DNA barcodes expose unexpected diversity in Canadian mites

Morphological Ontogeny, Ecology, and Biogeography of Fuscozetes fuscipes (Acari, Oribatida, Ceratozetidae)

The systematic status of Fuscozetes Sellnick, 1928, is not clear in the literature. Therefore, the morphological ontogeny of F. fuscipes (C.L. Koch, 1844), the type species of this genus, was investigated and compared with its congeners in this study, and a new diagnosis of Fuscozetes is given. The juveniles of F. fuscipes are light brown, with a brown prodorsum, sclerites, epimeres, and legs. In all juveniles, a humeral organ and a humeral macrosclerite are present. The gastronotum of the larva has 12 pairs of setae (h3 is present), whereas the nymphs have 15 pairs. In the larva, the gastronotal shield is weakly developed, and most gastronotal setae are short except for a slightly longer h2. Most of the gastronotal setae are inserted on the microsclerites except for h3, and several other macrosclerites and many microsclerites are present on the hysterosoma. In the nymphs, the gastronotal shield is well developed, with 10 pairs of setae (d-, l-, and h-series, and p1), and setae p2 and p3 are located on a large posteroventral macrosclerite. In all the instars, femora I and II are oval in cross-section, without a large ventral carina. Mitochondrial COI sequence data revealed a deep split between the Nearctic and Palearctic populations of F. fuscipes, and a less, but significant, divergence within each continent. These strong geographical barriers were contrasted with multiple cases of shared haplotypes over long distances in the Palearctic, indicating high migration rates in modern times.

Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils

Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.

Bat ectoparasites: chigger mites (Trombiculidae), ticks (Ixodidae and Argasidae), and bugs (Cimicidae) in the Eastern Palaearctic

Nine species-level taxa of bat ectoparasites, three chigger mites (Trombiculidae), three hard (Ixodidae), and one soft tick (Argasidae) species, as well as two bug (Cimicidae) species from nine bat species hosts were detected in the Eastern Palaearctic. Trombiculid larvae of Leptotrombidium schlugerae, Leptotrombidium album, and Ascoschoengastia latyshevi were first recorded on bats in the temperate zone of eastern Russia. L. schlugerae was more abundant than A. latyshevi in the same study sites in Eastern Siberia, and the main hosts of both chigger species were Plecotus ognevi and Eptesicus nilssonii. Ixodid ticks Dermacentor marginatus, Ixodes simplex, and Ixodes sp. were sampled from bats in Kazakhstan, the Far East, and Eastern Siberia, respectively. Phylogenetic analysis based on Cox1, 16S rDNA, and ITS2 sequences of I. simplex showed that the specimens from the Far East grouped into a clade distributed in the Eastern Palaearctic and India. In turn, the specimen of Ixodes sp. from Eastern Siberia was most closely related to Ixodes soricis and Ixodes angustus with p-distance of 9.8-10.7% (Cox1), suggesting that this tick probably belongs to a new species. Argas vespertilionis larvae were collected from three widespread bat species in Kazakhstan. Two bug species, Cimex pipistrelli and Cimex aff. lectularius, were recorded in the Far East and Eastern Siberia, respectively. Specimens from Transbaikalia were morphologically identified as Cimex lectularius. However, they differed from the latter by 12.5-12.9% of Cox1 sequences, indicating that C. aff. lectularius may be a new species.

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.

Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.

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.

Two Lineages of Oribatid Mites Morphologically Correspond to the Circumpolar Species Ameronothrus nigrofemoratus (Acari, Oribatida) but Differ Genetically as Distinct Species Are Revealed on the Kolguev Island

Data reported from Northern Canada were until recently the only available data on the genetic characteristics of the oribatid mite Ameronothrus nigrofemoratus, which has a circumpolar distribution on the coasts of Arctic seas. A partial cytochrome oxidase I gene (COI) mtDNA sequence was examined in mites morphologically assigned to this species from the Kolguev Island. Two highly divergent phylogenetic lineages of A. nigrofemoratus (7% divergence) were revealed, neither of which was found on the Canadian coast. Four COI amino acid substitutions distinguished one of the lineages from North American A. nigrofemoratus, corresponding to the degree of difference between A. nigrofemoratus and its sister species A. lineatus.

