scholarly journals Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter

2019 ◽  
Vol 8 (1) ◽  
pp. 13
Author(s):  
Julia Hassa ◽  
Daniel Wibberg ◽  
Irena Maus ◽  
Alfred Pühler ◽  
Andreas Schlüter
Keyword(s):  
Microbial Community ◽  
Biogas Production ◽  
Gc Content ◽  
Production Scale ◽  
Circular Chromosome ◽  
Hydrogenotrophic Methanogenesis ◽  
Complex Process ◽  
Indigenous Microbial Community ◽  
Genome Analyses ◽  
And Function

In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.

Co-digestion of organic and mineral wastes for enhanced biogas production: Reactor performance and evolution of microbial community and function

2019 ◽  
Vol 87 ◽  
pp. 313-325 ◽  
Author(s):  
Burhan Shamurad ◽  
Neil Gray ◽  
Evangelos Petropoulos ◽  
Shamas Tabraiz ◽  
Kishor Acharya ◽  
...  
Keyword(s):  
Microbial Community ◽  
Biogas Production ◽  
Reactor Performance ◽  
Mineral Wastes ◽  
And Function

scholarly journals Metagenomic Approach: Transforming In-Silico Research for Improved Biogas Production

2019 ◽  
Vol 7 (1) ◽  
pp. 6-11 ◽  
Author(s):  
Roushney Fatima Mukti ◽  
Sanjida Sakhawat Sinthee
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Sequence Data ◽  
Biogas Production ◽  
Biogas Plant ◽  
Rational Approach ◽  
Production Scale ◽  
Specific Element ◽  
Metagenomic Approach ◽  
Metagenome Sequence

The complexity of the microbial communities and metabolic pathways involved in the microbiological process of biogas production is poorly understood and numerous microorganisms in the fermentation sample of the biogas plant are still unclassified or unknown. The structure and function of microbial communities and the effects of the addition of trace elements are needed to be known, to control and channel the energy sources microbes produce and to capture and store the useful by-products or for targeted screening of novel enzymes. In this review, we discussed an emerging idea that Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production. The composition and gene content of a biogas-producing consortium can be determined through metagenomic approach which allows the design of the optimal microbial community structure for any biogas plant for the significant progress in the efficacy and economic improvement of biogas production and biofertilizer of either balanced nutrition or rich in specific element for plant growth produced from the sludge of biogas plant. Biogas-producing microbial community from different production-scale biogas plants supplied with different raw materials as substrates can be analyzed by polyphasic approach to find out the best raw material composition for biogas production. The phylogenetic structure of the microbial community residing in a fermentation sample from a biogas plant can be analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Int. J. Appl. Sci. Biotechnol. Vol 7(1): 6-11

scholarly journals Genome Analyses of a New Mycoplasma Species From the scorpion Centruroides vittatus

2018 ◽  
Author(s):  
Tsunemi Yamashita ◽  
Douglas D. Rhoads ◽  
Jeff Pummill
Keyword(s):  
Ribosomal Proteins ◽  
Gc Content ◽  
Fluoroquinolone Resistance ◽  
Mycoplasma Species ◽  
Virulence Determinants ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Centruroides Vittatus ◽  
Genome Analyses ◽  
Single Circular Chromosome

ABSTRACTArthropod Mycoplasma are little known endosymbionts in insects, primarily known as plant disease vectors. Mycoplasma in other arthropods such as arachnids are unknown. We report the first complete Mycoplasma genome sequenced, identified, and annotated from a scorpion, Centruroides vittatus, and designate it as Mycoplasma vittatus. We find the genome is at least a 683,827 bp single circular chromosome with a GC content of 43.7% and with 1,010 protein-coding genes. The putative virulence determinants include 20 genes associated with the virulence operon associated with protein synthesis (SSU ribosomal proteins) and nine genes with fluoroquinolone resistance. Comparative analysis revealed that the M. vittatus genome is smaller than other Mycoplasma genomes and exhibits a higher GC content. Phylogenetic analysis shows M. vittatus as part of the Hominis group of Mycoplasma. As arthropod genomes accumulate, further novel Mycoplasma genomes may be identified and characterized.

scholarly journals Operational and biochemical aspects of co-digestion (co-AD) from sugarcane vinasse, filter cake and deacetylation liquor

