Biology subjects

Hall, R.

Publications and source records attributed to Hall, R..

At least 19 recordsLinked to original sources

bioRxiv2025

Genomic analysis of Megalocytivirus genomes reveals widespread recombination

Megalocytiviruses are pathogens of global significance that can lead to substantial economic losses in aquaculture. Recombination among megalocytiviruses is typically assumed to be rare, although it has been relatively understudied. Here, we uncover widespread recombination within megalocytiviruses through detailed analyses of 63 Megalocytivirus genomes, including two which are newly sequenced and assembled. We also identify a number of genes which megalocytiviruses have likely obtained from outside the family Iridoviridae (iridovirids). These results have serious implications for the biosecurity management of megalocytiviruses, as they indicate that Megalocytivirus strains could be misclassified based on traditional approaches which target individual loci in the genome. We use this new knowledge of recombination to estimate updated phylogenetic trees of megalocytiviruses at the family-, genus-, and species-level. These trees show strong support for the designation of two novel species within the genus Megalocytivirus and highlight the difficulty of placing highly recombinant genomes in a single phylogenetic framework. We discuss the implications of our work for disease management, and the importance of genome-wide recombination detection and phylogenomic analysis in the classification and genetic characterisation of megalocytiviruses.

evolutionary biology↗

bioRxiv2025

Endothelial CYB5R3 couples store-operated calcium entry to TRPV2 activation and vascular fitness

NADH-cytochrome b5 reductase 3 (CYB5R3) is a flavoprotein that governs nitric oxide (NO) signaling and supports NADPH oxidase 4-derived hydrogen peroxide production via coenzyme Q reduction in endothelium. While CYB5R3 expression is decreased during aging, the downstream consequences of CYB5R3 loss are not understood. Here, we demonstrate that depletion of CYB5R3 in primary human aortic endothelial cells activates a Ca2+ influx network characterized by the upregulation of calcium release-activated calcium (CRAC) channel subunits ORAI2 and ORAI3, as well as the non-selective cation channel transient receptor potential vanilloid 2 (TRPV2). When endoplasmic-reticulum Ca2+ stores were depleted, CYB5R3-deficient cells had increased Ca2+ entry through the plasma membrane, part of which was insensitive to classical store-operated Ca2+ entry (SOCE) blockers and was mediated by TRPV2, as demonstrated by genetic knockdown and pharmacologic inhibition. Mechanistically, loss of CYB5R3 increased Ca2+-dependent NO production through elevated CRAC channel activity, which oxidatively inhibited the protein tyrosine phosphatase non-receptor type 1 (PTPN1). This prevented TRPV2 dephosphorylation, thereby maintaining Janus kinase 1 (JAK1)-dependent channel activation downstream of SOCE. It also enhanced the responsiveness of TRPV2 to physiological heat stimuli. Thus, CYB5R3 normally acts as a brake, limiting NO-dependent PTPN1 oxidation and restraining TRPV2 activity. In vivo, endothelial-specific Cyb5r3 deletion enhanced acetylcholine-induced vasorelaxation and improved exercise capacity, demonstrating a physiological function for this pathway in vascular adaptation. Together, these findings identify a CYB5R3-NO-SOCE- PTPN1-TRPV2 signaling axis that couples endothelial redox balance to Ca2+ dynamics and vascular function. SIGNIFICANCEEndothelial cells rely on receptor-regulated Ca2+ signals to produce vasodilators and control vascular function; however, the molecular mechanisms coordinating these pathways are incompletely understood. We identify CYB5R3 as a key redox switch that couples store-operated Ca2+ entry to the non-selective cation channel TRPV2. Loss of CYB5R3 enhances TRPV2 activity downstream of SOCE through NO-dependent oxidative inhibition of the phosphatase PTPN1, sustaining Janus kinase-mediated TRPV2 channel activation. This novel mechanism expands the physiological scope of CYB5R3 by redefining how redox enzymes intersect with Ca2+ signaling, linking endothelial CYB5R3 to vascular relaxation and exercise capacity in vivo. This positions CYB5R3 as a central regulator of vascular function with broad implications for cardiovascular health and disease.

cell biology↗

bioRxiv2024

Wildlife provisioning selects for higher pathogen virulence in hosts with incomplete immunity