Complete mitochondrial genomes of Thyreophagus entomophagus and Acarus siro (Sarcoptiformes: Astigmatina) provide insight into mitogenome features, evolution, and phylogeny among Acaroidea mites

Mites from the Acaroidea (Sarcoptiformes: Astigmatina) are important pests of various stored products, posing potential threats to preserved foods. In addition, mites can cause allergic diseases. Complete mitochondrial genomes (mitogenomes) are valuable resources for different research fields, including comparative genomics, molecular evolutionary analysis, and phylogenetic inference. We sequenced and annotated the complete mitogenomes of Thyreophagus entomophagus and Acarus siro. A comparative analysis was made between mitogenomic sequences from 10 species representing nine genera within Acaroidea. The mitogenomes of T. entomophagus and A. siro contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region. In Acaroidea species, mitogenomes have highly conserved gene size and order, and codon usage. Among Acaroidea mites, most PCGs were found to be under purifying selection, implying that most PCGs might have evolved slowly. Our findings showed that nad4 evolved most rapidly, whereas cox1 and cox3 evolved most slowly. The evolutionary rates of Acaroidea vary considerably across families. In addition, selection analyses were also performed in 23 astigmatid mite species, and the evolutionary rate of the same genes in different superfamilies exhibited large differences. Phylogenetic results are mostly consistent with those identified by previous phylogenetic studies on astigmatid mites. The monophyly of Acaroidea was rejected, and the Suidasiidae and Lardoglyphidae appeared to deviate from the Acaroidea branch. Our research proposed a review of the current Acaroidea classification system.

DNA Barcoding Reveals Generalization and Host Overlap in Hummingbird Flower Mites: Implications for the Mating Rendezvous Hypothesis

AbstractHummingbird flower mites are assumed to monopolize single host plant species owing to sexual selection for unique mating rendezvous sites. We tested the main assumption of the mating rendezvous hypothesis-extreme host specialization-by reconstructing interactions among tropical hummingbird flower mites and their host plants using DNA barcoding and taxonomic identifications. We collected 10,654 mites from 489 flowers. We extracted DNA from 1,928 mite specimens and amplified the cytochrome c oxidase I (CO1) DNA barcode. We analyzed the network structure to assess the degree of generalization or specialization of mites to their host plants. We recorded 18 species of hummingbird flower mites from three genera (Proctolaelaps, Rhinoseius, and Tropicoseius) interacting with 14 species of plants. We found that generalist mites are common, and congeneric mite species often share host plants. Our results challenge the assumption of strict specialization that supports this system as an example of mating rendezvous evolution.

How Phylogenetics Can Elucidate the Chemical Ecology of Poison Frogs and Their Arthropod Prey

The sequestration by neotropical poison frogs (Dendrobatidae) of an amazing array of defensive alkaloids from oribatid soil mites has motivated an exciting research theme in chemical ecology, but the details of mite-to-frog transfer remain hidden. To address this, McGugan et al. (2016, Journal of Chemical Ecology 42:537-551) used the little devil poison frog (Oophaga sylvatica) and attempted to simultaneously characterize the prey mite alkaloids, the predator skin alkaloids, and identify the mites using DNA sequences. Heethoff et al. (2016, Journal of Chemical Ecology 42:841-844) argued that none of the mite families to which McGugan et al. allocated the prey was thought to possess alkaloids. Heethoff et al. concluded from analyses including additional sequences that the mite species were unlikely to be close relatives of the defended mites. We re-examine this by applying more appropriate phylogenetic methods to broader and denser taxonomic samples of mite sequences using the same gene (CO1). We found, over trees based on CO1 datasets, only weak support (except in one case) for branches critical to connecting the evolution of alkaloid sequestration with the phylogeny of mites. In contrast, a well-supported analysis of the 18S ribosomal gene suggests at least two independent evolutionary origins of oribatid alkaloids. We point out impediments in the promising research agenda, namely a paucity of genetic, chemical, and taxonomic information, and suggest how phylogenetics can elucidate at a broader level the evolution of chemical defense in prey arthropods, sequestration by predators, and the impact of alkaloids on higher-order trophic interactions.

DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea)

Eriophyoid mites (Acari: Eriophyoidea) are among the smallest of terrestrial arthropods and the most species-rich group of herbivorous mites with a high host specificity. However, knowledge of their species diversity has been impeded by the difficulty of their morphological differentiation. This study assembles a DNA barcode reference library that includes 1,850 mitochondrial COI sequences which provides coverage for 45% of the 930 species of eriophyoid mites known from China, and for 37 North American species. Sequence analysis showed a clear barcode gap in nearly all species, reflecting the fact that intraspecific divergences averaged 0.97% versus a mean of 18.51% for interspecific divergences (minimum nearest-neighbor distances) in taxa belonging to three families. Based on these results, we used DNA barcoding to explore the species diversity of eriophyoid mites as well as their host interactions. The 1,850 sequences were assigned to 531 Barcode Index Numbers (BINs). Analyses examining the correspondence between these BINs and species identifications based on morphology revealed that members of 45 species were assigned to two or more BINs, resulting in 1.16 times more BINs than morphospecies. Richness projections suggest that over 2,345 BINs occurred at the sampled locations. Host plant analysis showed that 89% of these mites (BINs) attack only one or two congeneric host species, but the others have several hosts. Furthermore, host-mite network analyses demonstrate that eriophyoid mites are high host-specific, and modularity is high in plant-mite networks. By creating a highly effective identification system for eriophyoid mites in BOLD, DNA barcoding will advance our understanding of the diversity of eriophyoid mites and their host interactions.

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.

Temporal diversity patterns for fungi and mites associated with decaying Sporobolus pumilus (Spartina patens) in the Minas Basin, Nova Scotia

Coastal salt marshes provide many ecosystem services; however, little is known of the biology of decomposer taxa in these systems. This study employed aboveground and belowground litterbags to characterize the fungal and mite communities associated with the dominant salt marsh grass, Sporobolus pumilus, in the Minas Basin, Nova Scotia. Decomposition rates of aboveground and belowground tissues and environmental variables were quantified to contextualize temporal patterns in community composition. Aboveground litterbag mass loss peaked in July and decreased consistently over succeeding months, which positively correlated with fungal richness. Fungal and mite richness displayed inverse relationships over time, with mites gradually increasing in diversity before peaking in November, suggesting the presence of a complex detrital network where mites and fungi respond to different and possibly unrelated environmental cues. This study offers a first look at temporal community dynamics of two neglected groups of decomposers associated with S. pumilus in Canada.

Hidden biodiversity in microarthropods (Acari, Oribatida, Eremaeoidea, Caleremaeus)

A challenge for taxonomists all over the world and across all taxonomic groups is recognizing and delimiting species, and cryptic species are even more challenging. However, an accurate identification is fundamental for all biological studies from ecology to conversation biology. We used a multidisciplinary approach including genetics as well as morphological and ecological data to assess if an easily recognizable, widely distributed and euryoecious mite taxon represents one and the same species. According to phylogenetic (based on mitochondrial and nuclear genes) and species delimitation analyses, five distinct putative species were detected and supported by high genetic distances. These genetic lineages correlate well with ecological data, and each species could be associated to its own (micro)habitat. Subsequently, slight morphological differences were found and provide additional evidence that five different species occur in Central and Southern Europe. The minuteness and the characteristic habitus of Caleremaeus monilipes tempted to neglect potential higher species diversity. This problem might concern several other "well-known" euryoecious microarthropods. Five new species of the genus Caleremaeus are described, namely Caleremaeus mentobellus sp. nov., C. lignophilus sp. nov., C. alpinus sp. nov., C. elevatus sp. nov., and C. hispanicus sp. nov. Additionally, a morphological evaluation of C. monilipes is presented.

Elevational Diversity Patterns of Green Lacewings (Neuroptera: Chrysopidae) Uncovered With DNA Barcoding in a Biodiversity Hotspot of Southwest China

