Biology subjects

Smith, J. A.

Publications and source records attributed to Smith, J. A..

At least 19 recordsLinked to original sources

bioRxiv2026

'Who Goes There?' Quantifying Scavenger-Carcass Activity at Mass Mortality Events

1.Mass mortality events (MMEs) create sudden pulses of carrion that can alter how vertebrate scavengers use carcass resources, including the frequency, duration, and timing of species-carcass contacts. These changes could have implications for pathogen transmission at the scavenger-carcass interface. We aimed to develop and apply a reproducible analytical framework for using camera-trap data to quantify transmission-relevant vertebrate activity at carcass sites under differing carrion biomass scenarios. We studied experimental carcass plots (single carcass [~]43 kg; mass mortality plots [10 carcasses, >350 kg total]; 6 of each) in Australias alpine ecosystem. The framework integrated descriptive summaries (bipartite network analysis, Kaplan-Meier curves) and marked temporal point-process models to characterise structural and temporal dimensions of species-carcass activity. Mass mortality plots had greater overall visitation duration, occurring as sustained activity (50% of visitation event volume by day 17), compared with intense then rapidly declining activity at single carcasses (50% by day 8). Mass mortality plots also had higher predicted daily arrival probability and contact hours across most species, indicating an extended window for pathogen transmission. This framework provides empirically derived contact parameters for MME-related disease spread models using camera-trap data to identify potential transmission pathways at the scavenger-carcass interface.

ecology↗

bioRxiv2026

Functional Roles of the World's Recovered Predators

Terrestrial predator populations have declined globally due to anthropogenic pressures with cascading consequences throughout ecosystems. As a result, recent efforts have sought to restore predator populations both passively (via habitat conservation and connectivity) and actively (via conservation translocations and reintroductions). Predator recovery efforts often cite restoration of ecological responses as a central goal, yet few studies monitor and report ecological outcomes of predator restoration. We conducted a comprehensive global meta-analysis of ecological responses to predator recovery, specifically investigating drivers of the magnitude of responses and, crucially, their alignment with local conservation objectives. Our analysis revealed that recovered predators overall elicit strong responses from the wildlife community, with most responses aligning with local conservation management preferences. Recovery effort techniques and biological community characteristics influenced the strength of community response and alignment with conservation goals. Although our results suggest that predator recovery is largely beneficial to ecosystem function, clarifying the goals of predator restoration will be essential for successful evaluation of ecological restoration and development of coexistence strategies.

ecology↗

bioRxiv2025

Methods for estimating location from spatial patterns in species composition: a fishing location case study

The location at which a species assemblage is observed can be uncertain, for example in fisheries where catch composition is recorded accurately but location data may be coarse or inaccurate. In such cases, spatial signals in observed species compositions can help identify and refine uncertain locations. This study explored three approaches for location estimation using species composition data: 1) a hierarchical species distribution model (SDM) that jointly estimates species distributions and location uncertainty, 2) an inverse prediction method that uses a fitted SDM to identify the most likely location given new species data, and 3) the direct modeling of location as the response variable. Each approach requires a subset of observations with accurate locations to quantify the spatial patterns in species distributions. All three methods were useful and reasonably accurate: for the simulated data the average distance error (distance to true location) was 15% the size of the domain, and for the real data this error was 20-100 km. When only some locations are uncertain, the hierarchical approach is valuable due to its integrated estimation of location and species parameters. When many locations are uncertain, the other approaches seem more suitable. Inverse prediction is ideal when prior information is available to constrain the location estimation. Direct modelling (although causally spurious) is well suited to large datasets, with multivariate random forests often providing the most accurate location estimates. These methods can enhance spatial data quality in ecological monitoring and help develop tools for improving inaccurate or deliberately misreported fishing locations.

ecology↗

bioRxiv2025

Positive Selection Screen for Natural Product β-Catenin Inactivators

Many genetically validated targets in cancer, including the transcription factor {beta}-catenin ({beta}-cat), have historically been viewed as undruggable. Cell-based phenotypic screening of chemical compounds can reveal new biological and pharmacological principles. Natural products are powerful probes because of their superior structural diversity, drug-like properties, and biological activities as compared to unoptimized synthetic compounds. We screened 326,304 natural product mixtures (40,744 extracts and 285,560 fractions derived from them) using mammalian cells expressing an oncogenic version of {beta}-cat fused to a suicide protein. Multiple fractions degraded the {beta}-cat fusion protein or drove it into a compartment where both fusion partners were apparently inactive. The active natural product from one of the latter specifically activates novel, but not classical, protein kinase Cs (PKCs) and thereby relocates {beta}-cat to juxtamembrane vacuolar structures. These findings suggest a path for inactivating oncogenic {beta}-cat and underscore the power of screening natural product collections with robust phenotypic assays.

