Biology subjects

Flynn, T. M.

Publications and source records attributed to Flynn, T. M..

4 recordsLinked to original sources

bioRxiv2024

Effects of Soluble Electron Shuttles on Microbial Iron Reduction and Methanogenesis

In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 V and -0.340 V. Fe(III) reduction coupled to acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2,-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment. ImportanceIron is the fourth most abundant element in the Earths crust and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes are capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments is unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on the microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.

microbiology↗

bioRxiv2022

Inhibition of Microbial Methane Oxidation by 2-Chloro-6-Methylpyridine

Several pyridine derivatives including the pesticide nitrapyrin [2-chloro-6-(trichloromethyl) pyridine] are strong inhibitors of methane monooxygenase, a key enzyme of aerobic methane (CH4) oxidation. In this study we examined the effects of 2-chloro-6-methylpyridine (2C6MP) concentration on aerobic CH4 oxidation and the development of populations of putative methanotrophs in sediment from Old Woman Creek, a freshwater estuary in Huron Co., Ohio. Experimental systems were prepared in serum bottles containing minimal medium with a headspace containing 20% O2 and 10% CH4. The microcosms were spiked with 2C6MP to achieve concentrations of 0, 0.1, 1, or 10 mM and inoculated with sediment. When headspace CH4 concentrations decreased from 10% to < 2%, subsamples were taken for DNA extraction and sequencing of 16S rRNA gene amplicons. There was minimal effect of 2C6MP on CH4 oxidation at concentrations of 0.1, and 1 mM, but complete inhibition for > 20 months was observed at 10 mM. ANOSIM of weighted UniFrac distances between groups of triplicate samples supported a primary distinction of the inoculum relative to the enrichments (R=0.999) and a secondary distinction between bottles containing 2C6MP versus those without (R=0.464 [0.1 mM]; R=0.894 [1 mM]). The inoculum was dominated by members of the Proteobacteria (49.9{+/-}1.5%), and to a lesser extent by Bacteroidetes (8.8{+/-}0.2%), Acidobacteria (8.9{+/-}0.4%), and Verrucomicrobia (4.4{+/-}0.3%). In enrichments with or without 2C6MP, Proteobacteria expanded to comprise 65-70% of the total. In the absence of inhibitor, members of the Methylococcaceae and Methylophilaceae increased in relative abundance from < 0.1% of the inoculum to 8.5{+/-}1.0% and 13.4{+/-}2.3%, of the total community respectively. At both 0.1 and 1 mM concentrations of the inhibitor, the Methylococcaceae were much less abundant, representing 3.3{+/-}0.5% and 2.8{+/-}3.3% respectively. No inhibition of the Methylophilaceae was seen at the lower concentration of 2C6MP, but at the higher concentration this taxon was only 7.8{+/-}1.1% of the total. In contrast, members of the Crenotrichaceae, another group of methane oxidizers, increased in relative abundance with greater amounts of inhibitor, representing 8.6{+/-}3.6% of the total at 0.1 mM and 12.0{+/-}4.5% at 1 mM, compared to only 4.1{+/-}0.4% when no inhibitor was present. These results clearly show changes in the populations of putative aerobic methanotrophs relative to the amount of 2C6MP present.

microbiology↗

bioRxiv2020

Contrasting Variable and Stable Subsurface Microbial Populations: an ecological time series analysis from the Deep Mine Microbial Observatory, South Dakota, USA

The deep subsurface contains a vast reservoir of microbial life. While recent studies have revealed critical details about this biosphere including the sheer diversity of microbial taxa and their metabolic potential, long-term monitoring of deep subsurface microbial populations is rare, thus limiting our understanding of subsurface microbial population dynamics. Here we present a four-year time series analysis of subsurface microbial life from the Deep Mine Microbial Observatory (DeMMO), Lead, SD, USA. We find distinct and diverse populations inhabiting each of 6 sites over this ~1.5 km deep slice of terrestrial crust, corresponding to distinct geochemical habitats. Alpha diversity decreases with depth and beta diversity measures clearly differentiate samples by site over time, even during substantial perturbations. Population dynamics are driven by a subset of variable (and often relatively abundant) OTUs, but the vast majority of detected OTUs are stable through time, constituting a core microbial community. The phylogenetic affiliations of both stable and variable taxa, including putative sulfate reducers, methanogens, spore formers, and many uncultivated lineages, are similar to those found previously in subsurface environments. This work reveals the dynamic nature of the terrestrial subsurface, contributing to a more holistic understanding than can be achieved when viewing shorter timeframes. Originality-Significance StatementThis four-year record of deep mine microbial diversity and geochemistry is the first of its kind and allows for direct investigation of temporal trends in deep subsurface biogeochemistry. We identify disparate populations of variable and stable taxa, suggesting the presence of a core deep subsurface microbiome with unique niche partitioning.

ecology↗

bioRxiv2017

Community dynamics in parallelized, aerobic, single carbon-source enrichments

Here we seek to test the extent to which laboratory enrichments mimic natural community processes and the degree to which the initial structure of a community determines its response to a press disturbance via the addition of environmentally-relevant carbon compounds. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from 6 different classes of organic compound (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 hours, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still is strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g. Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g. Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Niche selection therefore seems to play a strong role in shaping the communities in the substrate arrays, although some stochasticity is seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to a changing environment.

microbiology↗