scholarly journals Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

2021 ◽  
Vol 9 (6) ◽  
pp. 1162
Author(s):  
Seyedbehnam Hashemi ◽  
Sayed Ebrahim Hashemi ◽  
Kristian M. Lien ◽  
Jacob J. Lamb
Keyword(s):  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Biogas Production ◽  
Operating Time ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Analysis Tool ◽  
High Resolution Data ◽  
On Line ◽  
Insight Into

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

scholarly journals Evaluation of DNA Extraction Methods of Mule Dung

2019 ◽  
Vol 4 (3) ◽  
pp. 170-174
Author(s):  
Rajesh Kumar Vaid ◽  
Taruna Anand ◽  
Priyanka Batra ◽  
Ram Avtar Legha ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Dna Isolation ◽  
Community Analysis ◽  
Extraction Methods ◽  
Microbial Community Analysis ◽  
Animal Dung ◽  
Microbial Community Analyses ◽  
Dna Extraction Methods ◽  
Selection Of

DNA isolation is a critical step in microbial community analysis of animal dung. DNA isolation from mule dung is challenging due to microbial diversity, composition and chemical nature of mule dung. Therefore, selection of an appropriate DNA isolation method is important to analyse the complete microbial diversity. In the current study, we evaluated the DNA isolation from mule dung samples (n=11) using QiAmp Mini stool kit as per manufacturer’s procedure with modifications. The results suggest that modifications in proprietary column based method improved the DNA quality and quantity suitable for mule dung microbial community analyses.

Bacterial Community Analysis of Mine Contaminated Soils in Hechi City

2020 ◽  
Vol 14 (4) ◽  
pp. 476-486
Author(s):  
Tingting Liu ◽  
Caoping Pang ◽  
Fengcai Ye ◽  
Dafei Gong ◽  
Jieling Luo ◽  
...  
Keyword(s):  
Microbial Community ◽  
Genetic Engineering ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Mine Soils ◽  
Sequencing Technology ◽  
Autonomous Region

Four mine contaminated soils located in northwest of Guangxi autonomous region were selected for microbial community analysis. These mine soils were contaminated by chromium (Cr) and cadmium (Cd). Microbial communities were described by high-throughput sequencing technology, which showed 39 different phyla in four samples. Among these phyla, Proteobacteria was the most abundant phylum in all samples. Acidobacteria, Actinobacteria, Planctomycetes, Firmicutes, Gemmatimonadetes, Bacteroidetes and Chloroflexi showed higher relative abundances than other phyla. In addition, a wide diversity of bacteria with the potential of bioremediation, such as Sphingomonas, Lysobacter and Gemmatimonas were detected in the tested mine contaminated soils. The results of microbial community analysis will provide a new target for isolation of microorganisms with the potential of bioremediation and lay the foundation for a great enhancement of bioremediation ability through the genetic engineering modification of indigenous microorganisms in future.

scholarly journals CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

2019 ◽  
Author(s):  
Vanessa R. Marcelino ◽  
Philip T.L.C. Clausen ◽  
Jan P. Buchmann ◽  
Michelle Wille ◽  
Jonathan R. Iredell ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Fold Increase ◽  
Community Analysis ◽  
Biological Data ◽  
Microbial Community Analysis ◽  
Metagenomic Data ◽  
Reference Database ◽  
Comprehensive Overview ◽  
Accurate Identification

AbstractHigh-throughput sequencing of DNA and RNA from environmental and host-associated samples (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a sample. Taxonomic identification software usually align individual short sequence reads to a reference database, sometimes containing taxa with complete genomes only. This is a challenging task given that different species can share identical sequence regions and complete genome sequences are only available for a fraction of organisms. A recently developed approach to map sequence reads to reference databases involves weighing all high scoring read-mappings to the data base as a whole to produce better-informed alignments. We used this novel concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Using simulated fungal and bacterial metagenomes, we demonstrate that CCMetagen substantially outperforms other commonly used metagenome classifiers, attaining a 3 – 1580 fold increase in precision and a 2 – 922 fold increase in F1 scores for species-level classifications when compared to Kraken2, Centrifuge and KrakenUniq. CCMetagen is sufficiently fast and memory efficient to use the entire NCBI nucleotide collection (nt) as reference, enabling the assessment of species with incomplete genome sequence data from all biological kingdoms. Our pipeline efficiently produced a comprehensive overview of the microbiome of two biological data sets, including both eukaryotes and prokaryotes. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.

Performance, Microbial Community Analysis and Fertilizer Value of Anaerobic Co-digestion of Cattle Manure with Waste Kitchen Oil

2019 ◽  
Vol 35 (2) ◽  
pp. 239-248 ◽  
Author(s):  
Ricardo Galbiatti Sandoval Nogueira ◽  
Teng Teeh Lim ◽  
Haoqi Wang ◽  
Paulo Henrique Mazza Rodrigues
Keyword(s):  
Anaerobic Digestion ◽  
Hydraulic Retention Time ◽  
Biogas Production ◽  
Preliminary Test ◽  
Community Analysis ◽  
Cattle Manure ◽  
Microbial Community Analysis ◽  
Fertilizer Value ◽  
Replication Control ◽  
Mesophilic Conditions

Abstract. Co-digestion trials of beef cattle manure and waste kitchen oil (WKO) were conducted to evaluate potential increase of biogas production for a local beef farm anaerobic digester. The trials were conducted using laboratory-scale, semi-continuously loaded digesters under mesophilic conditions, with 21-day hydraulic retention time (HRT). In a preliminary test, WKO was added at 0%, 0.5%, 1.0%, 1.5%, and 2.0% by volume, each with replicate digesters (n=2), except for the 0% level, which had one digester (n=1). Methane (CH4) yield per week increased linearly with WKO levels. Populations of bacteriodetes decreased, while clostridiales and synergistales increased with the WKO levels. A second test was conducted using treatments with more replication: control (n=3), and 1.0% (n=3) and 2% (n=3) WKO levels. Methane yields of the 1.0% and 2.0% WKO levels were 79.1% and 203% higher than the control, respectively. Addition of WKO have resulted in changes of the metagenomics of the digesters. Populations of clostridiales increased, while bacteroidales and euryarchaeota methanomicrobia YC-E6 decreased with the WKO levels. The findings confirm adding low amounts (1% and 2%) of WKO as co-digestion feedstock can be an effective way to increase CH4 yield for beef operation anaerobic digestion, especially when there are available feedstock nearby. Keywords: Anaerobic digestion, Biogas, Methane, Semi-continuous digesters.

Enhanced biogas production by co-digestion of crude glycerol and ethanol with palm oil mill effluent and microbial community analysis

2021 ◽  
Vol 148 ◽  
pp. 106037
Author(s):  
Poonsuk Prasertsan ◽  
Chonticha Leamdum ◽  
Sukonlarat Chantong ◽  
Chonticha Mamimin ◽  
Prawit Kongjan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Palm Oil ◽  
Crude Glycerol ◽  
Biogas Production ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Palm Oil Mill Effluent ◽  
Palm Oil Mill
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