cancer biology↗

bioRxiv2025

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

India is the most populous country globally, yet genetic studies involving Indian individuals remain limited. The Indian population is composed of many founder groups and has a mixed genetic ancestry, including an ancestral component not observed anywhere outside of India. This presents a unique opportunity to uncover novel disease variants and develop more tailored medical interventions. To facilitate genetic research in India, a crucial first step is to create a foundational resource that serves as a benchmark for future population studies and methods development. To this end, we have constructed the largest and most nationally representative linkage disequilibrium and genotype imputation reference panels in India to date, using high-coverage whole-genome sequencing data of 2,680 Indian participants from the Longitudinal Aging Study in India-Harmonized Diagnostic Assessment of Dementia (LASI-DAD). As an LD reference panel, LASI-DAD includes 69.5 million variants, representing 170% and 213% increases relative to the 1000 Genomes Project (1000G) and TOP-LD panels, respectively. Besides serving as an LD lookup panel, LASI-DAD facilitates various statistical analyses that rely on precise LD estimates. In a polygenic risk score (PRS) analysis, LASI-DAD improved the predictive performance of PRS by 2.1% to 35.1% across traits and studies. As an imputation reference panel, LASI-DAD improved the imputation accuracy by 3% to 101% (mean = 38%) compared to the TOPMed panel (Version R3) and by 3% to 73% (mean = 27%) compared to the Genome Asia Pilot (GAsP) panel across different minor allele frequencies. The LASI-DAD reference panel is publicly available to benefit future studies.

genetics↗

bioRxiv2025

Interaction of Ricin and RCA-I lectin with Human Serum Glycoproteins and Lung Cells

The plant protein ricin is one of the most toxic substances known and has been used in crimes internationally. Ricin binds to cell surface galactose as on glycoproteins and becomes endocytosed to kill cells. Blood contains high levels of galactosylated proteins which could bind to ricin and the related protein RCA-I from the same plant Ricinus communis. While blood proteins would be among targets for injected ricin, inhaled ricin would also bind to lung epithelial cells. Ricin and RCA-I are reported to have very similar or identical binding specificity. Thus, it is useful to increase the knowledge of proteins in blood and A549 cells that bind to ricin and RCA-I. Ricin and RCA-I staining of blots of electrophoresis gels of serum showed binding to serum proteins of 200-kDa and four between 75-kDa and 25-kDa for RCA-I and proteins between 150-kDa and 37-kDa for ricin which bound much less strongly. Both ricin and RCA-I bound to purified human immunoglobulin G heavy chain and transferrin but not to 2 HS glycoprotein which contains high amounts of sialic acid. Sambucus nigra agglutinin which binds sialic acid bound to 2 HS glycoprotein and transferrin but not to immunoglobulin G. Ricin bound to human lung A549 proteins of 150 kDa, 100 kDa and several proteins in human cell free salivary fluid between greater than 200 kDa to 25 kDa and binding to these proteins was diminished in the presence of serum. In fluorescence microscopy, RCA-I bound more strongly than ricin to A549 cells and this binding was diminished in the presence of human serum. RCA-I also bound much more strongly than ricin to human serum proteins coated on microtiter plate wells.

