Biology subjects

Dworatzek, S.

Publications and source records attributed to Dworatzek, S..

4 recordsLinked to original sources

bioRxiv2024

What we can find in what's left behind: DNA metabarcoding of semi-aquatic insect exuviae

Semi-aquatic insects contribute to critical ecological functioning of freshwater habitats in both the aquatic and terrestrial phase of their life. Traditional methods of studying their emergence rely on the capture of insects as they emerge, and morphological identification with taxonomic keys. This is not only time consuming but can have large impacts on the study population, obstacles that can be removed by the use of DNA. This study investigated the potential of using exuviae collected from the water surface as DNA source. Both emergence trap samples and insect exuviae were collected from a constructed wetland and a small creek in southern Ontario. Metabarcoding provided a total of 40 samples with 254 distinct taxa from emergence traps (26 samples), and 135 from exuviae (14 samples). There were many similarities between both two sample types, especially for the rich chironomid diversity. Nonetheless, the exuviae samples were able to identify more orders containing semi-aquatic insects. Furthermore, they showed a higher level of diversity within these orders. This higher level of diversity seen in exuviae samples may be due to limitations of emergence traps, such as they only account for a small defined surface area. In contrast, exuviae are representing a much larger area and are free floating, thus collection of emerging taxa is not limited to the emerging site. We were able to show that identification of emerging aquatic insects through metabarcoding of exuviae is a useful method for the study of insect emergence.

ecology↗

bioRxiv2023

A multifunctional Dehalobacter? Tandem chloroform and dichloromethane degradation in a mixed microbial culture

Chloroform (CF) and dichloromethane (DCM) contaminate groundwater sites around the world, which can be remediated through bioaugmentation. Although several strains of Dehalobacter restrictus can reduce CF to DCM, and multiple Peptococcaceae can ferment DCM, these processes cannot happen simultaneously due to CF sensitivity in the known DCM-degraders or electron donor competition. Here we present a mixed microbial culture that can simultaneously metabolize CF and DCM to carbon dioxide and create an additional enrichment culture fed only DCM. Through species-specific qPCR, we find that a Dehalobacter strain grows both while CF alone and DCM alone are converted, indicating its involvement in both metabolic steps. Additionally, the culture was maintained for over 1400 days without addition of exogenous electron donor, and through electron balance calculations we show that DCM mineralization produces sufficient reducing equivalents (likely hydrogen) for CF respiration. Together, these results suggest intraspecies electron transfer could occur to continually reduce CF in the culture. Minimizing the addition of electron donor reduces the cost of bioremediation, and understanding this mechanism informs strategies for culture maintenance and scale-up, and benefits contaminated sites where the culture is employed for remediation worldwide. SYNOPSISDechlorination of chloroform to dichloromethane and dichloromethane mineralization are performed concurrently by a Dehalobacter-containing mixed microbial community without provision of exogenous electron donor. TOC ART O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/552028v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@8e3002org.highwire.dtl.DTLVardef@f1d396org.highwire.dtl.DTLVardef@7a59dborg.highwire.dtl.DTLVardef@a179bc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Anaerobic Benzene Biodegradation Linked to Growth of Highly Specific Bacterial Clades

Reliance on bioremediation to remove benzene from anoxic environments has proven risky for decades but for unknown reasons. Years of research have revealed a strong link between anaerobic benzene biodegradation and the enrichment of highly specific microbes, namely Thermincola in the family Peptococcaceae and the deltaproteobacterial Candidate Sva0485 clade. Using aquifer material from Canadian Forces Base Borden, we compared five bioremediation approaches in batch microcosms. Under conditions simulating natural attenuation or sulfate biostimulation, benzene was not degraded after 1-2 years of incubation and no enrichment of known benzene-degrading microbes occurred. In contrast, nitrate-amended microcosms reported benzene biodegradation coincident with significant growth of Thermincola spp., along with a functional gene presumed to catalyze anaerobic benzene carboxylation (abcA). Inoculation with 2.5% of a methanogenic benzene-degrading consortium containing Sva0485 (Deltaproteobacteria ORM2) resulted in benzene biodegradation in the presence of sulfate or under methanogenic conditions. The presence of other hydrocarbon co-contaminants decreased rates of benzene degradation by a factor of 2-4. Tracking the abundance of the abcA gene and 16S rRNA genes specific for benzene-degrading Thermincola and Sva0485 is recommended to monitor benzene bioremediation in anoxic groundwater systems to further uncover growth rate limiting conditions for these two intriguing phylotypes. SYNOPSISAnaerobic benzene biodegradation was accelerated by biostimulation with nitrate or by bioaugmentation under methanogenic or sulfate-reducing conditions.

microbiology↗

bioRxiv2017

Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater

Individual Dehalococcoides mccartyi (Dhc) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes contained within their respective genomes. While thousands of rdhA genes have been sequenced, the activity of the corresponding proteins have been identified in only a handful of cases. Most effort has focused on identifying the enzymes that dechlorinate substrates including trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC) relevant to groundwater remediation. The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used to track growth and dechlorinating activity in DNA extracted from field samples. In this study, we augmented the typical suite of three characterized rdhA genes to include an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed Dhc-containing culture KB-1 to track population shifts within the culture and at two bioaugmented field sites. Quantitative PCR assays were developed for the 15 selected D. mccartyi rdhA genes and evaluated using 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to Dhc 16S gene copies indicated the presence of multiple distinct Dhc populations in each culture. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi populations and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples obtained from two bioaugmented field sites. Growth of the dominant D. mccartyi population in the KB-1 inoculum was detected in the UK site samples. At both field sites, the measurement of relative rdhA abundances revaled significant D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene, indicating that the selective pressure of the most abundant chlorinated electron acceptor that was observed in lab cultures was also occurring in the populations in the field. Understanding driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.

microbiology↗