Douglas J. H. Shyu’s research while affiliated with National Pingtung University of Science and Technology and other places

Microalgal biomass offers a promising biofertilizer option due to its nutrient-rich composition, adaptability, and environmental benefits. This study evaluated the potential of microalgal-based biofertilizers—microalgal Chlorella biomass, de-oiled microalgal biomass (DMB), and de-oiled and de-aqueous extract microalgal biomass (DAEMB)—in enhancing lettuce growth, soil nutrient dynamics, and microbial community composition. Lettuce seedlings were cultivated with these biofertilizers, and plant growth parameters, photosynthetic pigments, and nitrogen uptake were assessed. Soil incubation experiments further examined nutrient mineralization rates, while DNA sequencing analyzed shifts in rhizosphere microbial communities. Lettuce grown with these biofertilizers exhibited improved growth parameters compared to controls, with Chlorella biomass achieving a 31.89% increase in shoot length, 27.98% in root length, and a 47.33% increase in fresh weight. Chlorophyll a and total chlorophyll levels increased significantly in all treatments, with the highest concentrations observed in the Chlorella biomass treatment. Soil mineralization studies revealed that DMB and DAEMB provided a gradual nitrogen release, while Chlorella biomass exhibited a rapid nutrient supply. Microbial community analyses revealed shifts in bacterial and fungal diversity, with increased abundance of nitrogen-fixing and nutrient-cycling taxa. Notably, fungal diversity was enriched in biomass and DAEMB treatments, enhancing soil health and reducing pathogenic fungi. These findings highlight microalgal biofertilizers’ potential to enhance soil fertility, plant health, and sustainable resource use in agriculture.

Objectives: Indonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile. Data description: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503 S, 115.133452 E; (ii) Banjar, 8.210270 S, 114.967063 E; and (iii) Batur, 8.228806 S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop™ spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.

The steadily increasing presence of both natural and anthropogenic pollutants in our environment poses a considerable challenge, given the recalcitrance of many of these pollutants. Microbial bioremediation presents a promising and sustainable strategy that harnesses a diverse array of microorganisms, operating either concurrently or sequentially, to eliminate or mitigate the presence of pollutants within the environment. Recent years have witnessed the application of multiomics techniques to the study of biodegradation and bioremediation, yielding an abundance of novel data that enrich our comprehension of pivotal pathways and offer fresh perspectives on the adaptability of organisms amidst shifting environmental conditions. This book brings together recent progress in microbial bioremediation, emphasizing the emerging field of multiomics technologies. It serves as a valuable reference for microbiologists exploring multiomics applications and environmental scientists seeking innovative remediation solutions.

The steadily increasing presence of both natural and anthropogenic pollutants in our environment poses a considerable challenge, given the recalcitrance of many of these pollutants. Microbial bioremediation presents a promising and sustainable strategy that harnesses a diverse array of microorganisms, operating either concurrently or sequentially, to eliminate or mitigate the presence of pollutants within the environment. Recent years have witnessed the application of multiomics techniques to the study of biodegradation and bioremediation, yielding an abundance of novel data that enrich our comprehension of pivotal pathways and offer fresh perspectives on the adaptability of organisms amidst shifting environmental conditions. This book brings together recent progress in microbial bioremediation, emphasizing the emerging field of multiomics technologies. It serves as a valuable reference for microbiologists exploring multiomics applications and environmental scientists seeking innovative remediation solutions.

Solid waste treatment processes such as composting, anaerobic digestion and aerobic digestion rely on microbial communities to break down and transform organic matter into non-hazardous products without sanitary and pollution issues. The solutions that lead to converting valuable products or by-products are much more favourable. Profiling of microbial communities can help identify the dominant microbial species present in a particular environment and determine their roles in the solid waste treatment process. Microbial profiling can be achieved using conventional molecular techniques such as DNA sequencing, Polymerase Chain Reaction (PCR) amplification and fluorescent in situ hybridization. Moreover, advanced high-throughput microbial profiling approaches such as single-cell genome sequencing, single-cell RNA sequencing and metagenomic sequencing were developed. The process of composting involves microorganisms such as bacteria, fungi and actinomycetes that break down organic matter into simpler compounds such as carbon dioxide, water and humus and the role of microbial community in composting reduces the volume of waste, eliminate pathogens and reduce the concentration of heavy metals. For instance, in anaerobic digestion, the microbial community breaks down organic matter without oxygen, producing biogas, which can be used as a renewable energy source. The anaerobic process includes various bacteria and archaea, which work together to produce biogas and reduce the amount of organic matter in the waste. On the contrary, aerobic digestion consists of the microbial community that breaks down organic matter in the presence of oxygen, producing carbon dioxide, water and heat. The microbial community in aerobic digestion includes bacteria, fungi and protozoa, which work together to break down the organic matter and produce value-added products or by-products. Therefore, this chapter deals with the conventional and advanced high throughput molecular techniques that are important to achieve detailed microbial profiling and understanding the whole microbial community’s role in solid waste treatment that can help to improve the efficiency and effectiveness of the waste treatment process, leading to better waste management practices and a cleaner environment.

Profiling of Microbial Community and Their Role in Solid Waste Treatment