biochemistry↗

bioRxiv2025

Mechanisms of resistance to active state selective tri-complex RAS inhibitors

Tri-complex inhibitors (TCIs) act as molecular glues to recruit cyclophilin A (CYPA) to the active (GTP-bound or ON) conformation of RAS, which in turn prevents the activation of downstream effector proteins like RAF and PI3K. Emerging data demonstrate clinical activity, including tumor regressions, in patients with RAS driven cancers. Despite being promising therapeutic interventions, the mechanisms of resistance in patients treated with these inhibitors remain unknown. Here we studied matched baseline and post-progression specimens from patients treated with the RAS(ON) multi-selective inhibitor daraxonrasib (RMC-6236). Tissue or cell-free DNA specimens were collected from 40 patients with RAS-mutant non-small cell lung, colorectal, or other cancers. Eighteen patients (45%) were found to have acquired alterations in RAS signaling intermediates, including recurrent alterations in KRAS, BRAF, RAF1, MAP2K1/2 and PIK3CA. Preclinical resistance models mirrored the alterations observed in patients. We found that secondary KRAS Y64X mutations caused resistance by disrupting an important pi-pi interaction between KRAS and the indole ring of daraxonrasib, which lowers the affinity of the daraxonrasib:CYPA binary complex for active KRAS. We also identified kinase-dead and low-activity BRAF mutations in samples with acquired resistance. This is puzzling, because TCIs are expected to prevent the interaction between RAS and BRAF, which is needed for hypoactive mutants to dimerize and signal. We now show that RAF dimers are harder to displace from active RAS, as compared to their monomeric forms. Indeed, enhanced RAF dimerization attenuated the ability of TCIs to recruit CYPA to active RAS, resulting in diminished inhibition of oncogenic signaling and tumor growth. Thus, several clinical resistance alterations converge at attenuating the formation of the RAS:daraxonrasib:CYPA tri-complex, either by preventing daraxonrasib binding or by inducing RAF dimers.

cancer biology↗

bioRxiv2025

Persistent articular infection and host reactive response contribute to Brucella-induced spondyloarthritis in SKG mice

Brucellosis, one of the most prevalent zoonotic diseases worldwide, often results in osteoarticular complications including large joint and axial arthritis mimicking spondyloarthritis. To model this chronic manifestation, we infected autoimmunity-prone SKG mice containing a mutation in the T-cell adaptor ZAP-70 with Brucella species. B. melitensis infection resulted in a fully penetrant, readily scoreable disease involving large joint wrist and foot arthritis, peri-ocular inflammation, and less frequent scaly paw rash. Infection with B. abortus resulted in delayed arthritis onset, and B. neotomae revealed sex differences, with more severe disease and a dose response in females. Heat-killed Brucella did not induce arthritis, evincing a requirement for viable infection. Across species, splenic CFU correlated well with final clinical score at 12 weeks ({rho}=0.79 and p<0.001). In vivo imaging using luminescent B. neotomae revealed rapid colonization of the paws by one-week post-infection, more than a month prior to arthritis onset. Paw luminescence levels decreased after 2 weeks and then remained relatively static, even as clinical scores increased. Thus, the degree of arthritis did not strictly correlate with degree of paw infection but suggested an additional reactive component. Further, in examining a Brucella {Delta}tcpB mutant lacking a Type IV secretion system-dependent mediator, mice displayed an intermediate phenotype without significant differences in splenic CFU. Together these data suggest Brucella induced spondyloarthritis reflects both persistent colonization as well as excess host reactivity. Moreover, the sensitivity of the SKG model to different species and mutants will provide new opportunities for dissecting correlates of Brucella virulence and host immunity. ImportanceBrucellosis, a bacterial infection acquired from herd animals, remains one of the most common zoonotic diseases worldwide. Chronic infection often results in spondyloarthritis-like complications. Investigation into pathogenesis has been limited by the lack of overt disease in standard lab mice. We addressed this issue using spondyloarthritis-susceptible SKG mice. Upon infection with B. melitensis, SKG mice develop robust, fully penetrant large joint arthritis. Arthritis development required viable bacteria. Moreover, studies of colonization, gene expression and anatomic distribution using bioluminescent bacteria revealed active persistent infection in the mouse paws. However, peak paw infection occurred much earlier than arthritis onset, suggesting an added immune reactive component. Disease onset, severity and manifestations varied upon infection with different Brucella species and mutants. Together these results suggest this new model will be very useful to the scientific community for determining correlates of bacterial virulence leading to clinical disease.

microbiology↗

bioRxiv2025

Protective mechanisms against Alzheimer's Disease in APOE3-Christchurch homozygous astrocytes

The APOE3-Christchurch (APOE3-Ch) variant has been linked to reduced Alzheimers Disease (AD) risk, but its protective mechanisms remain unclear. This study explores the neuroprotective phenotype of APOE3-Ch astrocytes, focusing on lipid metabolism and tau processing. APOE3-Ch astrocytes demonstrate enhanced tau oligomer uptake via HSPG- and LRP1-mediated pathways, facilitated by elevated HSPG expression, and achieve superior tau degradation through lysosomal pathways and proteasomal pathways, in contrast to wild-type astrocytes, which primarily use proteasomal mechanisms. Transcriptomic analysis reveals upregulation of genes involved in endocytosis and cell projection assembly, explaining enhanced tau uptake and clearance in APOE3-Ch astrocytes. Lipidomic profiling identifies reduced levels of pathological lipids such as ceramides and gamma-linolenic acid (GLA), potentially mitigating neuroinflammation. These findings provide insight into the protective mechanisms of APOE3-Ch astrocytes and underscore their potential as therapeutic targets for tauopathy and neurodegeneration in AD. TeaserAPOE3-Christchurch astrocytes enhance tau clearance and mitigate neurotoxic lipid accumulation, unveiling protective mechanisms against Alzheimers.

