scholarly journals Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis

2020 ◽  
Vol 8 (2) ◽  
pp. 188 ◽  
Author(s):  
Haipeng Wang ◽  
Teng Teeh Lim ◽  
Cuong Duong ◽  
Wei Zhang ◽  
Congfeng Xu ◽  
...  
Keyword(s):  
Corn Stover ◽  
Loading Rate ◽  
Swine Manure ◽  
Preliminary Test ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
Sequencing Analysis ◽  
Degrading Bacteria

Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L−1 d−1 was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L−1 d−1 loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VSdes generation and carbon conversion efficiency (72.56 ± 3.40 mL g−1 and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.

Lysozyme Treatment Makes 16S rRNA Amplicon Sequencing Results Less Biased

2021 ◽  
Author(s):  
Yuting Jiao ◽  
Zijie Gao ◽  
Shiyu Gui ◽  
Lu Ren ◽  
Yongyue Lu ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
Effective Agent ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
16S Rrna Amplicon Sequencing ◽  
Structure Result ◽  
Total Bacteria

Abstract Background Amplicon sequencing is widely applied in gut bacteria structure analysis. However, the proportion of Gram-positive bacteria may greatly affect the results of microbial community analysis. Lysozyme is an effective agent to extract DNA of Gram-positive bacteria. In this study, we assessed the influence of lysozyme treatment on results of Bactrocere dorsalis rectal bacteria structure. Result The results indicated that the total bacteria content can be significantly increased in lysozyme treated samples. Moreover, rectal bacteria diversity was significantly higher in lysozyme treated samples. A detail analysis revealed that abundance of Gram-positive bacteria significantly increased in samples treated with lysozyme. Conclusion This study indicates that lysozyme treatment before DNA extraction is an effective way to reduce bias in bacteria structure analysis, especially for samples with high proportion of Gram-positive bacteria.

scholarly journals Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station

mSystems ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Kasthuri Venkateswaran ◽  
Nitin K. Singh ◽  
Aleksandra Checinska Sielaff ◽  
Robert K. Pope ◽  
Nicholas H. Bergman ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
International Space Station ◽  
Space Station ◽  
Food Poisoning ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Phenotypic Traits ◽  
International Space ◽  
Microbial Population Dynamics

ABSTRACT The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions. In an ongoing Microbial Observatory investigation of the International Space Station (ISS), 11 Bacillus strains (2 from the Kibo Japanese experimental module, 4 from the U.S. segment, and 5 from the Russian module) were isolated and their whole genomes were sequenced. A comparative analysis of the 16S rRNA gene sequences of these isolates showed the highest similarity (>99%) to the Bacillus anthracis-B. cereus-B. thuringiensis group. The fatty acid composition, polar lipid profile, peptidoglycan type, and matrix-assisted laser desorption ionization–time of flight profiles were consistent with the B. cereus sensu lato group. The phenotypic traits such as motile rods, enterotoxin production, lack of capsule, and resistance to gamma phage/penicillin observed in ISS isolates were not characteristics of B. anthracis. Whole-genome sequence characterizations showed that ISS strains had the plcR non-B. anthracis ancestral “C” allele and lacked anthrax toxin-encoding plasmids pXO1 and pXO2, excluding their identification as B. anthracis. The genetic identities of all 11 ISS isolates characterized via gyrB analyses arbitrarily identified them as members of the B. cereus group, but traditional DNA-DNA hybridization (DDH) showed that the ISS isolates are similar to B. anthracis (88% to 90%) but distant from the B. cereus (42%) and B. thuringiensis (48%) type strains. The DDH results were supported by average nucleotide identity (>98.5%) and digital DDH (>86%) analyses. However, the collective phenotypic traits and genomic evidence were the reasons to exclude the ISS isolates from B. anthracis. Nevertheless, multilocus sequence typing and whole-genome single nucleotide polymorphism analyses placed these isolates in a clade that is distinct from previously described members of the B. cereus sensu lato group but closely related to B. anthracis. IMPORTANCE The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions.

scholarly journals Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Liyou Wu ◽  
Chongqing Wen ◽  
Yujia Qin ◽  
Huaqun Yin ◽  
Qichao Tu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Analysis ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis

scholarly journals To rarefy or not to rarefy: Enhancing microbial community analysis through next-generation sequencing

2020 ◽  
Author(s):  
Ellen S. Cameron ◽  
Philip J. Schmidt ◽  
Benjamin J.-M. Tremblay ◽  
Monica B. Emelko ◽  
Kirsten M. Müller
Keyword(s):  
Microbial Community ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
List Type ◽  
Sequencing Data ◽  
Water And Wastewater Treatment ◽  
Library Size ◽  
Size Selection ◽  
The Impact

AbstractThe application of amplicon sequencing in water research provides a rapid and sensitive technique for microbial community analysis in a variety of environments ranging from freshwater lakes to water and wastewater treatment plants. It has revolutionized our ability to study DNA collected from environmental samples by eliminating the challenges associated with lab cultivation and taxonomic identification. DNA sequencing data consist of discrete counts of sequence reads, the total number of which is the library size. Samples may have different library sizes and thus, a normalization technique is required to meaningfully compare them. The process of randomly subsampling sequences to a selected normalized library size from the sample library—rarefying—is one such normalization technique. However, rarefying has been criticized as a normalization technique because data can be omitted through the exclusion of either excess sequences or entire samples, depending on the rarefied library size selected. Although it has been suggested that rarefying should be avoided altogether, we propose that repeatedly rarefying enables (i) characterization of the variation introduced to diversity analyses by this random subsampling and (ii) selection of smaller library sizes where necessary to incorporate all samples in the analysis. Rarefying may be a statistically valid normalization technique, but researchers should evaluate their data to make appropriate decisions regarding library size selection and subsampling type. The impact of normalized library size selection and rarefying with or without replacement in diversity analyses were evaluated herein.Highlights▪ Amplicon sequencing technology for environmental water samples is reviewed▪ Sequencing data must be normalized to allow comparison in diversity analyses▪ Rarefying normalizes library sizes by subsampling from observed sequences▪ Criticisms of data loss through rarefying can be resolved by rarefying repeatedly▪ Rarefying repeatedly characterizes errors introduced by subsampling sequences

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.

scholarly journals Dehalobium species implicated in 2,3,7,8-tetrachloro-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary

2021 ◽  
Author(s):  
Matthew Lee ◽  
Gan Liang ◽  
Sophie I Holland ◽  
Casey O'Farrell ◽  
Keith Osborne ◽  
...  
Keyword(s):  
Enrichment Culture ◽  
Sediment Cores ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
Reductive Dehalogenation ◽  
Anthropogenic Activity ◽  
Contamination Source ◽  
16S Amplicon Sequencing ◽  
Sydney Harbour

Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They are naturally occurring and by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g-1) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) the most toxic and concerning of the PCDD/F congeners. Comparison of congener profiles at the contamination source with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as a more amenable growth substrate enriched only the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TCDD and octachlorodibenzo-p-dibenzodioxin to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F degradation in a marine environment.

scholarly journals A critical perspective on interpreting amplicon sequencing data in soil ecological research

2021 ◽  
Author(s):  
Lauren V. Alteio ◽  
Joana Séneca ◽  
Alberto Canarini ◽  
Roey Angel ◽  
Ksenia Guseva ◽  
...  
Keyword(s):  
Statistical Power ◽  
Marker Gene ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Data Availability ◽  
Microbial Community Analysis ◽  
Sequencing Data ◽  
Spatio Temporal ◽  
Complementary Techniques ◽  
The Impact

Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing studies in soil and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation and availability to improve the rigor of future studies.

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