Creating wildlife habitat using artificial structures: a review of their efficacy and potential use in solar farms.

The biodiversity crisis is exacerbated by a growing human population modifying nearly three-quarters of the Earth's land surface area for anthropogenic uses. Habitat loss and modification represent the largest threat to biodiversity and finding ways to offset species decline has been a significant undertaking for conservation. Landscape planning and conservation strategies can enhance habitat suitability for biodiversity in human-modified landscapes. Artificial habitat structures such as artificial reefs, nest boxes, chainsaw hollows, artificial burrows, and artificial hibernacula have all been successfully implemented to improve species survival in human-modified and fragmented landscapes. As the global shift towards renewable energy sources continues to rise, the development of photovoltaic systems is growing exponentially. Large-scale renewable projects, such as photovoltaic solar farms have large space requirements and thus have the potential to displace local wildlife. We discuss the feasibility of 'conservoltaic systems' - photovoltaic systems that incorporate elements tailored specifically to enhance wildlife habitat suitability and species conservation. Artificial habitat structures can potentially lessen the impacts of industrial development (e.g., photovoltaic solar farms) through strategic landscape planning and an understanding of local biodiversity requirements to facilitate recolonization.

How turtles keep their cool: Seasonal and diel basking patterns in a tropical turtle.

Behavioural thermoregulation by ectotherms is an important mechanism for maintaining body temperatures to optimise physiological performance. Experimental studies suggest that nocturnal basking by Krefft's river turtles (Emydura macquarii krefftii) in the tropics may allow them to avoid high water temperatures, however, this hypothesis has yet to be tested in the field. In this study, we examined the influence of environmental temperature on seasonal and diel patterns of basking in E. m. krefftii in tropical north Queensland, Australia. Wildlife cameras were used to document turtle basking events for seven consecutive days and nights for each month over a year (April 2020-March 2021). Air and water temperatures were recorded simultaneously using temperature loggers. We used a negative binomial mixed effects model to compare mean basking durations (min) occurring among four environmental temperature categories based on population thermal preference (26 °C): 1) air temperature above and water temperature below preferred temperature; 2) air temperature below and water temperature above preferred temperature; 3) air and water temperatures both above preferred temperature; and 4) air and water temperatures both below preferred temperature. Basking behaviour was influenced significantly by the relationship between air and water temperature. During the day, turtles spent significantly less time basking when both air and water temperatures were above their preferred temperatures. Conversely, at night, turtles spent significantly more time basking when water temperatures were warm and air temperatures were cool relative to their preferred temperature. This study adds to the growing body of work indicating pronounced heat avoidance as a thermoregulatory strategy among tropical reptile populations.

Comparison of home range size, habitat use and the influence of resource variations between two species of greater gliders (Petauroides minor and Petauroides volans).

Knowledge of the spatial requirements of a species is fundamental to understanding its environmental requirements. However, this can be challenging as the size of a species' home range can be influenced by ecological factors such as diet and size-dependent metabolic demands, as well as factors related to the quality of their habitat such as the density and distribution of resources needed for food and shelter. Until recently, the genus Petauroides was thought to include only a single species with a widespread distribution across eastern Australia. However, a recent study has provided genetic and morphological evidence supporting Petauroides minor as a distinct northern species. Previous studies have focused on the ecology of P. volans, but there has been inadequate research on P. minor. Data on home range and habitat use were obtained for both species using a combination of techniques including GPS collar locations, radiotelemetry, and spotlighting and comparisons were made using consistent methodology. Home range sizes of P. minor (4.79 ha ± 0.97 s.d., KUD .95) were significantly larger than those of P. volans (2.0 ha ± 0.42 s.d., KUD .95). There were no significant differences between male and female home range sizes in either species. Both species showed site-specific preferences for tree species and for larger diameter trees for both forage and shelter. Tree size and biomass/ha were significantly greater in the P. volans study sites than the P. minor study sites and there was a negative correlation between home range size and eucalypt biomass. Larger home range size is likely driven by the substantial differences in biomass between northern (tropical) and southern (temperate) eucalypt-dominated habitats affecting the quality and quantity of resources for food and shelter. Understanding landscape use and habitat requirements within each species of Petauroides can provide important information regarding limiting factors and in directing conservation and management planning.

