Biology subjects

Yang, M. I.

Publications and source records attributed to Yang, M. I..

4 recordsLinked to original sources

bioRxiv2023

Microbial community organization during anaerobic wastewater treatment

Amplicon sequencing data and operating data from anaerobic wastewater treatment plants from three Canadian pulp and paper mills were explored using correlation and network modularization approaches to study the microbial community organization and identify relationships between organisms and operating conditions. Each of the digesters contain two or three modules consisting of organisms that cover all trophic stages of anaerobic digestion. These modules are functioning independently from each other, and their relative abundance changes in response to varying operating conditions. The time delay between a change in digester operation and the change in the abundance of microorganisms was investigated using time-lagged operating parameters. This time delay ranged between two to four days and is likely influenced by the growth rates of the anaerobic microorganisms and the digester hydraulic retention time. Digester upsets due to plant shutdown periods and organic overload caused a drastic increase in the population of acetoclastic methanogens, acidogenic fermenters, and syntrophic acid degraders. As a response to impaired process conditions, the same Methanothrix amplicon sequence variant (ASV) dominated methanogenesis in the digesters of all three mills. The common characteristics of the organisms represented by this ASV should be further investigated for their role in alleviating the impact of digester upset conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/553022v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@140e214org.highwire.dtl.DTLVardef@baa227org.highwire.dtl.DTLVardef@ebd2b8org.highwire.dtl.DTLVardef@573194_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Microbial Community Dynamics of a Sequentially Fed Anaerobic Digester Treating Solid Organic Waste

A 50 kg-scale high solids anaerobic digestor comprising six sequentially-fed leach beds with a leachate recirculation system and an upflow anaerobic sludge blanket reactor was operated at 37{degrees}C for 88 weeks. The feedstock contained a constant fibre fraction (a mix of cardboard, boxboard, newsprint, and fine paper) and varying proportions of food waste. Significantly enhanced co-digestion and methane production from the fibres was observed as the proportion of FW was increased. The most abundant 16S rRNA amplicon sequence variant (ASV), classified as Clostridium butyricum, was correlated with the amount of FW in the system and total methane yield. However, methane yield specifically from the fibre fraction was significantly correlated with organisms classified as Candidatus Roizmanbacteria and Spirochaetaceae. These ASVs together with ASVs classified as Anaerovorax and Methanoculleus correlated strongly to other ASVs in the microbial community, suggesting these are vitally important for ecosystem function and methane production. In addition, tracing the fate of microbes derived from incoming food waste helped to diagnose a poor batch of bulking agent. Table of Contents (TOC)/ Abstract Art O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/487789v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@2a191forg.highwire.dtl.DTLVardef@1d7497corg.highwire.dtl.DTLVardef@119a43aorg.highwire.dtl.DTLVardef@6d056e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2019

Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

Intensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient {gamma}-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of -, {beta}-, {gamma}-, and {delta}-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3 {micro}M/day to [~]12 {micro}M/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from {beta} (0.77{+/-}0.15), (0.55{+/-}0.09), {gamma} (0.13{+/-}0.02) to {delta} (0.06{+/-}0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance of Pelobacter and Dehalobacter, especially in the -HCH and {delta}-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of -, {beta}-, {gamma}-, and {delta}-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

microbiology↗

bioRxiv2019

Reductive dehalogenase gene biomarkers differentiate 1,1,1-trichloroethane from 1,1-dichloroethane dechlorination in microcosms and at a field site treated with granular ZVI and guar gum

Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic vs biotic mechanisms as both processes share common transformation products. In this study, we evaluated using the Dhb 16S rRNA gene and specific reductive dehalogenase genes as biomarkers for 1,1,1-TCA and 1,1-dichloroethane (1,1-DCA) dechlorination. We analyzed samples from laboratory groundwater microcosms and from an industrial site where a mixture of granular zero valent iron (ZVI) and guar gum was injected for 1,1,1-TCA remediation. Abiotic and biotic transformation products were monitored and the changes in dechlorinating organisms were tracked using quantitative PCR (qPCR) with primers targeting the Dhb 16S rRNA gene and two functional genes cfrA and dcrA encoding enzymes that dechlorinate 1,1,1-TCA to 1,1-DCA and 1,1-DCA to chloroethane (CA), respectively. The abundance of the cfrA- and dcrA-like genes confirmed that the two dechlorination steps were carried out by two distinct Dhb populations at the site. Using cell yields established in laboratory microcosms along with measured abundances of the Dhb 16S rRNA gene in site samples, biotic and abiotic transformation of 1,1,1-TCA at the site was estimated. The biomarkers used in this study proved useful for tracking biodechlorination of 1,1,1-TCA and 1,1-DCA where both abiotic (e.g. with ZVI) and biotic processes co-occur.

microbiology↗