Biology subjects

Perry, B. J.

Publications and source records attributed to Perry, B. J..

4 recordsLinked to original sources

bioRxiv2022

Cloacal virome of an ancient host lineage - the tuatara (Sphenodon punctatus) - reveals abundant and diverse diet-related viruses

1.Tuatara (Sphenodon punctatus) are one of the most phylogenetically isolated species and provide a unique host system to study virus evolution. While the tuatara genome, sequenced in 2020, revealed many endogenous viral elements, we know little of the exogenous viruses that infect tuatara. We performed a metatranscriptomics study of tuatara cloaca samples from a wild population on Takapourewa (Stephens Island), Aotearoa New Zealand. From these data we identified 49 potentially novel viral species that spanned 20 RNA viral families and/or orders, the vast majority (48) of which were likely dietary related. Notably, using a protein structure homology search, we identified a highly divergent novel virus within the Picornaviridae which may directly infect tuatara. Additionally, two endogenous tuatara adintoviruses were characterised that exhibited long-term viral-host co-divergence. Overall, our results indicate that the tuatara cloacal virome is highly diverse likely due a large number of dietary related viruses.

microbiology↗

bioRxiv2021

Metagenomic and Metatranscriptomic Analysis Reveals Enrichment for Xenobiotic-Degrading Bacterial Specialists and Xenobiotic-Degrading Genes in a Canadian Prairie Two-Cell Biobed System

Biobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, their microbiome dynamics remain largely understudied both taxonomically and functionally. As such, further characterization of these parameters may aid in the optimization of biobed management and deployment. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two-cell Canadian biobed system before and after a field season of pesticide application. These culture-independent approaches identified an enrichment of xenobiotic-degrading bacteria, such as Afipia, Sphingopyxis and Pseudomonas, and enrichment and transcription of xenobiotic-degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes to Pseudomonas, Oligotropha, Mesorhizobium, Rhodopseudomonas, and Stenotrophomonas taxa.

microbiology↗

bioRxiv2018

Functional and genetic characterization of an incF-type multidrug resistance plasmid isolated from fresh spinach.

The presence of antibiotic-resistant bacteria and clinically-relevant antibiotic resistance genes within raw foods is an on-going food safety concern. It is particularly important to be aware of the microbial quality of fresh produce because foods such as leafy greens including lettuce and spinach are minimally processed and often consumed raw therefore they often lack a microbial inactivation step. This study characterizes the genetic and functional aspects of a mobile, multidrug resistance plasmid, pLGP4, isolated from fresh spinach bought from a farmers market. pLGP4 was isolated using a bacterial conjugation approach. The functional characteristics of the plasmid were determined using multidrug resistance profiling and plasmid stability assays. pLGP4 was resistant to six of the eight antibiotics tested and included ciprofloxacin and meropenem. The plasmid was stably maintained within host strains in the absence of an antibiotic selection. The plasmid DNA was sequenced using an Illumina MiSeq high throughput sequencing approach and assembled into contigs using SPAdes. PCR mapping and Sanger DNA sequencing of PCR amplicons was used to complete the plasmid DNA sequence. Comparative sequence analysis determined that the plasmid was similar to plasmids that have been frequently associated with multidrug resistant clinical isolates of Klebsiella spp. DNA sequence analysis showed pLGP4 harboured qnrB1 and several other antibiotic resistance genes including three {beta}-lactamases: blaTEM-1, blaCTX-M-15 and blaOXA-1. The detection of a multidrug-resistant, clinically-relevant plasmid on fresh spinach emphasizes the importance for vegetable producers to implement evidence-based food safety approaches into their production practises to ensure the food safety of leafy greens.

microbiology↗

bioRxiv2018

Identifying the core bacterial and fungal communities within four agricultural biobeds used for the treatment of pesticide rinsates.

Bacterial and fungal communities of four pesticide rinsate treatment biobeds constructed in Alberta and Saskatchewan, Canada were profiled via high throughput DNA sequencing to assess the effect of biobed depth and pesticide application on microbial community composition. Biobeds differed in geographical location and biobed design, and composition of pesticide rinsates (including herbicides, fungicides, and insecticides). All biobeds achieved similar treatment efficacy and supported greater bacterial diversity relative to fungal diversity, yet selected for similar abundant bacterial orders of Actinomycetales, Acidobacteria, Rhizobiales, and Sphingobacteriales and fungal taxonomic groups of Dothideomycetes, Eurotiales, Hypocreales, and Sordariales. Biobeds differed in the presence of unique and differentiated genera and operational taxonomic units. Biobed depth did not uniformly impact the diversity and/or the microbial community structure. Overall, pesticide application increased bacterial diversity, but had limited effect on the more variable fungal diversity, therefore suggesting broader implication for the effect of applied fungicides on biobed fungal communities.\n\nHighlightsO_LIBiobeds support diverse bacterial and fungal communities\nC_LIO_LISpecific \"core\" bacterial and fungal taxa are abundant in biobeds of different design and treatment\nC_LIO_LIMicrobial diversity is not directly linked with pesticide type or diversity.\nC_LI

microbiology↗