Leech removal is not the primary driver of basking behavior in a freshwater turtle.

Leaving the water to bask (usually in the sun) is a common behavior for many freshwater turtles, with some species also engaging in "nocturnal basking." Ectoparasite removal is an obvious hypothesis to explain nocturnal basking and has also been proposed as a key driver of diurnal basking. However, the efficacy of basking, day or night, to remove leeches has not been experimentally tested. Therefore, we examined the number of leeches that were removed from Krefft's river turtles (Emydura macquarii krefftii) after experimentally making turtles bask at a range of times of day, durations, and temperatures. Turtles had high initial leech loads, with a mean of 32.1 leeches per turtle. Diurnal basking under a heat lamp for 3 hr at ~28°C significantly reduced numbers of leeches relative to controls. In diurnal trials, 90.9% of turtles lost leeches (mean loss of 7.1 leeches per turtle), whereas basking for 30 min under the same conditions was not effective (no turtles lost leeches, and all turtles were still visibly wet). Similarly, "nocturnal basking" at ~23°C for 3 hr was not effective at removing leeches. Only 18% of turtles lost leeches (one turtle lost one leech and another lost four leeches). Diurnal basking outdoors under direct sunlight for 20 min (mean temp = 34.5°C) resulted in a small reduction in leeches, with 50% of turtles losing leeches and an average loss of 0.7 leeches per turtle. These results indicate basking can remove leeches if temperatures are high or basking durations are long. However, it was only effective at unusually long basking durations in this system. Our data showed even the 20-min period was longer than 70.1% of natural diurnal basking events, many of which took place at cooler temperatures. Therefore, leech removal does not appear to be the purpose of the majority of basking events.

Geckos cling best to, and prefer to use, rough surfaces.

BACKGROUND: Fitness is strongly related to locomotor performance, which can determine success in foraging, mating, and other critical activities. Locomotor performance on different substrates is likely to require different abilities, so we expect alignment between species' locomotor performance and the habitats they use in nature. In addition, we expect behaviour to enhance performance, such that animals will use substrates on which they perform well. METHODS: We examined the associations between habitat selection and performance in three species of Oedura geckos, including two specialists, (one arboreal, and one saxicolous), and one generalist species, which used both rocks and trees. First, we described their microhabitat use in nature (tree and rock type) for these species, examined the surface roughnesses they encountered, and selected materials with comparable surface microtopographies (roughness measured as peak-to-valley heights) to use as substrates in lab experiments quantifying behavioural substrate preferences and clinging performance. RESULTS: The three Oedura species occupied different ecological niches and used different microhabitats in nature, and the two specialist species used a narrower range of surface roughnesses compared to the generalist. In the lab, Oedura geckos preferred substrates (coarse sandpaper) with roughness characteristics similar to substrates they use in nature. Further, all three species exhibited greater clinging performance on preferred (coarse sandpaper) substrates, although the generalist used fine substrates in nature and had good performance capabilities on fine substrates as well. CONCLUSION: We found a relationship between habitat use and performance, such that geckos selected microhabitats on which their performance was high. In addition, our findings highlight the extensive variation in surface roughnesses that occur in nature, both among and within microhabitats.

Nonlinear variation in clinging performance with surface roughness in geckos.

