Biology subjects

Eddie, B. J.

Publications and source records attributed to Eddie, B. J..

4 recordsLinked to original sources

bioRxiv2025

Microbial community of a colloidal activated carbon barrier at a perfluoroalkyl substance impacted site and sorption of perfluorooctanesulfonic acid by bacteria

Per- and polyfluorinated alkyl substances (PFAS) including perfluorooctanesulfonic acid (PFOS) are extremely refractory anthropogenic compounds that are widespread in the environment. Their fate and transport are of increasing interest, including the ways that biological activity may affect the efficiency of state-of-the-art mitigation efforts, such as colloidal activated carbon (CAC) injection. The microbial communities of sediments in and around a CAC barrier from 2.7 to 9 m below surface were investigated using 16S ribosomal RNA amplicon sequencing and strains isolated from the samples. The microbial community consisted of taxa commonly associated with the subsurface environment, including a high proportion of Bathyarchaeota in the deeper samples. The presence of PFAS or the CAC barrier used to treat it affected the microbial community. Bacteria in the order Peptococcales had higher relative abundance in the CAC barrier than upstream or downstream of it. The inverse Simpson index decreased with depth, indicating less variety in the microbes that were present, but was higher in the samples downstream of the CAC barrier, which may indicate an impact of the PFAS on the microbial community. The sorption of PFOS was investigated for six newly isolated strains as well as four other strains, and results indicate that sorption of PFOS by different species or genera of bacteria is more variable than previously thought. These results suggest that the microbial community could play a role in the mobility of PFAS within subsurface waters, and emphasizes the need to understand the subsurface microbial community and its interactions with PFAS.

microbiology↗

bioRxiv2022

Conservation of energetic pathways for electroautotrophy in the uncultivated candidate order Tenderiales

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics we identified conserved orthologous genes within the Tenderiales and nearest neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga". The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane bound energy transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggests the Tenderiales have an distribution unlimited ecological role coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. ImportanceElectromicrobiology enables enrichment and identification of chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation. The recently described order Tenderiales contains the uncultivated electroautotroph "Candidatus Tenderia electrophaga". The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome assembled genomes. This conservation extends to near neighbors of the Tenderiales, but not to other well-studied chemolithotrophs including iron and sulfur oxidizers. Our findings suggest that extracellular electron uptake may be pervasive among the Tenderiales and the geographic location from which metagenome assembled genomes were recovered offers clues to their natural ecological niche.

microbiology↗

bioRxiv2020

A Prokaryotic Membrane Sculpting BAR Domain Protein

Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here we report the first prokaryotic BAR domain protein, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and scaffolding OMEs into a consistent diameter and curvature. Cryogenic transmission electron microscopy reveals a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubes produced by the wild type strain. Overexpression of BdpA promotes OME formation during conditions where they are less common. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane curvature in vivo, we propose that BdpA and its homologs comprise a newly identified class of prokaryotic BAR (P-BAR) domains.

microbiology↗

bioRxiv2017

dRNA-seq implicates sulfide as master regulator of S(0) metabolism in Chlorobaculum tepidum and other green sulfur bacteria

The green sulfur bacteria (Chlorobiaceae) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S(0), and thiosulfate) as electron donors for photoautotrophic growth. Chlorobaculum tepidum, the model system for the Chlorobiaceae, both produces and consumes extracellular S(0) globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added to Cba. tepidum growing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e. specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA-seq (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S(0), and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor dependent transcriptional regulation. These motifs were conserved across homologous Chlorobiaceae promoters. Two lines of evidence suggest that sulfide mediated repression is the dominant regulatory mode in Cba. tepidum. First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the gene CT1277, encoding a putative regulatory protein, leads to constitutive over-expression of the sulfide:quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism in Cba. tepidum and the Chlorobiaceae. Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology in Cba. tepidum and perhaps other Chlorobiaceae.\n\nImportanceElemental sulfur is a key intermediate in biogeochemical sulfur cycling. The photoautotrophic green sulfur bacterium Chlorobaculum tepidum both produces and consumes elemental sulfur depending on the availability of sulfide in the environment. Our results reveal transcriptional dynamics of Chlorobaculum tepidum on elemental sulfur, and increase our understanding of the mechanisms of transcriptional regulation governing growth on different reduced sulfur compounds. This study identifies new genes and sequence motifs that likely play significant roles in the production and consumption of elemental sulfur. Beyond this focused impact, this study paves the way for the development of synthetic biology in Chlorobaculum tepidum and other Chlorobiaceae by providing a comprehensive identification of promoter elements to control gene expression, a key element of strain engineering.

microbiology↗