Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.

2020-03-06 | GSE146427 | GEO

Comparing Gut Microbial Composition and Functional Adaptations between SPF and Non-SPF pigs

Project description:The gut microbiota is closely associated with digestion, metabolism, immunity, and host health. The imbalance of the microbial community in livestock directly affects their well-being and, consequently, productivity. The composition and diversity of the gut microbiota are influenced not only by host genetics but also by environmental factors such as the microbial complexity of the rearing environment, feeds, and antibiotics. Here, we focus on the comparison of gut microbial communities in miniature pigs developed for xenotransplantation in specific pathogen-free (SPF) and conventional (non-SPF) facilities. To identify the disparities in gut microbial composition and functionality between these two environments, 16S RNA metagenome sequencing was conducted using fecal samples. The results revealed that the non-SPF pigs had higher gut microbiota diversity than the SPF pigs. The genera Streptococcus and Ruminococcus were more abundant in SPF pigs than in non-SPF pigs. Blautia, Bacteroides, and Roseburia were exclusively observed in SPF pigs, whereas Prevotella was exclusively found in non-SPF pigs. Carbohydrate and nucleotide metabolism, as well as environmental information processing, were predicted to be enriched in SPF pigs. In addition, energy and lipid metabolism, along with processes related to genetic information, cellular communication, and diseases, were predicted to be enriched in non-SPF pigs. This study makes an important contribution to elucidating the impact of environments harboring a variety of microorganisms, including pathogens, on the gut microbiota of miniature pigs. Furthermore, we sought to provide foundational data on the characteristics of the gut microbiota in genetically modified pigs, which serve as source animals for xenotransplantation.

2024-04-22 | GSE264183 | GEO

Composting of common organic wastes using microbial inoculants

Project description:It is important to use renewable resources to maximize crop yields and minimize the environmental hazards associated with chemical residues. Composting is an age old practice for the biological conversion of organic waste to a humus-like substance which can enhance physical, chemical and biological soil properties. To explore the effect of microorganisms in the composting process, three potent bacterial isolates were selected. Their morphological, cultural and biochemical characteristics were identified, and 16S rDNA studies identified isolates B1U/1 and D3L/1 as Bacillus subtilis and isolate RAT/5 as Pseudomonas sp. Common organic wastes were composted using the selected isolates individually and as a consortium. The C/N ratio of each substrate reduced gradually to 25–30:1 within 120 days and remained constant thereafter. The reduction in NH4+ and NO3− ion concentrations also indicated compost maturity after 120 days. The pH of the mature compost was typically 7.0 ± 0.2, and the PO4−3 ion concentration was high throughout the decomposition process. This study describes the optimization of the composting process using a consortium of isolates from composted soil.

| S-EPMC3376866 | biostudies-literature

Urban waterways microbial communities (Affymetrix)

Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3)

2014-12-22 | GSE64368 | GEO

Urban waterways microbial communities (GeoChip)

2014-12-22 | GSE64286 | GEO

microbial mat metagenome

Project description:microbial mat metagenome Metagenome

| PRJNA433474 | ENA