DNA barcodes enable higher taxonomic assignments in the Acari

Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases

Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.

Tick abundance and diversity are substantially lower in thinned vs. unthinned forests in the New Jersey Pinelands National Reserve, USA

Forest thinning is a management tool used in the New Jersey Pinelands and elsewhere to improve forest health and resilience, mitigate wildfire risk, and manage for wildlife. Forest thinning leads to warmer drier microclimates, which have been shown in both field and laboratory studies to reduce tick survival and reproduction. To directly assess the effects of forest thinning on the abundance and diversity of ticks and on the prevalence of tick-borne human pathogens, we sampled ticks weekly from March to November 2021 at three replicated pairs of thinned and unthinned forest sites composed primarily of pitch-pine, shortleaf pine, and various oak species. We characterized microclimate in the understory and forest floor at each sampling plot by deploying multiple data loggers to monitor temperature and relative humidity throughout the study period. As expected, we found that thinned plots were significantly drier and warmer than unthinned plots. We also found that average questing tick abundance was 92% lower in thinned as compared with unthinned plots. Of the three main tick species collected in unthinned plots (Amblyomma americanum, Ixodes scapularis, and Dermacentor albipictus) only A. americanum and a single I. scapularis were collected in thinned plots. Prevalence of Ehrlichia species in A. americanum did not differ between treatments, and the sole I. scapularis collected in a thinned plot was infected with Borrelia burgdorferi sensu lato. However, the significant and much lower tick abundance in thinned plots indicates a lower risk of human-tick encounters. Our results add to the growing evidence that landscape and forest management can reduce local tick abundance, thereby reducing tick-borne disease risk.

Unearthing soil arthropod diversity through DNA metabarcoding

DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.