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Bacterial community structure of the different steps of the vermicomposting process,

ABSTRACT: Bacterial community structure of the different steps of the vermicomposting process, Raw sequence reads

PROVIDER: PRJNA897901 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22220808_1.fastq.gz	Fastqsanger.gz
	SRR22220808_2.fastq.gz	Fastqsanger.gz
	SRR22220809_1.fastq.gz	Fastqsanger.gz
	SRR22220809_2.fastq.gz	Fastqsanger.gz
	SRR22220810_1.fastq.gz	Fastqsanger.gz

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Project description:Previous studies dealing with changes in microbial communities during vermicomposting were mostly performed at lab-scale conditions and by using low-throughput techniques. Therefore, we sought to characterize the bacterial succession during the vermicomposting of grape marc over a period of 91 days in a pilot-scale vermireactor. Samples were taken at the initiation of vermicomposting, and days 14, 28, 42, and 91, representing both active and mature stages of vermicomposting. By using 16S rRNA high-throughput sequencing, significant changes in the bacterial community composition of grape marc were found after 14 days and throughout the process (p < 0.0001). There was also an increase in bacterial diversity, both taxonomic and phylogenetic, from day 14 until the end of the trial. We found the main core microbiome comprised of twelve bacterial taxa (~16.25% of the total sequences) known to be capable of nitrogen fixation and to confer plant-disease suppression. Accordingly, functional diversity included increases in specific genes related to nitrogen fixation and synthesis of plant hormones (salicylic acid) after 91 days. Together, the findings support the use of grape marc vermicompost for sustainable practices in the wine industry by disposing of this high-volume winery by-product and capturing its value to improve soil fertility.

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Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure.

Project description:Anaerobic ammonia oxidation (anammox) combined with partial nitritation (PN) is an innovative treatment process for energy-efficient nitrogen removal from wastewater. In this study, we used genome-based metagenomics to investigate the overall community structure and anammox species enriched in suspended growth (SGR) and attached growth packed-bed (AGR) anammox reactors after 220 days of operation. Both reactors removed more than 85% of the total inorganic nitrogen. Metagenomic binning and phylogenetic analysis revealed that two anammox population genomes, affiliated with the genus Candidatus Brocadia, were differentially abundant between the SGR and AGR. Both of the genomes shared an average nucleotide identify of 83%, suggesting the presence of two different species enriched in both of the reactors. Metabolic reconstruction of both population genomes revealed key aspects of their metabolism in comparison to known anammox species. The community composition of both the reactors was also investigated to identify the presence of flanking community members. Metagenomics and 16S rRNA gene amplicon sequencing revealed the dominant flanking community members in both reactors were affiliated with the phyla Anaerolinea, Ignavibacteria, and Proteobacteria. Findings from this research adds two new species, Ca. Brocadia sp. 1 and Ca. Brocadia sp. 2, to the genus Ca. Brocadia and sheds light on their metabolism in engineered ecosystems.

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Project description:Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.

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Project description:While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300 as reported by Pelka et al. 2009, and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.

2018-07-10 | GSE116772 | GEO

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