Anthropogenic food provisioning provides massive inputs of food to wildlife, with profound ecological and evolutionary consequences. By altering wildlife condition, density, and behavior, provisioning can influence transmission of infectious diseases and thus may impose strong selection pressure on wildlife pathogens. But surprisingly, we lack theory on the eco-evolutionary consequences of provisioning for host-pathogen dynamics. Here we develop a mathematical model of the eco-evolutionary dynamics of a wildlife pathogen under provisioning, motivated by Mycoplasma gallisepticum, a bacterial pathogen that emerged, spread, and changed its virulence in provisioned house finches. We model how provisioning influences the evolution of pathogen virulence, defined here as mortality associated with infection. Consistent with past empirical work, house finches recover from infection and acquire incomplete immunity; this incomplete immunity is stronger if their initial infection was with a more virulent pathogen strain. We find that, even though provisioning improves body condition, it should still select for higher virulence, and thus may actually lead to declines in host populations. These negative effects arise because provisioning magnifies the impact of incomplete immunity, selecting for higher virulence and driving host populations down. Our results highlight that food provisioning can select for more virulent pathogens, with potentially far-reaching implications for conservation.

ecology↗

bioRxiv2024

New tools to monitor Pseudomonas aeruginosa infection and biofilms in vivo in C. elegans.

Antimicrobial resistance is a growing health problem. Pseudomonas aeruginosa is a pathogen of major concern because of its multidrug resistance and global threat, especially in health-care settings. The pathogenesis and drug resistance of P. aeruginosa depends on its ability to form biofilms, making infections chronic and untreatable as the biofilm protects against antibiotics and host immunity. A major barrier to developing new antimicrobials is the lack of in vivo biofilm models. Standard microbiological testing is usually performed in vitro using planktonic bacteria, without representation of biofilms, reducing translatability. Here we develop tools to study both infection and biofilm formation by P. aeruginosa in vivo to accelerate development of strategies targeting infection and pathogenic biofilms. Using the nematode Caenorhabditis elegans and P. aeruginosa reporters combined with in vivo imaging we show that fluorescent P. aeruginosa reporters that form biofilms in vitro can be used to visualise tissue infection. Using automated tracking of C. elegans movement, we find that that the timing of this infection corresponds with a decline in health endpoints. In a mutant strain of P. aeruginosa lacking RhlR, a transcription factor that controls quorum sensing and biofilm formation, we find reduced capacity of P. aeruginosa to form biofilms, invade host tissues and negatively impact healthspan and survival. Our findings suggest that RhlR could be a new antimicrobial target to reduce P. aeruginosa biofilms and virulence in vivo and C. elegans could be used to more effectively screen for new drugs to combat antimicrobial resistance.

microbiology↗

bioRxiv2024

HIV-1 Vpr causes separate cell cycle arrests in G2 and M that activate alternative DNA damage pathways

Vpr is a conserved primate lentiviral accessory protein that induces cell cycle arrest in G2. The precise mechanism of this arrest and its benefit to viral replication is unknown. Here, we show that in addition to G2 arrest, Vpr from HIV-1/SIVcpz and HIV-2 lineages separately induce mitotic arrest through the spindle assembly checkpoint, in contrast to other Vpr proteins that only cause G2 arrest. The G2 arrest was mediated solely by ATR (ataxia telangiectasia and Rad3 related) and this activity caused elevated cellular dNTP levels. The mitotic arrest required ATM (ataxia-telangiectasia mutated) as well as ATR activity and resulted from the formation of HIV-1 Vpr-induced ultra-fine anaphase bridges. Moreover, ectopic expression of the DNA structure-specific endonuclease, MUS81, prevented mitotic but not G2 arrest. Importantly, virion-incorporated Vpr was sufficient to induce cellular changes within 12h post-infection, implying that these events benefit the early stages of HIV infection. Author SummaryVpr is an accessory protein found in primate lentiviruses. Like other retroviral accessory proteins, it is not absolutely required for viral replication but is thought to overcome a cellular factor that negatively regulates infection. The most well-documented effect of Vpr expression is cell cycle arrest in G2. This has been linked to activation of the DNA damage response (DDR) pathway but there are conflicting reports in the literature as to the mechanism behind this. Here, we show that Vpr from some lentiviruses, in fact, cause two separate cell cycle blocks, in G2 and M, that require different DDR pathways. Other Vpr proteins only cause arrest in G2. Furthermore, we show that degradation of one reported target of Vpr, MUS81, is specifically linked to M but not G2 arrest. This indicates that not all Vpr functions are conserved and helps explain contradictory published results. Additionally, we found that virion-incorporated Vpr protein was able to induce cellular changes, including elevated dNTP levels, within 12 hours of infection suggesting that these events enhance early HIV-1 replication events.

microbiology↗

bioRxiv2024

Sediment-associated processes drive spatial variation in ecosystem respiration in the Yakima River basin

Hyporheic zones (HZ) can contribute substantially to total stream ecosystem respiration (ERtot). HZ-focused process-based models may, therefore, effectively predict ERtot across sites, yet this remains untested under variable environmental conditions. Here we evaluate whether spatial variation in HZ respiration predicted via a process-based model explains spatial variation in field-estimates of ERtot across 33 sites in the Yakima River basin in Washington State, USA. We found that HZ respiration predictions did not explain spatial variation in field estimates of ERtot. To investigate further, we partitioned ERtot contributions into water column respiration (ERwc) and sediment-associated respiration (ERsed). ERsed contributed >50% of ERtot at 88% of sites, though relative contributions varied substantially. Despite this dominance, modeled HZ respiration explained neither spatial variation in ERtot nor in ERsed, suggesting that the HZ model alone does not capture the drivers of sediment-associated respiration across these sites. Instead, ERsed spatial variation was primarily explained by gross primary production, stream slope, velocity, and total dissolved nitrogen rather than median grain size, a primary control of HZ respiration predicted by the process-based model. Consistent with recent studies, our results indicate that improving basin-scale ERtot predictions requires integrating hydrologic and biogeochemical processes across hyporheic, benthic, and water column zones.

ecology↗

bioRxiv2023

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Until recent events, the Antarctic was the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) had never previously been detected. The current panzootic of H5N1 HPAIV has decimated wild bird populations across Europe, North America, and South America. Here we report on the detection of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands, respectively. We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8th October 2023. Since this detection, mortalities were observed in brown skuas, kelp gulls, South Georgia shag, Antarctic tern, elephant seals and fur seals at multiple sites across South Georgia. Subsequent testing confirmed H5N1 HPAIV across several sampling locations in multiple avian species and two seal species. Simultaneously, we also confirmed H5N1 HPAIV in southern fulmar and black-browed albatross in the Falkland Islands. Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Critically, genetic assessment of sequences from mammalian species demonstrates no increased risk to human populations. Here we describe the detection, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region. We also speculate on the threat to specific populations following recent reports in the area.

microbiology↗

bioRxiv2023

Loss of type VI secretion systems in multi-drug resistant Escherichia coli clones

The repeated emergence of multi-drug resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonisation observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug resistant E. coli clones. We employed large scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20,000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterised the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones. Data SummaryThe genome sequence data generated in this study is publicly available from NCBI under BioProject PRJNA943186, alongside a complete assembly in GenBank under accessions CP120633-CP120634. All other sequence data used in this paper has been taken from ENA with the appropriate accession numbers listed within the methods section. The E. coli genome data sets used in this work are from a previous publication, the details of which can be found in the corresponding supplementary data files 10.6084/m9.figshare.21360108 [1]. Impact StatementEscherichia coli is a globally significant pathogen that causes the majority of urinary tract infections. Treatment of these infections is exacerbated by increasing levels of drug resistance. Pandemic multi-drug resistant (MDR) clones, such as ST131-C2/H30Rx, contribute significantly to global disease burden. MDR E. coli clones are able to colonise the human gut and displace the resident commensal E. coli. It is important to understand how this process occurs to better understand why these pathogens are so successful. Type VI secretion systems may be one of the antagonistic systems employed by E. coli in this process. Our findings provide the first detailed characterisation of the T6SS loci in ST410 and ST131 and shed light on events in the evolutionary pathways of the prominent MDR pathogens ST410-B4/H42RxC and ST131-C2/H30Rx.

