Mohd Fadzli Ahmad

Microbial communities are play a crucial role in the breakdown of organic waste, the production of biogas, and the reduction of environmental impact at landfills, which are complex ecosystems more than just places to dispose of waste. This study provides a comprehensive overview of the current knowledge of microbial diversity in landfills based on metagenomics studies. Metagenomics studies show that various microorganisms, including bacteria, archaea, and fungi, are found in landfills and interact to break down waste. Environmental factors such as pH, temperature, and waste composition impact these microbial communities. This review investigate how landfill age, waste composition, and operational methods impact microbial communities. Important microbial group functions in the waste breakdown, greenhouse gas emission, and soil leachate composition are also highlighted in this paper. The review examine how technologies, such as bioinformatics tools and high-throughput sequencing, enhance our knowledge of the landfill microbiome. Through metagenomics, researchers can identify the microbial genes responsible for important activities, including pollution bioremediation, production of methane, and organic matter breakdown. High-throughput sequencing methods such as 16S rRNA sequencing and shotgun metagenomics have improved the current understanding of landfill microbiomes by identifying new microbes with specialized metabolic roles. Identifying the plastic-degrading microbes and their enzymes is an emerging area of interest with potential for that may help develop biotechnological solutions to landfill plastic pollution. Metagenomics provides the opportunity to develop sustainable landfill management techniques and microbial-based waste treatment methods by identifying these microbial processes. This review emphasis the need of using the microbial processes for a better waste management and the significance of metagenomics in optimising landfill operations.

Cholesterol oxidase is an important enzyme that catalyzes the oxidation of cholesterol to cholest-4-en-3-one, with the simultaneous reduction of oxygen to hydrogen peroxide. It has gained significant attention due to its wide range of applications in medical diagnostics, pharmaceuticals, and food processing. Cholesterol oxidase is crucial in reducing cholesterol levels by breaking it into less harmful byproducts, making it a valuable tool in managing cholesterol-related health issues. The enzyme is primarily produced through microbial fermentation using microorganisms. However, the yield and efficiency of cholesterol oxidase production are highly dependent on fermentation conditions, including temperature, pH, and agitation rate, which significantly influence microbial growth, enzyme stability, and overall productivity. The initial production of cholesterol oxidase and cell growth under non-optimized conditions revealed suboptimal performance, with enzyme activity and cell dry weight (DCW) peaking at lower levels.

A landfill is a site for disposal of waste material by burying it in the ground. Understanding the impact of landfill ecosystems and studying the bioremediation methods require an understanding of their microbial diversity and functional ability. However, little is known about the microbial communities that found in landfill sites, especially in tropical areas. In order to further our knowledge of water quality and environmental sustainability, this study aims to outline the metabolic pathways and microbial community structure in soil and leachate samples from Jeram landfill. Sample of soil and leachate were carefully collected at the selected sites within the Jeram Landfill in Selangor, Malaysia. Metagenomic DNA was extracted and Illumina shotgun sequencing was performed for taxonomic and functional analysis. Taxonomic profiling showed that bacteria dominated in both soil (55.31%) and leachate (30.98%), whereas archaea were significantly more common in leachate (8.91%) than in soil (1.74%). Leachate contained a high percentage of unidentified sequences (59.60%), indicating the presence of a new or unknown microorganisms. The most prevalent species in the soil sample were Bacteroides graminisolvens, Methanosarcina barkeri, and Klebsiella pneumoniae. Methanogens like Methanoculleus bourgensis and Methanosarcina mazei, as well as Arcobacter species known for their roles in the nitrogen cycling, was dominant in leachate samples. KEGG pathway functional analysis revealed that metabolic pathway, biosynthesis of secondary metabolites, and carbon metabolism were the most common in both soil and leachate samples. However, leachate showed a significantly greater methane metabolism thus indicating the active anaerobic breakdown processes. These findings highlight how important microbial communities are to the breakdown of the organic matter, nitrogen cycling, and methane production which have a significant impact on the stability of landfills and the likelihood of water. This study enhances our knowledge of waste degrading processes and the implications for environmental sustainability and water resource management by providing insight into the metabolic processes and microbial diversity found in landfill sites. The findings provide an outline for further research on landfill impact assessment, bioremediation, and pollution control.

