The large variety of serovars found in jungle areas was consistent with similar previous findings of diverse serovar infections in troops who had operated in Malaysian jungles.
Global warming is the main concern in today’s century as it comes with numerous side effects to the natural environment. Open Top Chambers (OTC) consist of metal constructions with transparent vertical side-walls and a frustum on top. An opening in the middle of the frustum allows an air exchange to reduce temperature and humidity effects in the chamber. The size of the open top chamber which is located in Universiti Putra Malaysia is slanted 60o, 50cm tall, 2.08m basal diameter hexagon chamber. The Open Top Chamber experiments were carried out to determine how much global warming has affected and is still affecting the temperature, pH, the moisture and the growth of the microbes in the tropical soil. The aim of this study is to elucidate the effects of temperature increase on the soil microbes’ population and on the pH of the soil. The study was conducted to observe the effect of heat on the population of soil microbes and the pH of the soil which was collected on the same day for 6 consecutive months. The microbes from the samples were grown on agar plates. The population of microbes on the plates were used as values were for Colony Forming Unit (CFU) value calculations. The effects of OTCs on mean temperature showed a large range of CFU values throughout the 6 months but did not differ significantly between studies. Increases in mean monthly and diurnal temperature were strongly related, indicating that the presence of warming effect by the OTCs. Such predictive power allows a better mechanistic understanding of observed biotic response to experimental warming. This study will be useful for the understanding of the global warming effect on microbes. The Open Top Chamber experiment has proven to be one of the effective model for global warming research and data collected especially on the growth of soil microbial obtained would be of great use for further experiments.
The data reported in this paper are among the first relating to the microbiology of hyper-arid, very high altitude deserts and they provide base line information on the structure of actinobacterial communities. The high mountain Cerro Chajnantor landscape of the Central Andes in northern Chile is exposed to the world's most intense levels of solar radiation and its impoverished soils are severely desiccated. The purpose of this research was to define the actinobacterial community structures in soils at altitudes ranging from 3000 to 5000 m above sea level. Pyrosequencing surveys have revealed an extraordinary degree of microbial dark matter at these elevations that includes novel candidate actinobacterial classes, orders and families. Ultraviolet-B irradiance and a range of edaphic factors were found to be highly significant in determining community compositions at family and genus levels of diversity.
Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.
Vast amounts of plastic waste are causing serious environmental issues and urge to develop of new remediation methods. The aim of the study is to determine the role of inorganic (nitric acid), organic (starch addition), and biological (Pseudomonas aeruginosa) soil amendments on the degradation of Polyethylene (PE) and phytotoxic assessment for the growth of lettuce plant. The PE-degrading bacteria were isolated from the plastic-contaminated soil. The strain was identified as Pseudomonas aeruginosa (OP007126) and showed the highest degradation percentage for PE. PE was pre-treated with nitric acid as well as starch and incubated in the soil, whereas P. aeruginosa was also inoculated in PE-contaminated soils. Different combinations were also tested. FTIR analysis and weight reduction showed that though nitric acid was efficient in degradation, the combined application of starch and bacteria also showed effective degradation of PE. Phytotoxicity was assessed using morphological, physiological, and biochemical parameters of plant. Untreated PE significantly affected plants' physiology, resulting in a 45% reduction in leaf chlorophyll and a 40% reduction in relative water content. It also had adverse effects on the biochemical parameters of lettuce. Bacterial inoculation and starch treatment mitigated the harmful impact of stress and improved plants' growth as well as physiological and biochemical parameters; however, the nitric treatment proved phytotoxic. The observed results revealed that bacteria and starch could be effectively used for the degradation of pre-treated PE.
A novel kinetic model has been developed to explain the degradation of total petroleum hydrocarbons. Microbiome engineered biochar amendment may result in a synergistic impact on degradation of total petroleum hydrocarbons (TPHs). Therefore, the present study analyzed the potential of hydrocarbon-degrading bacteria A designated as Aeromonas hydrophila YL17 and B as Shewanella putrefaciens Pdp11 morphological characterized as rod shaped, anaerobic and gram-negative immobilized on biochar, and the degradation efficiency was measured by gravimetric analysis and gas chromatography-mass spectrometry (GC-MS). Whole genome sequencing of both strains revealed the existence of genes responsible for hydrocarbon degradation. In 60 days remediation setup, the treatment consisting of immobilization of both strains on biochar proved more efficient with less half-life and better biodegradation potentials compared to biochar without strains for decreasing the content of TPHs and n-alkanes (C12-C18). Enzymatic content and microbiological respiration showed that biochar acted as a soil fertilizer and carbon reservoir and enhanced microbial activities. The removal efficiency of hydrocarbons was found to be a maximum of 67% in soil samples treated with biochar immobilized with both strains (A + B), followed by biochar immobilized with strain B 34%, biochar immobilized with strain A 29% and with biochar 24%, respectively. A 39%, 36%, and 41% increase was observed in fluorescein diacetate (FDA) hydrolysis, polyphenol oxidase and dehydrogenase activities in immobilized biochar with both strains as compared to control and individual treatment of biochar and strains. An increase of 35% was observed in the respiration rate with the immobilization of both strains on biochar. While a maximum colony forming unit (CFU/g) was found 9.25 with immobilization of both strains on biochar at 40 days of remediation. The degradation efficiency was due to synergistic effect of both biochar and bacteria based amendment on the soil enzymatic activity and microbial respiration.