Elevational diversity patterns can reflect the responses of biodiversity to climate change spatially. We investigate the species diversity patterns of green lacewings (an important predatory group of insects) along the gradient of elevation from the Shaluli Mountains (Mts. Shaluli), which belong to the Hengduan Mountains in southwestern China, one of the important hotspots of global biodiversity. We combined multiple approaches, including Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning analysis (ASAP), General Mixed Yule Coalescent (GMYC), Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), to delimit the green lacewings species based on the standard barcoding region of cytochrome c oxidase subunit I (COI). The α-diversity and β-diversity patterns of green lacewings from the Mts. Shaluli along the gradient of elevation were analyzed, with further exploration on how the temperature effect elevational-diversity pattern on broad-scale (county scale) elevational gradients. The DNA barcoding reference library consisted of 40 green lacewing species from the Mts. Shaluli. The α-diversity of green lacewings decreased with the increasing elevation. The temperature was found to have a significant effect on the abundance and Shannon-Wiener diversity index but not on the species richness. Nestedness replaced turnover as the main component of Sørensen’s dissimilarity with the increasing elevation, and greater nestedness occurred at low temperature areas. The combination of a reliable DNA barcoding database could improve the accuracy and efficiency to investigate the species diversity patterns of green lacewings. Temperature, resource, and resultant interspecific competitions may have important roles in explaining the species diversity patterns of green lacewings from the Mts. Shaluli. Priority of conservation should be given to the species at low elevation, middle elevation, and relatively high temperature regions under the background of global climate warming.

Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956

Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.

DNA barcodes enable higher taxonomic assignments in the Acari

Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem's identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID's capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success.

Long-term stasis in acariform mites provides evidence for morphologically stable evolution: Molecular vs. morphological differentiation in Linopodes (Acariformes; Prostigmata)

Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY.

DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.

Urban emergence of Dermanyssus gallinae lineage L1 and Ornithonyssus sylviarum in Hungary: phylogenetic differentiation between the roles of migrating vs transported synanthropic birds

Background

Among Dermanyssoidea, the chicken red mite (Dermanyssus gallinae) and the northern fowl mite (Ornithonyssus sylviarum) are considered to be the cause of high economic losses endured by the poultry industry in the Holarctic region, with O. sylviarum predominating in North America and D. gallinae in Europe. Both species have a short life-cycle (thereby allowing a rapid build-up of massive infestations), a wide range of hosts, synanthropic presence and the ability to bite humans. The aim of this study was to analyze dermanyssoid mite specimens, collected in two human dwellings and two racing pigeon premises in different urban areas in Hungary, with molecular–phylogenetic methods.

Methods

Mite species were identified morphologically. This was followed by DNA extraction and molecular–phylogenetic analyses of selected mites, based on the cytochrome c oxidase subunit I (cox1) and 28S rRNA (28S) genes.

Results

Mites that had invaded a home from a pigeon nest and were linked to human dermatitis were morphologically and molecularly identified as D. gallinae special lineage L1. Specimens collected at all other sampling sites were identified as O. sylviarum, including mites that had invaded a home from a house martin (Delichon urbicum) nest, as well as those which were collected from racing pigeons. House martin- or pigeon-associated O. sylviarum specimens showed the highest sequence identity and closest phylogenetic relationship with conspecific mites reported in GenBank from Israel or Canada, respectively.

Conclusions

Detailed morphological and molecular–phylogenetic analyses of D. gallinae lineage L1 confirmed its status as a cryptic species within D. gallinae (s.l.). Taking into account the well-documented latitudinal migratory routes of house martins between Hungary and Africa, O. sylviarum associated with this bird species most likely arrived on its host from the eastern Mediterranean region. On the other hand, mites collected from pigeons in Hungary showed cox1 genetic homogeneity with North American O. sylviarum, which can only be explained by a long-distance (west-to-east intercontinental) connection of birds and their mites as part of human activity (e.g. transportation to exhibitions or trading). In summary, this is the first molecularly confirmed and phylogenetically analyzed case of O. sylviarum infestation of birds in Hungary, implicating urban environment and involving distant parts of the country. This is also the first report of D. gallinae lineage L1 in central Europe.

Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles

Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.

Discriminating larvae of two syntopic Cychramus species (Coleoptera, Nitidulidae) by means of bar-HRM analysis

Molecular genetic methods are increasingly used to supplement or substitute classical morphology-based species identification. Here, we employ a COI mini-barcode coupled high-resolution melting analysis to quickly, cost-efficiently and reliably determine larvae of two closely related Cychramus (Coleoptera, Nitidulidae) species. Euclidean distance comparison (p < 0.01) and a Welch t-test of the melting point temperatures (p < 0.01) provide highly significant statistical evidence for species specific differences in melting and fluorescence curves, thus allowing the assignment of larvae to either of the two species. This protocol serves as a fast, low-cost and low-tech method to discriminate between pairs or groups of closely related species and can be adapted and applied to various ecological research questions.

The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype-level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.

Water Mite Diversity (Acariformes: Prostigmata: Parasitengonina: Hydrachnidiae) from Karst Ecosystems in Southern of Mexico: A Barcoding Approach

Water mites represent the most diverse and abundant group of Arachnida in freshwater ecosystems, with about 6000 species described; however, it is estimated that this number represents only 30% of the total expected species. Despite having strong biotic interactions with their community and having the potential to be exceptional bioindicators, they are frequently excluded from studies of water quality or ecology, due to actual and perceived difficulties of taxonomic identification in this group. The objective of this study is to use the variations in the sequences of the mitochondrial cytochrome oxidase subunit I (COI), also known as the DNA barcodes region, as a tool to assess the diversity of water mites at 24 sites in the Yucatan Peninsula of Mexico. We found 77 genetic groups or putative species corresponding to 18 genera: Arrenurus, Atractides, Centrolimnesia, Eylais, Geayia, Hydrodroma, Hydryphantes, Hygrobates, Koenikea, Krendowskia, Limnesia, Limnochares, Mamersellides, Mideopsis, Neumania, Piona, Torrenticola, and Unionicola. This was significant, since there are only 35 species described for this region. Furthermore, this molecular information has allowed us to infer that there are characteristic assemblies per site. These data will facilitate the incorporation of water mites in different studies while the curatorial work continues to assign a Linnaean name.

Urbanization and plant invasion alter the structure of litter microarthropod communities

Anthropogenic activity underpins the creation of urban ecosystems, often with introduced or invasive species playing a large role in structuring ecological communities. While the effects of urbanization on charismatic taxa such as birds, bees or butterflies have received much attention, the impacts on small and inconspicuous organisms remain poorly understood. Here, we assess how the community structure of leaf litter-inhabiting microarthropods in city parks varies along an urbanization gradient in Toronto, Canada. At each park, we established paired forest understorey plots which were either dominated by native vegetation or dog-strangling vine Vincetoxicum rossicum, an invasive species that is spreading throughout northeastern North America and abundant in urban areas. We compared microarthropod richness, abundance and diversity in ecological traits between invaded and non-invaded plots as well as compositional dissimilarities among plots across the urbanization gradient. We recorded 123 genera and found (a) there was a negative effect of urbanization on microarthropod richness and abundance but only in invaded plots; (b) richness and abundance increased continuously with urbanization in non-invaded plots, but peaked at intermediate urbanization levels in invaded plots and (c) there was significant turnover with increasing urbanization, with distinct communities represented in highly urbanized areas compared to less urbanized areas, regardless of whether invaded. We also found litter microarthropod richness and abundance increased with soil ammonium and decreased with nitrate. These trends were especially strong for fungivorous microarthropods; however, there was no relationship between soil nutrients and urbanization or invasion. Urbanization and biological invasion drive biodiversity change, and there is a need to disentangle these effects on ecological communities and related ecosystem processes. We show microarthropod communities change with urbanization, with the effects of invasion most prominent in non-urban areas. Here, there is high richness and abundance but low ecological trait diversity, possibly because certain feeding traits are excluded and others overrepresented. Understanding of urban ecological systems must include knowledge of the microarthropods that interact widely across food webs, form distinct communities in highly urban areas and drive many of the important ecological functions upon which people in cities depend.

A DNA Barcoding Survey of an Arctic Arthropod Community: Implications for Future Monitoring

Accurate and cost-effective methods for tracking changes in arthropod communities are needed to develop integrative environmental monitoring programs in the Arctic. To date, even baseline data on their species composition at established ecological monitoring sites are severely lacking. We present the results of a pilot assessment of non-marine arthropod diversity in a middle arctic tundra area near Ikaluktutiak (Cambridge Bay), Victoria Island, Nunavut, undertaken in 2018 using DNA barcodes. A total of 1264 Barcode Index Number (BIN) clusters, used as a proxy for species, were recorded. The efficacy of widely used sampling methods was assessed. Yellow pan traps captured 62% of the entire BIN diversity at the study sites. When complemented with soil and leaf litter sifting, the coverage rose up to 74.6%. Combining community-based data collection with high-throughput DNA barcoding has the potential to overcome many of the logistic, financial, and taxonomic obstacles for large-scale monitoring of the Arctic arthropod fauna.