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.

– Soil pH affects the microbial community's composition and diversity, although research on microorganisms in preserved peat swamp forests is rare. In terms of soil acidity, peat swamp forest has been classified as one of the most nutrient-deficient areas of the planet. To have a more comprehensive understanding of the ecology and function of these microbial communities, profiling of peat swamp soil microbial community and structure was conducted with Raja Musa Peat Swamp Forest Reserved (RMFR) in Selangor for its pristine soil that refers to its stability of the microbial community and soil compositions, while focusing on pH response against the microbial community. This study was conducted by using Whole Genome Sequences analysis complemented with Next Generation Sequencing (NGS) and whole shotgun metagenomic. The focus was to clarify whether the naturally occurring pH variations, specifically acid stress and osmotic stress in stress response, affected the soil microbial functional biodiversity and composition. Details analysis from MG-RAST has shown that bacteria has dominated the community with 98 percent abundance while eucaryote with 1 percent and archaea 1 percent. At the phylum level, the four highest abundances recorded which Proteobacteria hits with 51 percent abundances, Actinobacteria 18 percent, Acidobacteria 9 percent, and firmicutes 7 percent. At the genus level, the five highest abundances have been identified: Burkholderia has recorded 6 percent abundances, Candidatus Solibacter 4 percent of abundances, Bradyrhizobium has 4 percent abundances, Streptomyces 4 percent of abundances, and Rhodopseudomonas has 3 percent of abundances,. Amino acid metabolism analysis has identified a significant percentage of valine, leucine, and isoleucine involved with stress response genes that contribute to acid stress and osmotic stress with the microbial genus of the highest abundances has involved where Burkholderia has 10 percent abundances, Bradyrhizobium 10 percent abundances, Rhodopseudomonas 10 percent of abundances, Mycobacterium 8 percent abundances, and Frankia 7 percent abundances.

The microalgae-based industries are trending upwards, particularly as the feed ingredient for aquaculture. Therefore, a sustainable and reasonably priced source of nutrients to support the mass cultivation of microalgae is in great demand. The present study explored the feasibility of using extracts from virgin soil as natural growth-promoting nutrients for the cultivation of Nannochloropsis oculata, Nannochloropsis oceanica, and Chlorella sorokiniana. The extracts were obtained from Bera Lake Forest using five different treatment methods. The greatest retrieval of dissolved organic carbon, total dissolved nitrogen, and total dissolved phosphorus were observed with the autoclave treatment method at 121 °C twice, yielding a respective concentration of 336.56 mg/L, 13.40 mg/L, and 0.14 mg/L, respectively. The highest growth was recorded with Nannochloropsis oculata resulting in an optical density of 0.488 ± 0.009 (×10³ cell mL⁻¹), exhibiting 43% and 44% enhanced growth in comparison to Nannochloropsis oceanica and Chlorella sorokiniana, respectively. The specific growth rate (0.114 ^a ± 0.007 d⁻¹) was the highest for Nannochloropsis oculata when the 24 h-extraction method was used, whereas the utilization of the autoclave 121 °C twice treatment method contributed to the highest specific growth of Nannochloropsis ocenica (0.069 ^a ± 0.003 d⁻¹) and Chlorella sorokiniana (0.080 ^a ± 0.001 d⁻¹). Collectively, these findings suggested that the addition of soil extracts which is sustainable and inexpensive promoted the growth of microalgae compared to the control system. A further study investigating the optimum culture conditions for enhanced microalgae growth will be carried out for the mass production of microalgae biomass.

