@article {3051, title = {Direct microbial electron uptake as a mechanism for stainless steel corrosion in aerobic environments.}, journal = {Water Res}, volume = {219}, year = {2022}, month = {2022 Jul 01}, pages = {118553}, abstract = {

Shewanella oneidensis MR-1 is an attractive model microbe for elucidating the biofilm-metal interactions that contribute to the billions of dollars in corrosion damage to industrial applications each year. Multiple mechanisms for S. oneidensis-enhanced corrosion have been proposed, but none of these mechanisms have previously been rigorously investigated with methods that rule out alternative routes for electron transfer. We found that S. oneidensis grown under aerobic conditions formed thick biofilms (\~{}50~{\textmu}m) on stainless steel coupons, accelerating corrosion over sterile controls. H and flavins were ruled out as intermediary electron carriers because stainless steel did not reduce riboflavin and previous studies have demonstrated stainless does not generate H. Strain ∆mtrCBA, in which the genes for the most abundant porin-cytochrome conduit in S. oneidensis were deleted, corroded stainless steel substantially less than wild-type in aerobic cultures. Wild-type biofilms readily reduced nitrate with stainless steel as the sole electron donor under anaerobic conditions, but strain ∆mtrCBA did not. These results demonstrate that S. oneidensis can directly consume electrons from iron-containing metals and illustrate how direct metal-to-microbe electron transfer can be an important route for corrosion, even in aerobic environments.

}, keywords = {Biofilms, Corrosion, Electron Transport, Electrons, Metals, Oxidation-Reduction, Stainless Steel, Steel}, issn = {1879-2448}, doi = {10.1016/j.watres.2022.118553}, author = {Zhou, Enze and Li, Feng and Zhang, Dawei and Xu, Dake and Li, Zhong and Jia, Ru and Jin, Yuting and Song, Hao and Li, Huabing and Wang, Qiang and Wang, Jianjun and Li, Xiaogang and Gu, Tingyue and Homborg, Axel M and Mol, Johannes M C and Smith, Jessica A and Wang, Fuhui and Lovley, Derek R} } @article {3060, title = {Microbial corrosion of metals: The corrosion microbiome.}, journal = {Adv Microb Physiol}, volume = {78}, year = {2021}, month = {2021}, pages = {317-390}, abstract = {

Microbially catalyzed corrosion of metals is a substantial economic concern. Aerobic microbes primarily enhance Fe oxidation through indirect mechanisms and their impact appears to be limited compared to anaerobic microbes. Several anaerobic mechanisms are known to accelerate Fe oxidation. Microbes can consume H abiotically generated from the oxidation of Fe. Microbial H removal makes continued Fe oxidation more thermodynamically favorable. Extracellular hydrogenases further accelerate Fe oxidation. Organic electron shuttles such as flavins, phenazines, and possibly humic substances may replace H as the electron carrier between Fe and cells. Direct Fe-to-microbe electron transfer is also possible. Which of these anaerobic mechanisms predominates in model pure culture isolates is typically poorly documented because of a lack of functional genetic studies. Microbial mechanisms for Fe oxidation may also apply to some other metals. An ultimate goal of microbial metal corrosion research is to develop molecular tools to diagnose the occurrence, mechanisms, and rates of metal corrosion to guide the implementation of the most effective mitigation strategies. A systems biology approach that includes innovative isolation and characterization methods, as well as functional genomic investigations, will be required in order to identify the diagnostic features to be gleaned from meta-omic analysis of corroding materials. A better understanding of microbial metal corrosion mechanisms is expected to lead to new corrosion mitigation strategies. The understanding of the corrosion microbiome is clearly in its infancy, but interdisciplinary electrochemical, microbiological, and molecular tools are available to make rapid progress in this field.

