Biology subjects

Elias, D. A.

Publications and source records attributed to Elias, D. A..

3 recordsLinked to original sources

bioRxiv2022

Transcriptional control of hgcAB by an ArsR-like regulator in Pseudodesulfovibrio mercurii ND132

The hgcAB gene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg-methylator Pseudodesulfovibrio mercurii ND132, we specifically evaluated transcriptional control of hgcAB by a putative ArsR encoded upstream and co-transcribed with hgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosyl-homocysteine (SAH) responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR in Pseudodesulfovibrio mercurii ND132. Using qPCR and RNA-seq analyses we confirmed this ArsR regulates hgcAB transcription, and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link between hgcAB activity and arsenic transformations by Pseudodesulfovibrio mercurii ND132, with significant up-regulation of other ArsR-regulated arsenic resistance operons alongside hgcAB. Interestingly, wild-type ND132 was less sensitive to AsV (but not AsIII) than an hgcAB knockout strain, supporting the idea that hgcAB may be linked to arsenic resistance. Arsenic significantly impacted Hg-methylation rates by ND132, however, responses varied with culture conditions. Differences in growth and overall metabolic activity did not account for arsenic impacts on methylation. One goal of this research is to better predict MeHg production in nature. However, we found that hgcAB gene and transcript abundance was not a good predictor of Hg-methylation rates. Our finding that hgcAB activity is linked to arsenic may hold clues to the possible environmental drivers of horizontal transfer of hgcAB. IMPORTANCEThis work reveals a link between microbial mercury methylation and arsenic resistance and may hold clues to the evolution of mercury methylation genes (hgcAB). Microbes with hgcAB produce methylmercury, a strong neurotoxin that readily accumulates in the food web. This study addresses a critical gap in our understanding about the environmental factors that control hgcAB expression. We show that hgcAB expression is controlled by an ArsR-like regulator responsive to both arsenic and S-adenosyl-homocysteine in our model organism, Pseudodesulfovibrio mercurii ND132. Exposure to arsenic also significantly impacted Pseudodesulfovibrio mercurii ND132 mercury methylation rates. However, expression of hgcAB was not always a good predictor of Hg methylation rates, highlighting the roles of Hg bioavailability and other biochemical mechanisms in methylmercury production. This study improves our understanding of the controls on hgcAB expression which is needed to better predict environmental methylmercury production.

microbiology↗

bioRxiv2020

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate-reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.

microbiology↗

bioRxiv2019

Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated environments. To provide site assessment for a larger study, we processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater from the ENIGMA Field Research Site at the United States Department of Energy (DOE) Oak Ridge Reservation (ORR). We compared fresh core sediments by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including contaminants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. This environmental systems approach provided detailed site-specific biogeochemical information from the various properties of subsurface media to reveal the influences of solid, liquid, and gas phases. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate- reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. This suggested that groundwater predominantly flowed through preferential paths with high flux and little mixing with water in the interstices of sediment particles, which could impact microbial activity. The abundant clay minerals with high surface area and high water-holding capacity of micro-pores of the fine clay rich layer suggest suppression of nutrient supply to microbes from the surface. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of highly toxic elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.

systems biology↗