neuroscience↗

bioRxiv2024

Glucose alters the evolutionary response to gentamicin in uropathogenic Escherichia coli

Urinary tract infections (UTI) are a major health and economic concern. Uropathogenic Escherichia coli (UPEC) are the leading cause of UTI, and antibiotic resistant UPEC are increasingly common. The microenvironment of the urinary tract is metabolically distinct, and there is growing interest in understanding the extent to which metabolism may influence UPEC infection and response to antibiotics, and how this varies between individuals. Diabetes, characterised in part by glycosuria, is a known risk factor for UTI and is associated with more severe infections. The role that glucose plays in driving UPEC evolution is unclear. Here, we found that a pathologically-relevant glucose concentration reduced the efficacy of the antibiotic gentamicin against a UPEC strain. Through experimental evolution, we identified mutations in the RNA polymerase sigma factor rpoS associated with long-term glucose exposure. We found that the presence of gentamicin resulted in mutations in genes including trkH, encoding a potassium ion uptake system and linked previously to aminoglycoside resistance, and in the autotransporter hyxB. Strikingly, these mutations were not present in populations exposed to a combination of both glucose and gentamicin. Together, this suggests that whilst glucose may reduce growth inhibition by gentamicin, it may also influence mutation acquisition, providing new avenues for understanding the evolution and treatment of UPEC-mediated UTI in high-risk individuals.

microbiology↗

bioRxiv2024

Multiple Unfolded Protein Response pathways cooperate to link cytosolic dsDNA release to Stimulator of Interferon Gene (STING) activation

The double-stranded DNA (dsDNA) sensor STING has been increasingly implicated in responses to "sterile" endogenous threats and pathogens without nominal DNA or cyclic di-nucleotide stimuli. Previous work showed an endoplasmic reticulum (ER) stress response, known as the unfolded protein response (UPR), activates STING. Herein, we sought to determine if ER stress generated a STING ligand, and to identify the UPR pathways involved. Induction of IFN-{beta} expression following stimulation with the UPR inducer thapsigargin (TPG) or oxygen glucose deprivation required both STING and the dsDNA-sensing cyclic GMP-AMP synthase (cGAS). Furthermore, TPG increased cytosolic mitochondrial DNA, and immunofluorescence visualized dsDNA punctae in murine and human cells, providing a cGAS stimulus. N-acetylcysteine decreased IFN-{beta} induction by TPG, implicating reactive oxygen species (ROS). However, mitoTEMPO, a mitochondrial oxidative stress inhibitor did not impact TPG-induced IFN. On the other hand, inhibiting the inositol requiring enzyme 1 (IRE1) ER stress sensor and its target transcription factor XBP1 decreased the generation of cytosolic dsDNA. iNOS upregulation was XBP1-dependent, and an iNOS inhibitor decreased cytosolic dsDNA and IFN-{beta}, implicating ROS downstream of the IRE1-XBP1 pathway. Inhibition of the PKR-like ER kinase (PERK) pathway also attenuated cytoplasmic dsDNA release. The PERK-regulated apoptotic factor Bim was required for both dsDNA release and IFN-{beta} mRNA induction. Finally, XBP1 and PERK pathways contributed to cytosolic dsDNA release and IFN-induction by the RNA virus, Vesicular Stomatitis Virus (VSV). Together, our findings suggest that ER stressors, including viral pathogens without nominal STING or cGAS ligands such as RNA viruses, trigger multiple canonical UPR pathways that cooperate to activate STING and downstream IFN-{beta} via mitochondrial dsDNA release.

immunology↗

bioRxiv2024

Combining in vivo and in vitro approaches to better understand host-pathogen interactions

Nutrition often shapes the outcome of host-parasite interactions, however understanding the mechanisms by which this occurs is confounded by the intimate nature of the association and by the fact that the host and parasite may compete for the same limiting nutrients. One way of disentangling this interaction is to combine in vivo and in vitro approaches. Here, we explore the role of host nutrition in determining the outcome of infections using a model insect-bacterium system: the cotton leafworm Spodoptera littoralis and the blood-borne bacterium Xenorhabdus nematophila. Spodoptera littoralis larvae were reared on one of a series of 20 chemically-defined diets ranging in their protein: carbohydrate (P:C) ratio and caloric density. They were then challenged with either a fixed dose of X. nematophila cells (live or dead) or were sham-injected. Survivorship of larvae challenged with live bacterial cells was strongly dependent on the protein levels of the diet, with mortality being highest on low-protein diets. This trend was reflected in the bacterial growth rate in vivo, which peaked in larvae fed low-protein diets. To determine whether in vivo bacterial growth rates were driven by blood nutrients, rather than an enhanced host immune response, we generated 20 synthetic haemolymphs ( nutribloods) that mimicked the nutritional content of host blood. Bacterial growth rate in the nutribloods was also negatively impacted by their protein content suggesting that nutrient availability and not host immunity was driving the interaction. By comparing standardized bacterial growth rates in vivo and in vitro, we conclude that the outcome of this host-parasite interaction is largely driven by bottom-up effects of nutrients on bacterial growth, rather than by top-down effects of nutrients on host-mediated immune responses. The outcome of host-parasite interactions is typically assumed to be strongly determined by the host immune response. The direct effects of nutrition have been underexplored and may have broad consequences for host-parasite interactions across taxa.

ecology↗

bioRxiv2024

Nutribloods: novel synthetic lepidopteran haemolymphs for understanding insect-microbe interactions in vitro

Understanding the role of nutrients in microbial population dynamics relies on a sound appreciation of their nutritional environment and how this may vary in different habitats. For microbial pathogens and commensals, this can be especially challenging because the microbe may share nutritional resources with its host. Here we design a series of 20 synthetic haemolymphs (nutribloods) that mimic haemolymph nutrient profiles of caterpillars fed on one of 20 chemically-defined diets, that vary in their protein:carbohydrate (P:C) ratio and caloric density. Using these, we are able to simulate the range of nutritional conditions that insect blood pathogens might face, providing a model system for understanding the role of nutrition in microbial growth. We tested this using the entomopathogen, Xenorhabdus nematophila, a gram-positive extracellular bacterium of insect hosts. This revealed that whilst bacterial fitness peaked in nutriblood nutrient space that was high in carbohydrates and low in proteins, levels of amino acids in the nutribloods also appear to be an important driving force for bacterial growth. Using synthetic haemolymphs that had average levels of all nutrients other than carbohydrate, protein or amino acids, we also established that bacterial growth is generally enhanced by carbohydrate and amino acids but reduced by proteins. Here, we have established a tractable model system for examining the role that nutrition plays in the growth of an entomopathogenic bacterium. In future work, this model host-pathogen system can be used to test a range of nutritionally-driven processes, including competition during co-infection and interactions with the host microbiome, as well as comparative studies of other entomopathogens.

physiology↗

bioRxiv2024

Downregulation of NR4A3 During Inactivity Alters Glucose Metabolism and Impairs Translation in Human Skeletal Muscle

The transcription factor NR4A3 is regulated by exercise and a potent modulator of skeletal muscle metabolism. We report here that physical inactivity decreased skeletal muscle NR4A3 levels, concomitant with mitochondrial function and proteostasis pathways. Silencing of NR4A3 in myotubes decreased glucose oxidation and increased lactate production. This coincided with greater signalling downstream of AMPK and elevated rates of fatty acid oxidation. While NR4A3 silencing reduced protein synthesis, mTORC1 signalling, and ribosomal transcription, overexpression of the canonical NR4A3 protein isoform augmented translation and cellular protein content. Moreover, restoration of NR4A3 levels rescued glucose oxidation in NR4A3-silenced myotubes and restored phosphorylation of mTORC1 substrates. NR4A3 depletion reduced myotube area and altered the abundance of contractile elements. Thus, downregulation of NR4A3 has adverse effects on skeletal muscle metabolism, myotube size, and contractile apparatus by directing mTORC1 signalling and ribosomal biogenesis. Our data demonstrate that NR4A3 controls skeletal muscle atrophy associated with physical inactivity.

physiology↗

bioRxiv2024

Searching the Pinus taeda foliar mycobiome for emerging pathogens among brown spot needle blight and needlecast outbreaks in the Southeast United States

Needle pathogens cause the discoloration, death, or premature abscission of conifer foliage, which reduce growth and vigor, and repeated defoliation may eventually result in tree mortality. Since 2016, forest managers in the southeast United States have reported an increasing scale, frequency, and severity of needle disease outbreaks on the regions principal timber species, loblolly pine (Pinus taeda L.). These recent outbreaks are raising concern throughout the region, as needle diseases are not traditionally considered a threat to P. taeda. Lecanosticta acicola (Thum.) Syd., the native causal agent of brown-spot needle blight, has been recovered from some outbreaks, however, the full array of fungi associated with symptoms has not been explored. In this research, P. taeda foliage was collected from affected stands throughout the region and analyzed to identify fungi associated with needle disease symptoms. We employed both targeted molecular diagnostics, to confirm the presence or absence of L. acicola, and DNA metabarcoding, to characterize the foliar mycobiome and screen for other potential pathogens. Lecanosticta acicola was detected among symptomatic needles from multiple states, particularly in western portions of the P. taeda range but rarely from stands in eastern states. Fungal ITS1 metabarcoding revealed multiple pathogens in symptomatic needles and identified associations between known pathogens fungi and differing symptoms. Additionally, the fungal community composition of needles varied with patterns of symptom presentation. This study is the first regionwide assessment of fungi associated with recent large-scale needle disease outbreaks on P. taeda and identifies multiple pathogens that warrant study in greater detail.

microbiology↗

bioRxiv2024

50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences

India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India--including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups--providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry through gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover [~]1.5 Gb (or 50%) of the introgressing Neanderthal and [~]0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.

evolutionary biology↗

bioRxiv2023

Electrobiocorrosion by Microbes without Outer-Surface Cytochromes

Anaerobic microbial corrosion of iron-containing metals causes extensive economic damage. Some microbes are capable of direct metal-to-microbe electron transfer (electrobiocorrosion), but the prevalence of electrobiocorrosion among diverse methanogens and acetogens is poorly understood because of a lack of tools for their genetic manipulation. Previous studies have suggested that respiration with 316L stainless steel as the electron donor is indicative of electrobiocorrosion because, unlike pure Fe0, 316L stainless steel does not abiotically generate H2 as an intermediary electron carrier. Here we report that all of the methanogens (Methanosarcina vacuolata, Methanothrix soehngenii, and Methanobacterium strain IM1) and acetogens (Sporomusa ovata, Clostridium ljungdahlii) evaluated respired with pure Fe0 as the electron donor, but only M. vacuolata, Mx soehngenii, and S. ovata were capable of stainless steel electrobiocorrosion. The electrobiocorrosive methanogens required acetate as an additional energy source in order to produce methane from stainless steel. Co-cultures of S. ovata and Mx. soehngenii demonstrated how acetogens can provide acetate to methanogens during corrosion. Not only was Methanobacterium strain IM1 not capable of electrobiocorrosion, but it also did not accept electrons from Geobacter metallireducens, an effective electron- donating partner for direct interspecies electron transfer to all methanogens that can directly accept electrons from Fe0. The finding that M. vacuolata, Mx. soehngenii, and S. ovata are capable of electrobiocorrosion, despite a lack of the outer-surface c-type cytochromes previously found to be important in other electrobiocorrosive microbes, demonstrates that there are multiple microbial strategies for making electrical contact with Fe0. Impact StatementUnderstanding how anaerobic microbes receive electrons from Fe0 is likely to lead to novel strategies for mitigating the corrosion of iron-containing metals, which has an enormous economic impact. Electrobiocorrosion, is a relatively recently recognized corrosion mechanism. It was previously demonstrated in pure cultures when Fe0 oxidation was inhibited by deletion of genes for outer-surface c-type cytochromes known to be involved in other forms of extracellular electron exchange. However, many methanogens and acetogens lack obvious outer-surface electrical connections and are difficult to genetically manipulate. The study reported here provides an alternative approach to evaluating whether microbes are capable of electrobiocorrosion that does not require genetic manipulation. The results indicate that Methanobacterium strain IM1, is not electrobiocorrosive, in contrast to previous speculation. However, some methanogens and acetogens without known outer-surface c-type cytochromes do appear to be capable of electrobiocorrosion, suggesting that this corrosion mechanism may be more widespread than previously thought.

microbiology↗

bioRxiv2023

Detrimental Impact of a Type VI Secretion System on Direct Interspecies Electron Transfer

Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells, eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular activated carbon, consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasize the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCEDirect interspecies electron transfer (DIET) is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity in establishing syntrophic relationships.

microbiology↗