}, keywords = {Corrosion, Electron Transport, Metals, Microbiota, Oxidation-Reduction}, issn = {2162-5468}, doi = {10.1016/bs.ampbs.2021.01.002}, author = {Lekbach, Yassir and Liu, Tao and Li, Yingchao and Moradi, Masoumeh and Dou, Wenwen and Xu, Dake and Smith, Jessica A and Lovley, Derek R} } @article {3062, title = {Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species.}, journal = {ISME J}, volume = {15}, year = {2021}, month = {2021 Oct}, pages = {3084-3093}, abstract = {

Microbial corrosion of iron-based materials is a substantial economic problem. A mechanistic understanding is required to develop mitigation strategies, but previous mechanistic studies have been limited to investigations with relatively pure Fe(0), which is not a common structural material. We report here that the mechanism for microbial corrosion of stainless steel, the metal of choice for many actual applications, can be significantly different from that~for Fe(0). Although H is often an intermediary electron carrier between the metal and microbes during Fe(0) corrosion, we found that H is not abiotically produced from stainless steel, making this corrosion mechanism unlikely. Geobacter sulfurreducens and Geobacter metallireducens, electrotrophs that are known to directly accept electrons from other microbes or electrodes, extracted electrons from stainless steel via direct iron-to-microbe electron transfer. Genetic modification to prevent H consumption did not negatively impact on stainless steel corrosion. Corrosion was inhibited when genes for outer-surface cytochromes that are key electrical contacts were deleted. These results indicate that a common model of microbial Fe(0) corrosion~by hydrogenase-positive microbes, in which H serves as an intermediary electron carrier between the metal surface and the microbe, may not apply to the microbial corrosion of stainless steel. However, direct iron-to-microbe electron transfer is a~feasible route for stainless steel corrosion.

}, keywords = {Corrosion, Electrons, Geobacter, Iron, Stainless Steel}, issn = {1751-7370}, doi = {10.1038/s41396-021-00990-2}, author = {Tang, Hai-Yan and Yang, Chuntian and Ueki, Toshiyuki and Pittman, Conor C and Xu, Dake and Woodard, Trevor L and Holmes, Dawn E and Gu, Tingyue and Wang, Fuhui and Lovley, Derek R} } @article {3102, title = {Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili.}, journal = {Sci Rep}, volume = {6}, year = {2016}, month = {2016 Mar 22}, pages = {23385}, abstract = {

The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.

}, keywords = {Electric Conductivity, Fimbriae, Bacterial, Geobacter, Models, Theoretical}, issn = {2045-2322}, doi = {10.1038/srep23385}, author = {Xiao, Ke and Malvankar, Nikhil S and Shu, Chuanjun and Martz, Eric and Lovley, Derek R and Sun, Xiao} } @article {3101, title = {Synthetic Biological Protein Nanowires with High Conductivity.}, journal = {Small}, volume = {12}, year = {2016}, month = {2016 Sep}, pages = {4481-5}, abstract = {

Genetic modification to add tryptophan to PilA, the monomer for the electrically conductive pili of Geobacter sulfurreducens, yields conductive protein filaments 2000-fold more conductive than the wild-type pili while cutting the diameter in half to 1.5 nm.

