Biology subjects

Macalady, J.

Publications and source records attributed to Macalady, J..

3 recordsLinked to original sources

bioRxiv2025

Metabolic diversity of the Ferrovales and potential contributions to iron oxidation

Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially-mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovales are a common Fe-oxidizing bacterial group observed in AMD globally and thus could be an exceptional target for bioremediation strategies. However, Ferrovales are difficult to culture and both phylogenetically and metabolically diverse. To better understand the potential for Ferrovales to contribute to AMD bioremediation, we circumvented limitations in culture-based approaches and analyzed 240 genomes and metagenome assembled genomes from the Ferrovales, including taxa from AMD sites with high iron oxidation rates. The phylogenetic and physiological diversity of this group was greater than previously known and multiple Ferrovales taxa can co-occur. For example, we observed taxa that varied in mobility (based on the presence or absence of flagellar biosynthesis genes) and taxa that encode multiple iron oxidation pathways. We also identified Ferrovales that are likely capable of anoxygenic photosynthesis. Our data suggest that differences in physiology promote niche differentiation along resource axes and co-occurrence of multiple taxa. Its possible that multiple co-occurring iron oxidizing taxa could support a more robust microbial community, resulting in higher iron oxidation rates and more efficient bioremediation. ImportanceAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation, the use of living things for the remediation of contaminated sites, because they drive biogeochemical processes in these ecosystems. Iron-oxidizing microbial species remove iron from AMD effluent, and the iron oxides sorb other trace metals. These communities vary across sites and differ in how rapidly they oxidize iron. Therefore, it is difficult to effectively use them for bioremediation. Ferrovales are common iron-oxidizing taxa in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovales to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovales in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovales as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity may lead to the co-occurrence of multiple Ferrovales species. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.

microbiology↗

bioRxiv2022

Convergent community assembly among globally separated acidic cave biofilms

Acidophilic bacteria and archaea inhabit extreme geochemical islands that can tell us when and how geographic barriers affect the biogeography of microorganisms. Here we describe microbial communities from extremely acidic (pH 0-1) biofilms known as "snottites" from hydrogen sulfide-rich caves around the world. Given the extreme acidity and subsurface location of these biofilms, and in light of earlier work showing strong geographic patterns among snottite Acidithiobacillus populations, we investigated their structure and diversity in order to understand how geography might impact community assembly. We used 16S rRNA gene cloning and fluorescence in situ hybridization (FISH) to investigate 26 snottite samples from four sulfidic caves in Italy and Mexico. All samples had very low biodiversity and were dominated by sulfur-oxidizing bacteria in the genus Acidithiobacillus. Ferroplasma and other archaea in the Thermoplasmatales ranged from 0 to 50% of total cells, and relatives of the bacterial genera Acidimicrobium and Ferrimicrobium were up to 15% of total cells. Rare phylotypes included Sulfobacillus spp. and members of the Dependentiae and Saccharibacteria (formerly TM6 and TM7). Although the same genera of acidophiles occurred in snottites on separate continents, most members of those genera represent substantially divergent populations with 16S rRNA genes that are only 95-98% similar. Our findings are consistent with a model of community assembly where sulfidic caves are stochastically colonized by microorganisms from local sources, which are strongly filtered through selection for extreme acid tolerance, and these different colonization histories are maintained by dispersal restrictions within and among caves. ImportanceMicroorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation. Understanding the factors that govern their ecology and distribution can help us better predict and utilize their activities in natural and engineered systems. However, extremely acidic habitats are unusual in that they are almost always isolated within circumneutral landscapes. So where did their acid-adapted inhabitants come from, and how do new colonists arrive and become established? In this study, we took advantage of a unique natural experiment in Earths subsurface to show how isolation may have played a role in the colonization history, community assembly, and diversity of highly acidic microbial biofilms.

microbiology↗

bioRxiv2019

Another chemolithotrophic metabolism missing in nature--sulfur comproportionation

Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation-reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy ({Delta}Gr) can identify whether a reaction is thermodynamically favorable, and the accompanying energy yield at the temperature, pressure, and chemical composition in the system of interest. Based on carefully calculated values of {Delta}Gr, we predict a novel microbial metabolism--sulfur comproportionation (3H2S + SO42- + 2H+ = 4S0 + 4H2O). We show that at elevated concentrations of sulfide and sulfate in acidic environments over a broad temperature range, this putative metabolism can be exergonic ({Delta}Gr<0), yielding [~]30-50 kJ/mol. We suggest that this may be sufficient energy to support a chemolithotrophic metabolism currently missing in nature. Other versions of this metabolism, to thiosulfate (H2S + SO42- = S2O32- + H2O) and to sulfite (H2S + 3SO42- = 4SO32- + 2H+), are only moderately exergonic or endergonic even at ideal geochemical conditions. Natural and impacted environments, including sulfidic karst systems, shallow-sea hydrothermal vents, sites of acid mine drainage, and acid-sulfate crater lakes, may be ideal hunting grounds for finding microbial sulfur comproportionators.

microbiology↗