Microalgae are a source of high-value substances beneficial for industrial applications. To augment the mass production of microalgae in an artificial culture medium, growth-promoting nutrients are essential. The effect of soil extracts (SEs) on four microalgae species was investigated in this study. Artificial Conway media were supplemented with SE collected from the Ayer Hitam Forest Reserve and Raja Musa Forest Reserve (RM), tested using a microplate-incubation technique. The samples were cultured for nine days at 25°C and 30°C, with a light intensity of 33.75 mol photons m−2 seconds−1 and a 12-hour light/dark cycle. Incubation at 25°C showed a higher specific growth rate (SGR) for Nannochloropsis oculata (0.32–0.39 d−1), while, at 30°C, a higher SGR was observed for Dunaliella tertiolecta in all soil treatments (0.31–0.34 d−1). In terms of SEs, media + RM SE showed a higher SGR from 0.25 to 0.39 d−1 for four microalgae. Chlorella sorokiniana and N. oculata grew well at 25°C in all soil treatments, while D. tertiolecta and Dunaliella primolecta grew well at 30°C. This study shows that the RM medium was the optimum soil treatment for all microalgae tested due to the higher concentration of organic matter.

Microalgae are widely utilized in commercial industries. The addition of a modified artificial medium (soil extract) could enhance their growth. Soil extract collected from the Raja Musa peat swamp and mineral soil from the Ayer Hitam Forest Reserve (AHFR), Selangor, Malaysia, were treated using various extraction methods. Carteria radiosa PHG2-A01, Neochloris conjuncta, and Nephrochlamys subsolitaria were grown in microplates at 25 °C, light intensity 33.75 µmol photons m⁻²s⁻¹ for 9 days. N. conjuncta dominated the growth in 121 °C twice extraction method AFHR samples, with 47.17% increment. The highest concentrations of ammonia and nitrate were detected in the medium with soil extract treated with 121 °C twice extraction method, yielding the concentrations of 2 mg NL⁻¹ and 35 mg NL⁻¹ for ammonia and nitrate of RM soil and 2 mg NL⁻¹ and 2.85 mg NL⁻¹ for the AH soil. These extracts are proved successful as a microalgal growth stimulant, increasing revenue and the need for enriched medium. The high rate of nutrient recovery has the potential to serve as a growth promoter for microalgae.

The assessment of water-extractable organic matter using an autoclave can provide useful information on physical, chemical, and biological changes within the soil. The present study used virgin forest soils from Chini Forest Reserve, Langkawi Island, and Kenyir Forest Reserve (Malaysia), extracted using different extraction methods. The dissolved organic carbon (DOC), total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and ammonium-nitrate content were higher in the autoclave treatments, up to 3.0, 1.3, 1.2, and 1.4 times more than by natural extraction (extracted for 24 h at room temperature). Overall, the highest extractable DOC, TDN, TDP, ammonium and nitrate could be seen under autoclaved conditions 121 °C 2×, up to 146.74 mg C/L, 8.97 mg N/L, 0.23 mg P/L, 5.43 mg N mg/L and 3.47 N mg/L, respectively. The soil extracts became slightly acidic with a higher temperature and longer duration. Similar trends were observed in the humic and nonhumic substances, where different types of soil extract treatments influenced the concentrations of the fractions. Different soil extraction methods can provide further details, thus widening the application of soil extracts, especially in microbes.

Soil extracts are useful nutrients to enhance the growth of microalgae. Therefore, the present study attempts for the use of virgin soils from Peninsular Malaysia as growth enhancer. Soils collected from Raja Musa Forest Reserve (RMFR) and Ayer Hitam Forest Reserve (AHFR) were treated using different extraction methods. The total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and dissolved organic carbon (DOC) concentrations in the autoclave methods were relatively higher than natural extraction with up to 132.0 mg N/L, 10.7 mg P/L, and 2629 mg C/L, respectively for RMFR. The results of TDN, TDP, and DOC suggested that the best extraction methods are autoclaved at 121 °C twice with increasing 87%, 84%, and 95%, respectively. Chlorella vulgaris TRG 4C dominated the growth at 121 °C twice extraction method in the RMRF and AHRF samples, with increasing 54.3% and 14%, respectively. The specific growth rate (µ) of both microalgae were relatively higher, 0.23 d⁻¹ in the Ayer Hitam Soil. This extract served well as a microalgal growth promoter, reducing the cost and the needs for synthetic medium. Mass production of microalgae as aquatic feed will be attempted eventually. The high recovery rate of nutrients has a huge potential to serve as a growth promoter for microalgae.