Understanding the challenges faced by organisms moving within their environment is essential to comprehending the evolution of locomotor morphology and habitat use. Geckos have developed adhesive toe pads that enable exploitation of a wide range of microhabitats. These toe pads, and their adhesive mechanisms, have typically been studied using a range of artificial substrates, usually significantly smoother than those available in nature. Although these studies have been fundamental in understanding the mechanisms of attachment in geckos, it is unclear whether gecko attachment simply gradually declines with increased roughness as some researchers have suggested, or whether the interaction between the gekkotan adhesive system and surface roughness produces nonlinear relationships. To understand ecological challenges faced in their natural habitats, it is essential to use test surfaces that are more like surfaces used by geckos in nature. We tested gecko shear force (i.e., frictional force) generation as a measure of clinging performance on three artificial substrates. We selected substrates that exhibit microtopographies with peak-to-valley heights similar to those of substrates used in nature, to investigate performance on a range of smooth surfaces (glass), and fine-grained (fine sandpaper) to rough (coarse sandpaper). We found that shear force did not decline monotonically with roughness, but varied nonlinearly among substrates. Clinging performance was greater on glass and coarse sandpaper than on fine sandpaper, and clinging performance was not significantly different between glass and coarse sandpaper. Our results demonstrate that performance on different substrates varies, probably depending on the underlying mechanisms of the adhesive apparatus in geckos.

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

Heat seekers: A tropical nocturnal lizard uses behavioral thermoregulation to exploit rare microclimates at night.

Environmental temperatures play a vital role in the physiological and behavioral activity of ectotherms. Behavioral thermoregulation allows animals to modify their body temperature to optimize functions critical to fitness, including digestion, growth, reproduction, and locomotor performance. Diurnal reptiles are a classic model system to answer questions related to thermal ecology, whereas behavioral thermoregulation in nocturnal species is thought to be strongly constrained by low environmental thermal heterogeneity at night. The few studies describing the thermal ecology of nocturnal reptiles indicate a majority of thermoregulatory behavior (if any) occurs during the day within diurnal retreats, but few examined this behavior throughout the night. In tropical systems, thermal heterogeneity may remain high, even at night, allowing nocturnal ectotherms to thermoregulate through conduction on surfaces that retain heat after sunset. We investigated the thermoregulatory behavior of a tropical nocturnal gecko (Australian house gecko, Gehyra dubia) by measuring its preferred temperature in a thermal gradient, and selected body temperatures using radio telemetry, in relation to available operative environmental temperatures obtained using thermal models. Preferred body temperatures of geckos ranged from 31.4 ±â€¯0.59-34.5 ±â€¯0.55 °C in a laboratory thermal gradient. In the field, during winter, geckos were more effective thermoregulators than in the summer. In low thermal quality habitats, geckos sought rare, warm microclimates at night to maintain body temperatures warmer than most available environmental temperatures, and were highly effective thermoregulators. For ectotherms, appropriate environmental temperatures are a vital resource for survival, similar to food or shelter. The ability to exploit rare microclimates is especially important for nocturnal species, as heterogeneity of environmental temperatures is reduced at night compared to the day. In a warming world, it is vital to understand the thermal ecology of nocturnal ectotherms, as other species may shift to become more nocturnal to avoid lethal diurnal temperatures.

Predation risk is a function of alternative prey availability rather than predator abundance in a tropical savanna woodland ecosystem.

Typically, factors influencing predation risk are viewed only from the perspective of predators or prey populations but few studies have examined predation risk in the context of a food web. We tested two competing hypotheses regarding predation: (1) predation risk is dependent on predator density; and (2) predation risk is dependent on the availability of alternative prey sources. We use an empirical, multi-level, tropical food web (birds-lizards-invertebrates) and a mensurative experiment (seasonal fluctuations in abundance and artificial lizards to estimate predation risk) to test these hypotheses. Birds were responsible for the majority of attacks on artificial lizards and were more abundant in the wet season. Artificial lizards were attacked more frequently in the dry than the wet season despite a greater abundance of birds in the wet season. Lizard and invertebrate (alternative prey) abundances showed opposing trends; lizards were more abundant in the dry while invertebrates were more abundant in the wet season. Predatory birds attacked fewer lizards when invertebrate prey abundance was highest, and switched to lizard prey when invertebrate abundance reduced, and lizard abundance was greatest. Our study suggests predation risk is not predator density-dependent, but rather dependent on the abundance of invertebrate prey, supporting the alternative prey hypothesis.

PATRIC as a unique resource for studying antimicrobial resistance.