microbiology↗

bioRxiv2023

A Horizontal View of Primary Metabolomes in Vegetative Desiccation Tolerance

Vegetative desiccation tolerance (VDT), the ability of such tissues to survive the near complete loss of cellular water, is a rare but polyphyletic phenotype. It is a complex multifactorial trait, typified by some near universal (core) factors but with many and varied adaptations due to plant architecture, biochemistry and biotic/abiotic dynamics of particular ecological niches. The ability to enter into a quiescent biophysically stable state is what ultimately determines desiccation tolerance. Thus, understanding of the metabolomic complement of plants with VDT gives insight into the nature of survival as well as evolutionary aspects of VDT. In this study we measured the soluble carbohydrate profiles and the polar, TMS-derivatisable metabolomes of 7 phylogenetically diverse species with VDT, in contrast with 3 desiccation sensitive (DS) species, under conditions of full hydration, severe water deficit stress, and desiccated. Our study confirmed the existence of core mechanisms of VDT systems relying on either constitutively abundant trehalose, or the accumulation of raffinose family oligosaccharides and sucrose, with threshold ratios conditioned by other features of the metabolome. DS systems did not meet these ratios. Considerable chemical variations among VDT species suggest that similar stresses, e.g. photosynthetic stress, are dealt with using different chemical regimes. Furthermore, differences in timing of metabolic shifts suggest there is not a single "desiccation programme", but that subprocesses are coordinated differently at different phases of drying. There is likely to be constraints on the composition of a viable dry state and how different adaptive strategies interact with the biophysical constraints of VDT.

plant biology↗

bioRxiv2023

Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two subassemblies; Retriever composed of VPS35L, VPS26C and VPS29, and the CCC complex which contains ten subunits COMMD1-COMMD10 and two coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy and in silico predictions we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilised by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a sixteenth subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.

biochemistry↗

bioRxiv2022

Longitudinal, Multi-platform Metagenomics Yields a High-quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities

Microbiomes are intricately intertwined with human health, geochemical cycles and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combine longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese, co-existence of closely related Psychrobacter species, and enabled the prediction of plasmid and phage diversity and their host associations. Combined with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. ImportanceMetagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, then allow the testing of these hypotheses in a controlled manner. Here, we first generate an extensive longitudinal metagenomic dataset. This dataset reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and functions associated with, cheese rind microbiomes.

microbiology↗

bioRxiv2022

SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export

SARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis. Author SummarySARS-CoV-2 is the virus responsible for the current COVID-19 pandemic. Coronaviruses, like SARS-CoV-2, replicate their genome in the cytoplasm of the host cell by hijacking the cellular machinery. In addition to structural proteins and viral enzymes, SARS-CoV-2 encodes 9 accessory proteins. Although these are not required for in vitro replication, they are thought to modulate the host cell environment to favour viral replication. In this work, we show that the ORF6 accessory protein can supress cellular protein production by blocking mRNA nuclear export through interacting with the cellular protein Rae1, a known mRNA export factor. We also investigated which cellular mRNAs were retained in the nucleus when ORF6 was overexpressed. Interestingly, we found that ORF6 inhibited the export of many different mRNAs, including those encoding antiviral factors, like IRF1 and RIG-I, even in the absence of stimulation by interferon. Importantly, we found that the export of these mRNAs was similarly affected in the context of SARS-CoV-2 infection. Therefore, we believe we have identified a novel mechanism that SARS-CoV-2 uses to suppress antiviral responses in order to make the cell more permissive to infection.

microbiology↗

bioRxiv2021

Ecological constraints on highly evolvable olfactory receptor genes and morphology

While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. Phyllostomid bats, an ecologically diverse clade that evolved plant-visiting from an insectivorous ancestor, suggest the evolution of novel food detection mechanisms is a key innovation: phyllostomids behaviorally rely strongly on olfaction, while echolocation is supplemental. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration is coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants -- a potential ecological constraint on sensory evolution. Significance StatementThe evolutionary relationship between genes and morphology is complex to decipher, and macroevolutionary trends are often measured independently; this is especially challenging to quantify in unstable genomic regions or hypervariable traits. Odorant cues are detected by proteins encoded by the largest and fasted-evolving gene family in the mammalian genome and expressed in epithelia distributed on elaborate bony structures in the nose, posing a challenge to quantification. Yet, the direct interaction of the olfactory system with environmental signals strongly suggest that selection shapes its immense diversity. In neotropical bats, where reliance on plant-visiting evolved from an insectivorous ancestor, we discovered clear dietary differences amongst species, but only after considering morphological and molecular data simultaneously, emphasizing the power of a coupled analysis.

evolutionary biology↗

bioRxiv2021

Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses

The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the interactions between these lagovirus variants we monitored their geographical distribution and relative incidence over time through a landscape-scale competition study, and from this, revealed potential drivers of epidemiological fitness. Within three years of the arrival of GI.1bP-GI.2 (RHDV2) into Australia, we observed the emergence of two novel recombinant lagovirus variants, GI.4eP-GI.2 (4e-recombinant) in New South Wales and GI.4cP-GI.2 (4c-recombinant) in Victoria. Although both novel recombinants contain the non-structural genes from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the 4c-recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both new recombinant variants replaced the previous dominant parental RHDV2 in their respective geographical areas, despite sharing an identical or near-identical (i.e., single amino acid change) major capsid protein with the parental virus. This suggests that epidemiological fitness of these recombinants was not driven by antigenic variation in the capsid, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the GI4.e recombination event in early to mid-2015, while the five GI.4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights an unprecedented frequency of these events, detectable only due to intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

microbiology↗

bioRxiv2021

Ecological habitat partitioning and feeding specialisations of coastal minke whales (Balaenoptera acutorostrata) using a designated MPA in northeast Scotland

In the design of protected areas for cetaceans, spatial maps rarely take account of the life-history and behaviour of protected species relevant to their spatial ambit, which may be important when modelling population trends or assessing susceptibility to anthropogenic threats. In the present study, we examined the distribution and feeding behaviours of minke whales by age-class (adults versus juveniles) from long-term studies in the Moray Firth in northeast Scotland, where a Marine Protected Area (MPA) has recently been designated. Data were collected from dedicated boat surveys between 2000 and 2019, during which 657 encounters with 774 whales of confirmed age-class (444 juveniles and 330 adults) were recorded from 50,041 km of survey effort, resulting in 224 individual follows. Feeding/foraging whales were documented in 84% of the encounters. Adults and juveniles were occasionally seen together, but their distributions were not statistically correlated, and GIS revealed spatial separation by age-class[-]with juveniles preferring shallow, inshore waters with sandy-gravel sediments and adults preferring deeper, offshore waters with steep benthic slope. Whilst adult minkes employed a range of "active" prey-entrapment specialisations, showing seasonal flexibility in their targeted prey with interindividual variation, juveniles almost exclusively used "passive" (low energy) feeding methods, targeting low-density patches of inshore prey. These findings corroborate the need to incorporate demographic/behavioural data into spatial models when identifying priority areas for protected cetaceans and may be important to adaptive management objectives for the species in the Moray Firth MPA.

ecology↗

bioRxiv2020

First description of Hepatitis E virus in Australian rabbits

We report the first detection of Hepatitis E virus in rabbits in Australia. While conducting metatranscriptomic sequencing of liver samples collected from domestic rabbits that had diedwe detected three samples positive for hepatitis E virus. Two viral genome sequences were obtained, which shared 96% nucleotide identity.

zoology↗

bioRxiv2019

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of the gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. We analysed the faecal microbiome of wild hares and rabbits from a sympatric environment, additionally comparing Illumina and Nanopore sequencing platforms. The faecal microbiomes varied significantly between hares and rabbits, despite both species occupying a similar habitat. Moreover, we identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria, and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the faecal microbiota between hares and rabbits in Australia may be associated with differences in diet, and potentially behaviour, of the host species in their non-native range, which may influence the environmental impacts that these species have in Australia.

ecology↗

bioRxiv2019

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Ectoparasites play an important role in virus transmission among vertebrates. However, little is known about the extent and composition of viruses that pass between invertebrates and vertebrates. In Australia, flies and fleas support the mechanical transmission of viral biological controls against wild rabbits - rabbit haemorrhagic disease virus (RHDV) and myxoma virus. We compared virome structure and composition in rabbits and these associated ectoparasites, sequencing total RNA from multiple tissues and gut contents of wild rabbits, fleas collected from these rabbits, and flies trapped sympatrically. Meta-transcriptomic analyses identified 50 novel viruses from multiple RNA virus families. Rabbits and their ectoparasites were characterised by markedly different viromes: although viral contigs from six virus families/groups were found in both rabbits and ectoparasites, none were vertebrate-associated. A novel calicivirus and picornavirus detected in rabbit caecal content were vertebrate-specific: the newly detected calicivirus was distinct from known rabbit caliciviruses, while the novel picornavirus clustered with the Sapeloviruses. Several Picobirnaviridae were also identified, falling in diverse phylogenetic positions suggestive of an association with co-infecting bacteria. The remaining viruses found in rabbits, and all those from ectoparasites, were likely associated with invertebrates, plants and co-infecting endosymbionts. While no full genomes of vertebrate-associated viruses were detected in ectoparasites, suggestive of major barriers to biological transmission with active replication, small numbers of reads from rabbit astrovirus, RHDV and other lagoviruses were present in flies. This supports the role of flies in the mechanical transmission of RHDV and implies that they may assist the spread of astroviruses.

microbiology↗