Biology subjects

Grettenberger, C. L.

Publications and source records attributed to Grettenberger, C. L..

5 recordsLinked to original sources

bioRxiv2026

Environmental filtering, dispersal limitation, and competition control the distribution of acidophilic iron oxidizers

Acid mine drainage is a global pollution problem characterized by low pH and high concentrations of metals. Active remediation is often cost-prohibitive, but Fe(II) oxidizing microbes may be used for passive bioremediation. To leverage these species, we must understand the factors that control their distribution. Here, we examine the environmental and ecological factors that control these species with the aim of determining if microbial seeding is a viable remediation strategy. Although stochastic processes appear to control the distribution of majority of taxa inhabiting AMD ecosystems, the distribution of Fe(II) oxidizers is driven by environmental filtering and competition. The abundance of all the major Fe(II) oxidizing genera have significant relationships with pH, with pH explaining 10 - 38% of the variation in their abundance. The genera appear to have pH preferences with Acidithiobacillus and Leptospirillum preferring environments below pH 3, Gallionella, Sideroxydans, and Ferritrophicum preferring environments above pH 3.5, and Ferrovum preferring intermediate pH environments. Once the effect of pH is removed, genera that share pH preferences are negatively correlated, indicating that they are likely competing for the Fe(II) oxidizing niche in their preferred environments. Communities are also shaped by dispersal limitation, which suggests that microbial seeding is possible in these environments. Future seeding attempts should consider species interactions and ecology more generally to inform their efforts.

microbiology↗

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↗

bioRxiv2020

Metagenome assembled genomes of novel taxa from an acid mine drainage environment

ABSTRACTAcid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and include one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies.IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.View Full Text

microbiology↗

bioRxiv2019

Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site

BackgroundFerrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY.\n\nResultsHere we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp.. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis.\n\nConclusionsPreviously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.

microbiology↗

bioRxiv2018

Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium

Atmospheric oxygen level rose dramatically around 2.4 billion years ago due to oxygenic photosynthesis by the Cyanobacteria. The oxidation of surface environments permanently changed the future of life on Earth, yet the evolutionary processes leading to oxygen production are poorly constrained. Partial records of these evolutionary steps are preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Melainabacteria, crown-group Cyanobacteria, and Gloeobacter, representing the earliest-branching Cyanobacteria capable of oxygenic photosynthesis. Here, we describe nearly complete, metagenome assembled genomes of an uncultured organism phylogenetically placed between the Melainabacteria and crown-group Cyanobacteria, for which we propose the name Candidatus Aurora vandensis {au.rora Latin noun dawn and vand.ensis, originating from Vanda}.\n\nThe metagenome assembled genome of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many extrinsic proteins associated with the photosystems in other species are, however, missing or poorly conserved. The assembled genome also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Based on the content of the genome, we propose an evolutionary model for increasing efficiency of oxygenic photosynthesis through the evolution of extrinsic proteins to stabilize photosystem II and I reaction centers and improve photon capture. This model suggests that the evolution of oxygenic photosynthesis may have significantly preceded oxidation of Earths atmosphere due to low net oxygen production by early Cyanobacteria.

microbiology↗