Global transcriptional analysis of Geobacter sulfurreducens under palladium reducing conditions reveals new key cytochromes involved

Abstract

Geobacter sulfurreducens is capable of reducing Pd(II) to Pd(0) using acetate as electron donor; however, the biochemical and genetic mechanisms involved in this process have not been described. In this work, we carried out transcriptome profiling analysis to identify the genes involved in Pd(II) reduction in this bacterium. Our results showed that 252 genes were upregulated while 141 were downregulated during Pd(II) reduction. Among the upregulated genes, 12 were related to energy metabolism and electron transport; 50 were classified as involved in protein synthesis; 42 were associated with regulatory functions and transcription, and 47 have no homologs with known function. RT-qPCR data confirmed upregulation of genes encoding PilA, the structural protein for the electrically conductive pili, as well as c-type cytochromes GSU1062, GSU2513, GSU2808, GSU2934, GSU3107, OmcH, OmcM, PpcA, PpcD under Pd(II)-reducing conditions. ΔpilA and ΔpilR mutant strains showed 20% and 40% decrease in the Pd(II)-reducing capacity, respectively, compared to the wild type strain, indicating the central role of the pili in this process. RT-qPCR data collected during Pd(II) reduction also confirmed downregulation of the omcB, omcC, omcZ, and omcS genes, which have been shown to be involved in Fe(III) reduction and electrodes. Based on these results, we propose mechanisms involved in Pd(II) reduction by G. sulfurreducens. ImportanceGeobacter sulfurreducens is a versatile microorganism, known for its ability to reduce a wide range of environmentally relevant metals. It has been reported that this bacterium synthesizes palladium nanoparticles successfully. Yet, the biochemical and genetic mechanisms involved in this process had not been described previously. By using a transcriptome profile analysis to identify genes implicated in this process and genetic and physiological data, we propose a model for the biological reduction of Pd(II) by G.sulfurreducens. Moreover, the study also revealed the microbial reduction of Pd(II) coupled to growth, which shows not only unexpected ideas about its complex metabolism, but some key cytochromes involved in this pathway, which have not been previously associated with other metal reducing process for this bacterium. In brief the present work contributes to a better understanding of the biochemical and genetic mechanisms involved in Pd(II) reduction and put forward novel insights about G. sulfurreducens metabolism.

Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov.

“…Members of the family Geobacteraceae were identified as Gram-stain negative, chemoheterotrophic, anaerobic, and capable of reducing Fe(III), Mn(IV), U(VI), elemental sulfur, and humic substances (Childers et al, 2002; Coppi et al, 2007; Prakash et al, 2010; Lovley et al, 2011). Some members were also reported to use other polluting metal ions as electron acceptors, such as Co(III), V(V), Cr(VI), Ag(I), Hg(II), Np(V), and Pu(IV), indicating that Geobacteraceae strains have important geochemical effects on natural environments (Lovley et al, 2011; Hernández-Eligio et al, 2018). Other features including extracellular electron transfer, dechlorinating activity, and indirectly contributing to methane production have been well-studied in Geobacteraceae (Lovley et al, 2011; Rotaru et al, 2014).…”

Characterization and significance of extracellular polymeric substances, reactive oxygen species, and extracellular electron transfer in methanogenic biocathode

“…Previous studies reported that some bacteria (e.g., Enterobacteriaceae , Desulfovibrio , etc.) found in cathode biofilms in this study could express different cytochromes and/or conductive pili (Gardy et al, 2003; Hernández-Eligio et al, 2020). The expression of these genes was quite comparable in both carbon fibers and stainless-steel cathode electrodes.…”

“…Notably, some bacteria (e.g., Enterobacteriaceae, Desulfovibrio, etc.) found in biocathode in this study could express different cytochromes and/or conductive pili 74,77 . Furthermore, a recent study suggested that Methanobacterium species could produce methane via DIET 78 .…”

“…These genes showed trivial differences in expression levels in anode biofilms between both reactors, suggesting that higher current density from the CF-SS reactor was not attributed to the overexpression of genes regulating anodic EET. The EET from EAB to the anode has been demonstrated to be facilitated via c-type cytochromes and conductive nanowire or pili (Hernández-Eligio et al, 2020), while fundamental aspects of EET mechanisms in methanogenic biocathode (i.e., direct electron transport from the electrode to methanogens) is still not well understood. Previous reports postulated that conductive pili and c-type cytochromes could play an important role in EET to electrotrophic methanogens from DIET-partners (i.e., electroactive bacteria) (Park et al, 2018b; Rotaru et al, 2014).…”

“…Based on the authors' knowledge, this study first reports the expression of EET genes for methanogenic biocathode. The EET from EAB to the anode has been demonstrated to be facilitated via c-type cytochromes and conductive nanowire or pili 74 , while the significance of EET in methanogenic biocathode is still ambiguous. However, previous reports postulated that conductive pili and c-type cytochromes could play an important role in DIET from EAB to methanogens 75,76 .…”