}, keywords = {Amino Acid Sequence, Electric Conductivity, Fimbriae, Bacterial, Geobacter, Nanowires, Proteins, Tryptophan}, issn = {1613-6829}, doi = {10.1002/smll.201601112}, author = {Tan, Yang and Adhikari, Ramesh Y and Malvankar, Nikhil S and Pi, Shuang and Ward, Joy E and Woodard, Trevor L and Nevin, Kelly P and Xia, Qiangfei and Tuominen, Mark T and Lovley, Derek R} } @article {756, title = {Genetic diversity of ixodid ticks parasitizing eastern mouse and dwarf lemurs in Madagascar, with descriptions of the larva, nymph and male of Ixodes lemuris (Acari: Ixodidae).}, journal = {J Parasitol}, year = {2012}, month = {2012 Aug 27}, abstract = {Abstract The ixodid ticks parasitizing small-bodied nocturnal mouse and dwarf lemurs (Primates, Cheirogaleidae) in Madagascar are poorly documented. At Tsinjoarivo, a high-altitude eastern rainforest, mouse and dwarf lemurs were parasitized by ticks of the genus Ixodes. At Ranomafana, a montane southeastern rainforest, dwarf lemurs hosted ticks of the genus Ixodes, whereas mouse lemurs were parasitized by ticks of the genus Haemaphysalis. Our Ixodes specimens represent all active stages and females are morphologically consistent with previous descriptions of Ixodes lemuris females, the only described stage in the literature. Morphological comparisons and genetic analysis using fragments of COI gene confirm all Ixodes ticks from Tsinjoarivo and Ranomafana forests belong to the same species, i.e., Ixodes lemuris. Thus, we are able to provide descriptions of the previously unknown larva, nymph and male. Mouse lemurs at both locations were parasitized only by immature stages of Ixodes lemuris (at Tsinjoarivo) or Haemaphysalis lemuris (at Ranomafana) whereas dwarf lemurs were parasitized by all stages of Ixodes lemuris. We suggest that ecological and biogeographical conditions may affect the pattern of tick infestation at Tsinjoarivo and Ranomafana. Additional studies are necessary to understand the tick-host associations of small-bodied nocturnal lemurs.}, issn = {1937-2345}, doi = {10.1645/GE-3183.1}, author = {Blanco, Marina Beatriz and Elfawal, Mostafa A and Durden, Lance A and Beati, Lorenza and Xu, Guang and Godfrey, Laurie R and Rich, Stephen M} } @article {760, title = {Resolving the phylogeny of malaria parasites.}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, year = {2011}, month = {2011 Aug 9}, pages = {12973-4}, keywords = {Animals, Evolution, Molecular, Malaria, Parasites}, issn = {1091-6490}, doi = {10.1073/pnas.1110141108}, author = {Rich, Stephen M and Xu, Guang} } @article {768, title = {Correlation between tick density and pathogen endemicity, New Hampshire.}, journal = {Emerg Infect Dis}, volume = {15}, year = {2009}, month = {2009 Apr}, pages = {585-7}, abstract = {To assess the endemicity of tick-borne pathogens in New Hampshire, we surveyed adult tick vectors. Pathogens were more prevalent in areas of high tick density, suggesting a correlation between tick establishment and pathogen endemicity. Infection rates in ticks correlated with disease frequency in humans.}, keywords = {Anaplasma phagocytophilum, Animals, Arachnid Vectors, Babesia microti, Babesiosis, Biosurveillance, Borrelia burgdorferi, Communicable Diseases, Emerging, Ehrlichiosis, Humans, Ixodes, Lyme Disease, New Hampshire}, issn = {1080-6059}, doi = {10.3201/eid1504.080940}, author = {Walk, Seth T and Xu, Guang and Stull, Jason W and Rich, Stephen M} } @article {767, title = {The origin of malignant malaria.}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, year = {2009}, month = {2009 Sep 1}, pages = {14902-7}, abstract = {Plasmodium falciparum, the causative agent of malignant malaria, is among the most severe human infectious diseases. The closest known relative of P. falciparum is a chimpanzee parasite, Plasmodium reichenowi, of which one single isolate was previously known. The co-speciation hypothesis suggests that both parasites evolved separately from a common ancestor over the last 5-7 million years, in parallel with the divergence of their hosts, the hominin and chimpanzee lineages. Genetic analysis of eight new isolates of P. reichenowi, from wild and wild-born captive chimpanzees in Cameroon and C{\^o}te d{\textquoteright}Ivoire, shows that P. reichenowi is a geographically widespread and genetically diverse chimpanzee parasite. The genetic lineage comprising the totality of global P. falciparum is fully included within the much broader genetic diversity of P. reichenowi. This finding is inconsistent with the co-speciation hypothesis. Phylogenetic analysis indicates that all extant P. falciparum populations originated from P. reichenowi, likely by a single host transfer, which may have occurred as early as 2-3 million years ago, or as recently as 10,000 years ago. The evolutionary history of this relationship may be explained by two critical genetic mutations. First, inactivation of the CMAH gene in the human lineage rendered human ancestors unable to generate the sialic acid Neu5Gc from its precursor Neu5Ac, and likely made humans resistant to P. reichenowi. More recently, mutations in the dominant invasion receptor EBA 175 in the P. falciparum lineage provided the parasite with preference for the overabundant Neu5Ac precursor, accounting for its extreme human pathogenicity.