The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need to perform genomic and other 'omic' data analyses. In response to mounting concern over antimicrobial resistance (AMR), the PATRIC team has been developing new tools that help researchers understand AMR and its genetic determinants. To support comparative analyses, we have added AMR phenotype data to over 15 000 genomes in the PATRIC database, often assembling genomes from reads in public archives and collecting their associated AMR panel data from the literature to augment the collection. We have also been using this collection of AMR metadata to build machine learning-based classifiers that can predict the AMR phenotypes and the genomic regions associated with resistance for genomes being submitted to the annotation service. Likewise, we have undertaken a large AMR protein annotation effort by manually curating data from the literature and public repositories. This collection of 7370 AMR reference proteins, which contains many protein annotations (functional roles) that are unique to PATRIC and RAST, has been manually curated so that it projects stably across genomes. The collection currently projects to 1 610 744 proteins in the PATRIC database. Finally, the PATRIC Web site has been expanded to enable AMR-based custom page views so that researchers can easily explore AMR data and design experiments based on whole genomes or individual genes.

Disparities in spread and control of influenza in slums of Delhi: findings from an agent-based modelling study.

OBJECTIVES: This research studies the role of slums in the spread and control of infectious diseases in the National Capital Territory of India, Delhi, using detailed social contact networks of its residents. METHODS: We use an agent-based model to study the spread of influenza in Delhi through person-to-person contact. Two different networks are used: one in which slum and non-slum regions are treated the same, and the other in which 298 slum zones are identified. In the second network, slum-specific demographics and activities are assigned to the individuals whose homes reside inside these zones. The main effects of integrating slums are that the network has more home-related contacts due to larger family sizes and more outside contacts due to more daily activities outside home. Various vaccination and social distancing interventions are applied to control the spread of influenza. RESULTS: Simulation-based results show that when slum attributes are ignored, the effectiveness of vaccination can be overestimated by 30%-55%, in terms of reducing the peak number of infections and the size of the epidemic, and in delaying the time to peak infection. The slum population sustains greater infection rates under all intervention scenarios in the network that treats slums differently. Vaccination strategy performs better than social distancing strategies in slums. CONCLUSIONS: Unique characteristics of slums play a significant role in the spread of infectious diseases. Modelling slums and estimating their impact on epidemics will help policy makers and regulators more accurately prioritise allocation of scarce medical resources and implement public health policies.

Isolation and molecular characterization of group B Streptococcus from laboratory Long-Evans rats (Rattus norvegicus) with and without invasive group B streptococcal disease.

Purpose. Group B Streptococcus (S. agalactiae, GBS) is a Gram-positive opportunistic pathogen that inhabits the respiratory, urogenital and gastrointestinal tracts of humans and animals. Maternal colonization of GBS is a risk factor for a spectrum of clinical diseases in humans and a principle cause of neonatal meningitis and septicaemia.Methodology. We describe polymicrobial sepsis including GBS in two gravid adult female Long-Evans rats experiencing acute mortality from a colony of long-term breeding pairs. Fluorescent in situ hybridization confirmed GBS association with pathological changes in affected tissues, including the heart and uterus.Results. Characterization of seven GBS strains obtained from clinically affected and non-affected animals indicated similar antibiotic resistance and susceptibility patterns to that of human strains of GBS. The rat strains have virulence factors known to contribute to pathogenicity, and shared serotypes with human invasive isolates. Phylogenetic analyses revealed that one rat-derived GBS strain was more closely related to human-derived strains than other rat-derived strains, strengthening the notion that interspecies transmission is possible.Conclusions. To our knowledge, this is the first investigation of genotypic and phenotypic features of rat-derived GBS strains and their comparison to human- and other animal-derived GBS strains. Since GBS commonly colonizes commercially available rats, its exclusion as a potential pathogen for immunocompromised or stressed animals is recommended.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.

The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by 'virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.

The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.