2021 ◽  
Author(s):  
Maria Paula C. Volpi ◽  
Antonio Djalma N. Ferraz ◽  
Telma T. Franco ◽  
Bruna S. Moraes
Keyword(s):  
Microbial Community ◽  
Ethanol Production ◽  
Filter Cake ◽  
Biogas Production ◽  
Organic Load ◽  
Continuous Stirred Tank Reactor ◽  
Operational Parameters ◽  
Hydrogenotrophic Methanogenesis ◽  
Oxidation Reduction ◽  
Pre Treatment

ABSTRACTThis work performed co-AD from the vinasse and filter cake (from 1G ethanol production) and deacetylation liquor (from the pre-treatment of sugarcane straw for 2G ethanol production) in a semi-Continuous Stirred Tank Reactor (s-CSTR) aiming to provide optimum operational parameters for continuous CH4 production. Using filter cake as co-substrate may allow the reactor to operate throughout the year, as it is available in the sugarcane off-season, unlike vinasse. A comparison was made from the microbial community of the seed sludge and the reactor sludge when CH4 production stabilized. Lactate, butyrate and propionate fermentation routes were denoted at the start-up of the s-CSTR, characterizing the acidogenic phase: the Oxidation-Reduction Potential (ORP) values ranged from -800 to -100 mV. Once the methanogenesis was initiated, alkalizing addition was no longer needed as its demand by the microrganisms was supplied by the alkali-characteriscs of the deacetylation liquor. The gradual increase of the applied Organic Load Rates (OLR) allowed stabilization of the methanogenesis from 3.20 gVS L-1 day-1: the highest CH4 yield (230 NmLCH4 gSV-1) and average organic matter removal efficiency (83% ± 13) was achieved at ORL of 4.16 gVS L-1day-1. The microbial community changed along the reactor operation, presenting different metabolic routes mainly due to the used lignocellulosic substrates. Bacteria from the syntrophic acetate oxidation (SAO) process coupled to hydrogenotrophic methanogenesis were predominant (∼ 2% Methanoculleus) during the CH4 production stability. The overall results are useful as preliminary drivers in terms of visualizing the co-AD process in a sugarcane biorefinery integrated to scale.KeypoitnsIntegration of 1G2G sugarcane ethanol biorefinery from co-digestion of its residues Biogas production from vinasse, filter cake and deacetylation liquor in a semi-CSTR Lignicellulosic substrates affected the biochemical routes and microbial community Biomol confirmed the stablismenht of thermophilic community from mesophilic sludge

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

scholarly journals Microbiological Activity during Co-Composting of Food and Agricultural Waste for Soil Amendment

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 928
Author(s):  
Vladimir Mironov ◽  
Anna Vanteeva ◽  
Alexander Merkel
Keyword(s):  
Microbial Community ◽  
Agricultural Waste ◽  
Temperature Changes ◽  
Culture Independent ◽  
Mineralization Of Organic Matter ◽  
Microbial Number ◽  
Mature Compost ◽  
Stimulate Plant Growth ◽  
And Function ◽  
Favorable Conditions

This study aims to establish the relationship between ambient parameters and the diversity, composition, and function of microbial communities that predominate at each stage of the co-composting of food and agricultural waste. Culture-based and culture-independent methods were used to investigate the changes in the microbiota. The favorable conditions of high initial humidity and C/N ratio caused a decrease in the richness and biodiversity of the microbiota when such conditions existed. During the thermophilic stage, the total microbial number increased, and active mineralization of organic matter was carried out by members of the genera Bacillus, Caldibacillus, Aspergillus, and Penicillium. The fungal community was sensitive to drastic temperature changes. Byssochlamys dominated among fungi during the transition from the mesophilic to the thermophilic stage and during cooling. The biodiversity increased with time and was associated with the dynamics of germination and nitrification indices, so that the more diverse the microbial community, the higher the properties of compost that stimulate plant growth and development. The microbial community of the mature compost, together with mineral plant nutrients ready for consumption and humic compounds, make this compost a good soil additive.

Insights into the mechanism of the interference of sulfadiazine on soil microbial community and function

2021 ◽  
pp. 126388
Author(s):  
Linlin Qiu ◽  
Tim J. Daniell ◽  
Steven A. Banwart ◽  
Muhammad Nafees ◽  
Jingjing Wu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Soil Microbial ◽  
And Function
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