}, keywords = {Amino Acid Sequence, Animals, Glycoproteins, Humans, Malaria, Molecular Sequence Data, Mutation, N-Acetylneuraminic Acid, Pan troglodytes, Phylogeny, Plasmodium, Plasmodium falciparum, Protozoan Infections, Animal, Protozoan Proteins, Sequence Alignment}, issn = {1091-6490}, doi = {10.1073/pnas.0907740106}, author = {Rich, Stephen M and Leendertz, Fabian H and Xu, Guang and LeBreton, Matthew and Djoko, Cyrille F and Aminake, Makoah N and Takang, Eric E and Diffo, Joseph L D and Pike, Brian L and Rosenthal, Benjamin M and Formenty, Pierre and Boesch, Christophe and Ayala, Francisco J and Wolfe, Nathan D} } @article {481, title = {Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production.}, journal = {Appl Environ Microbiol}, volume = {74}, year = {2008}, month = {2008 Jul}, pages = {4277-84}, abstract = {Although Pelobacter species are closely related to Geobacter species, recent studies suggested that Pelobacter carbinolicus may reduce Fe(III) via a different mechanism because it lacks the outer-surface c-type cytochromes that are required for Fe(III) reduction by Geobacter sulfurreducens. Investigation into the mechanisms for Fe(III) reduction demonstrated that P. carbinolicus had growth yields on both soluble and insoluble Fe(III) consistent with those of other Fe(III)-reducing bacteria. Comparison of whole-genome transcript levels during growth on Fe(III) versus fermentative growth demonstrated that the greatest apparent change in gene expression was an increase in transcript levels for four contiguous genes. These genes encode two putative periplasmic thioredoxins; a putative outer-membrane transport protein; and a putative NAD(FAD)-dependent dehydrogenase with homology to disulfide oxidoreductases in the N terminus, rhodanese (sulfurtransferase) in the center, and uncharacterized conserved proteins in the C terminus. Unlike G. sulfurreducens, transcript levels for cytochrome genes did not increase in P. carbinolicus during growth on Fe(III). P. carbinolicus could use sulfate as the sole source of sulfur during fermentative growth, but required elemental sulfur or sulfide for growth on Fe(III). The increased expression of genes potentially involved in sulfur reduction, coupled with the requirement for sulfur or sulfide during growth on Fe(III), suggests that P. carbinolicus reduces Fe(III) via an indirect mechanism in which (i) elemental sulfur is reduced to sulfide and (ii) the sulfide reduces Fe(III) with the regeneration of elemental sulfur. This contrasts with the direct reduction of Fe(III) that has been proposed for Geobacter species.}, keywords = {Acetoin, Cytochrome c Group, Deltaproteobacteria, Ethanol, Fermentation, Ferric Compounds, Gene Expression Profiling, Genome, Bacterial, Iron, Nitrilotriacetic Acid, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Reverse Transcriptase Polymerase Chain Reaction, RNA, Bacterial, Substrate Specificity, Sulfides, Sulfur, Sulfur-Reducing Bacteria, Thioredoxins}, issn = {1098-5336}, doi = {10.1128/AEM.02901-07}, author = {Haveman, Shelley A and Didonato, Raymond J and Villanueva, Laura and Shelobolina, Evgenya S and Postier, Bradley L and Xu, Bo and Liu, Anna and Lovley, Derek R} } @article {505, title = {Importance of c-Type cytochromes for U(VI) reduction by Geobacter sulfurreducens.}, journal = {BMC Microbiol}, volume = {7}, year = {2007}, month = {2007}, pages = {16}, abstract = {BACKGROUND: In order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated. RESULTS: The ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50-60\%) the ability of G. sulfurreducens to reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI) reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI) reduction. A subpopulation of both wild type and U(VI) reduction-impaired cells, 24-30\%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI) reduction-impaired and wild type G. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III) revealed no correlation between the impact of cytochrome deletion on U(VI) reduction and reduction of Fe(III) hydroxide and chelated Fe(III). CONCLUSION: This study indicates that c-type cytochromes are involved in U(VI) reduction by Geobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction by G. sulfurreducens but do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI) reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI) reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium reduction. Periplasmic uranium accumulation may reflect the ability of uranium to penetrate the outer membrane rather than the occurrence of enzymatic U(VI) reduction. Elimination of cytochromes rarely had a similar impact on both Fe(III) and U(VI) reduction, suggesting that there are differences in the routes of electron transfer to U(VI) and Fe(III). Further studies are required to clarify the pathways leading to U(VI) reduction in G. sulfurreducens.}, keywords = {Biodegradation, Environmental, Cytochrome c Group, Ferric Compounds, Geobacter, Microscopy, Electron, Transmission, Mutation, Oxidation-Reduction, Periplasm, Uranium}, issn = {1471-2180}, doi = {10.1186/1471-2180-7-16}, author = {Shelobolina, Evgenya S and Coppi, Maddalena V and Korenevsky, Anton A and DiDonato, Laurie N and Sullivan, Sara A and Konishi, Hiromi and Xu, Huifang and Leang, Ching and Butler, Jessica E and Kim, Byoung-Chan and Lovley, Derek R} } @article {789, title = {Animal propagation and genomic survey of a genotype 1 isolate of Cryptosporidium parvum.}, journal = {Mol Biochem Parasitol}, volume = {108}, year = {2000}, month = {2000 May}, pages = {187-97}, abstract = {Human cryptosporidiosis is attributed to two major Cryptosporidium parvum genotypes of which type 1 appears to be the predominant. Most laboratory investigations however are performed using genotype 2 isolates, the only type which readily infects laboratory animals. So far type 1 has only been identified in humans and primates. A type 1 isolate, obtained from an individual with HIV and cryptosporidiosis, was successfully adapted to propagate in gnotobiotic piglets. Genotypic characterization of oocyst DNA from this isolate using multiple restriction fragment length polymorphisms, a genotype-specific PCR marker, and direct sequence analysis of two polymorphic loci confirmed that this isolate, designated NEMC1, is indeed type 1. No changes in the genetic profile were identified during multiple passages in piglets. In contrast, the time period between infection and onset of fecal oocyst shedding, an indicator of adaptation, decreased with increasing number of passages. Consistent with other type 1 isolates, NEMC1 failed to infect mice. A preliminary survey of the NEMC1 genome covering approximately 2\% of the genome and encompassing 200 kb of unique sequence showed an average similarity of approximately 95\% between type 1 and 2 sequences. Twenty-four percent of the NEMC1 sequences were homologous to previously determined genotype 2 C. parvum sequences. To our knowledge, this is the first successful serial propagation of genotype 1 in animals, which should facilitate characterization of the unique features of this human pathogen.}, keywords = {Animals, Cryptosporidiosis, Cryptosporidium parvum, Genome, Protozoan, Genotype, Germ-Free Life, Humans, Mice, Mice, Knockout, Molecular Sequence Data, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Sequence Analysis, DNA, Swine}, issn = {0166-6851}, author = {Widmer, G and Akiyoshi, D and Buckholt, M A and Feng, X and Rich, S M and Deary, K M and Bowman, C A and Xu, P and Wang, Y and Wang, X and Buck, G A and Tzipori, S} } @article {831, title = {Replication fork assembly at recombination intermediates is required for bacterial growth.}, journal = {Proc Natl Acad Sci U S A}, volume = {96}, year = {1999}, month = {1999 Mar 30}, pages = {3552-5}, abstract = {PriA, a 3{\textquoteright} --> 5{\textquoteright} DNA helicase, directs assembly of a primosome on some bacteriophage and plasmid DNAs. Primosomes are multienzyme replication machines that contribute both the DNA-unwinding and Okazaki fragment-priming functions at the replication fork. The role of PriA in chromosomal replication is unclear. The phenotypes of priA null mutations suggest that the protein participates in replication restart at recombination intermediates. We show here that PriA promotes replication fork assembly at a D loop, an intermediate formed during initiation of homologous recombination. We also show that DnaC810, encoded by a naturally arising intergenic suppressor allele of the priA2::kan mutation, bypasses the need for PriA during replication fork assembly at D loops in vitro. These findings underscore the essentiality of replication fork restart at recombination intermediates under normal growth conditions in bacteria.}, keywords = {Bacteria, Bacteriophage phi X 174, Base Sequence, DNA Polymerase III, DNA Replication, DNA-Binding Proteins, Escherichia coli, Molecular Sequence Data, Oligodeoxyribonucleotides, Open Reading Frames, Recombination, Genetic, Replication Protein A, Templates, Genetic}, issn = {0027-8424}, author = {Liu, J and Xu, L and Sandler, S J and Marians, K J} }