UNLABELLED: Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical syndromes, most commonly skin infections in immunocompromised individuals. M. haemophilum exhibits a unique requirement for iron supplementation to support its growth in culture, but the basis for this property and how it may shape pathogenesis is unclear. Using a combination of Illumina, PacBio, and Sanger sequencing, the complete genome sequence of M. haemophilum was determined. Guided by this sequence, experiments were performed to define the basis for the unique growth requirements of M. haemophilum. We found that M. haemophilum, unlike many other mycobacteria, is unable to synthesize iron-binding siderophores known as mycobactins or to utilize ferri-mycobactins to support growth. These differences correlate with the absence of genes associated with mycobactin synthesis, secretion, and uptake. In agreement with the ability of heme to promote growth, we identified genes encoding heme uptake machinery. Consistent with its propensity to infect the skin, we show at the whole-genome level the genetic closeness of M. haemophilum with Mycobacterium leprae, an organism which cannot be cultivated in vitro, and we identify genes uniquely shared by these organisms. Finally, we identify means to express foreign genes in M. haemophilum. These data explain the unique culture requirements for this important pathogen, provide a foundation upon which the genome sequence can be exploited to improve diagnostics and therapeutics, and suggest use of M. haemophilum as a tool to elucidate functions of genes shared with M. leprae. IMPORTANCE: Mycobacterium haemophilum is an emerging pathogen with an unknown natural reservoir that exhibits unique requirements for iron supplementation to grow in vitro. Understanding the basis for this iron requirement is important because it is fundamental to isolation of the organism from clinical samples and environmental sources. Defining the molecular basis for M. haemophilium's growth requirements will also shed new light on mycobacterial strategies to acquire iron and can be exploited to define how differences in such strategies influence pathogenesis. Here, through a combination of sequencing and experimental approaches, we explain the basis for the iron requirement. We further demonstrate the genetic closeness of M. haemophilum and Mycobacterium leprae, the causative agent of leprosy which cannot be cultured in vitro, and we demonstrate methods to genetically manipulate M. haemophilum. These findings pave the way for the use of M. haemophilum as a model to elucidate functions of genes shared with M. leprae.

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

MOTIVATION: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. RESULTS: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. AVAILABILITY AND IMPLEMENTATION: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. CONTACT: anwarren@vt.edu SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

Effective scatterer diameter estimates for broad scatterer size distributions.

Acoustic form factors have been used to model the frequency dependence of acoustic scattering in phantoms and tissues. This work demonstrates that a broad range of scatterer sizes, individually well represented by Faran theory or a Gaussian form factor, is not accurately described by a single effective scatterer from either of these models. Contributions from a distribution of discrete scatterer sizes for two different form factor functions (Gaussian form factors and scattering functions from Faran's theory) were calculated and linearly combined. Composite form factors created from Gaussian distributions of scatterer sizes centered at 50 µm with standard deviations of up to σ = 40 µm were fit to each scattering model between 2 and 12 MHz. Scatterer distributions were generated using one of two assumptions: the number density of the scatterer diameter distribution was Gaussian distributed, or the volume fraction of each scatterer diameter in the distribution was Gaussian distributed. Each simulated form factor was fit to a single-diameter form factor model for Gaussian and exponential form factors. The mean-squared error (MSE) between the composite simulated data and the best-fit single-diameter model was smaller with an exponential form factor model, compared with a Gaussian model, for distributions with standard deviations larger than 30% of the centroid value. In addition, exponential models were shown to have better ability to distinguish between Faran scattering model-based distributions with varying center diameters than the Gaussian form factor model. The evidence suggests that when little is known about the scattering medium, an exponential scattering model provides a better first approximation to the scattering correlation function for a broad distribution of spherically symmetric scatterers than when a Gaussian form factor model is assumed.

PATRIC, the bacterial bioinformatics database and analysis resource.

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.

Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote-microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan's aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host-microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.

A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle.

We present the draft genome for the Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among Rickettsia species (Alphaproteobacteria: Rickettsiales), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes. In particular, an integrative conjugative element named RAGE (for Rickettsiales amplified genetic element), previously identified in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the tra genes encoded in the Rickettsia bellii and R. massiliae genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ~35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity.