Higher Taxa Research Articles

Toward a new classification of planthoppers Hemiptera Fulgoromorpha: 2. Higher taxa, their names and their composition

A synthesis of planthopper suprafamilial and familial classification is provided and discussed, solving some nomenclatural issues for the group, and adopting an enriched presentation with a clear distinction between the taxon name and its concept.

Review on Classification and Nomenclature of Viruses

Viruses are subcellular, infectious, non-living creatures that can only replicate and metabolize inside the cells of living hosts. Virus taxonomy is the classification of viruses into categories called taxa. The classification and nomenclature recently gained importance due to the exponentially increasing number of new viruses discovered. Hence the current review on classification and nomenclature of virus aimed to provide sufficient and updated information to readers. Current virus classification is increasingly performed using more complex phylogenetic approaches that move researchers closer to a rudimentary understanding of the origin, evolution, relatedness, and diversification of viruses. In the taxonomic hierarchy of virus, the highest taxa are real and the lowest rank is species. To categorize viruses, phenotypic traits like morphology, nucleic acid type, and mechanism of replication, host organisms, and the sort of disease they cause are taken into consideration. Mostly based on 1. Classical- e.g. Animal, plant, or bacterial virus system- e.g. Naked or enveloped virus. 2. Genomic-Baltimore classification by seven categories: I: dsDNA viruses (e.g. Adeno viruses, Herpes viruses, Pox viruses) II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvo viruses) III: dsRNA viruses (e.g. Reo viruses) IV: (+) ssRNA viruses (+ strand or sense) RNA (e.g. Corona viruses, Picorna viruses, Toga viruses) V: (−) ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxo viruses, Rhabdo viruses). VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retro viruses). VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g. Hepadna viruses). 3. Serology (a corona virus). There isn't a standardized format for virus species names yet, in contrast to the binomial nomenclature used for cellular species. The ICTV now requires that a species name comprise as few words as possible while still being distinct, and must not merely contain the term virus and the host. By responding to a series of questions based on contrasting traits, a species can be identified using the dichotomous key method.

The damselfly genus Furagrion Petrulevičius et al. (Odonata, Zygoptera) from the early Eocene Fur Formation of Denmark and the dysagrionoid grade.

The earliest Eocene odonate genus Furagrion Petrulevičius et al. from the Danish Fur Formation is revised based on eighteen specimens, two of which apparently have been lost since their publication. The holotype of Phenacolestes jutlandicus Henriksen, type species of Furagrion, is incomplete and lacks the characters currently used to differentiate species, genera and higher taxa in Odonata. We, therefore, propose that the holotype is set aside and a recently discovered nearly complete Fur Formation fossil is designated as neotype. Furagrion possesses all of the nine wing character states currently used along with head shape for diagnosing the Dysagrionidae; however, Furagrion has a characteristically zygopteran head, not the distinctive head shape of the suborder Cephalozygoptera. We, therefore, treat it as a zygopteran unassigned to family. These nine wing character states appear in different combinations not only in various Zygoptera and Cephalozygoptera, but also in the Frenguelliidae, an Eocene family of Argentina that may represent an unnamed suborder. We recognise these taxa as constituting a dysagrionoid grade, in which these character states appear either convergently or as symplesiomorphies. Furagrion morsi Zessin is synonymized with Phenacolestes jutlandicus Henriksen, syn. nov. and Morsagrion Zessin with Furagrion Petrulevičius, Wappler, Wedmann, Rust, and Nel, syn. nov.

Soil Microbiome in the Impact Zone of the Pechenganikel Plant Emissions (Murmansk Region)

The microbial parameters in Albic Podzol soil were analyzed along the pollution gradient (3, 16, 30, 50 km) with Pechenganickel plant emissions (Murmansk region). The amount and structure of the prokaryotes and fungi biomass were assessed by the method of luminescent microscopy; the content of microorganism’s ribosomal genes copies was determined by real-time PCR; the taxonomic diversity and abundance of culturable soil microfungi were studied. An increase in the number of genes copies of bacteria, archaea, and fungi close the source of emissions compared to remote areas was revealed. In all plots, the highest number of ribosomal genes copies was found for bacteria (from 3.21 × 1010 to 12 × 1010 per g of soil). For fungi and archaea, the number varied from 0.53 × 1010 to 1.59 × 1010 per g of soil and from 0.55 × 1010 to 11.41 × 1010 gene copies/g of soil, respectively. A significant increase in the actinomycetes biomass close the plant was noted, while the biomass of bacteria and fungi remained practically unchanged at different distances from the emission source. Mycelium and fungal spores in all areas are mainly represented by small forms with a diameter of 2–3 microns. The length of the fungal mycelium varied from 51.2 m/g near the plant to 397 m/g in remote areas, with no regularities in its distribution along the contamination gradient. A decrease in the diversity of soil microfungi at the level of genera and higher taxa along the pollution gradient with plant emissions was noted. A change in the structure of communities from polydominant (background site) to monodominant (near the plant) was revealed. The species Penicillium raistrickii dominated in all plots. Fungi Trichoderma viride, dark-colored yeasts Torula lucifuga (3 km) and Aureobasidium pullulans (16 km) also dominated in the zone 16 km from the emission source. In the background area, representatives of the orders Mucorales and Umbelopsidales were dominant.

Diet Analysis of the African Golden Wolf Canis anthus (Cuvier, 1820) in Tizi-ouzou, Kabylia Region (Algeria)

The diet of the African golden wolf Canis anthus was studied in the region of Tizi-Ouzou (North-Central Algeria), during a period from November 2016 to May 2017 by means of scat analysis. A total of 386 samples were collected in the study area, 206 in Yakouren and 180 in Ait-Zellal. Prey items found in the dung were assigned to species or higher taxa using identification guides and our collection of plant samples from the study area.The identification of the different items allowed us to classify the prey of this carnivore into 8 food categories Mammals, Arthropods, Birds, Energy plants, Non-energy plants, Reptiles, Molluscs and Waste. Plant material, mammals and birds are the most consumed food items in both study stations, with significant differences between the diet compositions of the two habitats. These results confirm that the feeding behaviour of golden wolves is generalist and opportunistic, the existence of a significant difference between the diet compositions in the two different habitats emphasises the influence of environmental factors on the feeding ecology of Canis anthus.

Evolution of genome size and GC content in the tribe Carduinae (Asteraceae)

Genome size and GC content are basic species-specific attributes often delimiting genera or higher taxa, which enable the identification of polyploidy, hybridization and other modes of genome or karyotype evolution. The evolution of these genomic traits can often occur as a result of the selective pressure of the environment. Here, we reconstruct the evolution of these genomic traits in subtribe Carduinae (Asteraceae) in the context of changes in chromosome numbers. Using flow cytometry, genome size and GC content were estimated for 119 taxa and mapped onto a phylogenetic tree constructed using sequences from seven genetic markers. In addition, the genomic data were compared with the length of stomatal guard cells and achene size (length, weight) to evaluate the extent to which genomic characters could evolve adaptively in this subtribe. We found strong phylogenetic signals for the analysed genomic and phenotypic traits, which delimited most Carduinae genera or clades in agreement with the reconstructed phylogeny. Monoploid genome size was positively correlated with genomic GC content and stomatal guard cell length. In Cirsium, whose species were the focus of the majority of the analyses, the large-genomed subgen. Lophiolepis had smaller guard cells, which might be related to it occurring in more xeric habitats compared to subgen. Cirsium. In contrast, the achenes of the large-genomed subgen. Lophiolepis were larger, possibly in response to the summer drought, whereas achene weight and length were independent of genome size across the subtribe. Thus, genome size in the subtribe Carduinae might evolve under weak environmental control, at least under that mediated by the size of guard cells or achenes. Achene size was related positively to GC content, which could have evolved adaptively in response to summer drought. In Carduus and the North American Cirsium taxa, there is an increase in average chromosome size with reduction in monoploid chromosome number, suggesting descending dysploidy associated with chromosomal fusion. Polyploidy is relatively rare in this subtribe and was confirmed only in five of the species studied, including Cirsium vulgare, an invasive species that likely originated via distant (intersubgeneric) hybridization, as suggested by its intermediate genomic and achene features combined with the conflict between its morphology and phylogenetic position. Phylogenetic reconstruction, differences in genomic parameters, as well as stomatal guard cell and achene sizes support the separation of a monophyletic Lophiolepis from the remainder of Cirsium. Genome and achene size results also indicate that the early diverging Cirsium italicum can be separated from the rest of the monophyletic Lophiolepis+Picnomon+Notobasis clade.

An evaluation of platforms for processing camera‐trap data using artificial intelligence

Abstract Camera traps have quickly transformed the way in which many ecologists study the distribution of wildlife species, their activity patterns and interactions among members of the same ecological community. Although they provide a cost‐effective method for monitoring multiple species over large spatial and temporal scales, the time required to process the data can limit the efficiency of camera‐trap surveys. Thus, there has been considerable attention given to the use of artificial intelligence (AI), specifically deep learning, to help process camera‐trap data. Using deep learning for these applications involves training algorithms, such as convolutional neural networks (CNNs), to use particular features in the camera‐trap images to automatically detect objects (e.g. animals, humans, vehicles) and to classify species. To help overcome the technical challenges associated with training CNNs, several research communities have recently developed platforms that incorporate deep learning in easy‐to‐use interfaces. We review key characteristics of four AI platforms—Conservation AI, MegaDetector, MLWIC2: Machine Learning for Wildlife Image Classification and Wildlife Insights—and two auxiliary platforms—Camelot and Timelapse—that incorporate AI output for processing camera‐trap data. We compare their software and programming requirements, AI features, data management tools and output format. We also provide R code and data from our own work to demonstrate how users can evaluate model performance. We found that species classifications from Conservation AI, MLWIC2 and Wildlife Insights generally had low to moderate recall. Yet, the precision for some species and higher taxonomic groups was high, and MegaDetector and MLWIC2 had high precision and recall when classifying images as either ‘blank’ or ‘animal’. These results suggest that most users will need to review AI predictions, but that AI platforms can improve efficiency of camera‐trap‐data processing by allowing users to filter their dataset into subsets (e.g. of certain taxonomic groups or blanks) that can be verified using bulk actions. By reviewing features of popular AI‐powered platforms and sharing an open‐source GitBook that illustrates how to manage AI output to evaluate model performance, we hope to facilitate ecologists' use of AI to process camera‐trap data.

Leishmania infantum infection does not affect the main composition of the intestinal microbiome of the Syrian hamster

BackgroundVisceral leishmaniasis (VL) is the most severe form of all leishmanial infections and is caused by infection with protozoa of Leishmania donovani and Leishmania infantum. This parasitic disease occurs in over 80 countries and its geographic distribution is on the rise. Although the interaction between the intestinal microbiome and the immune response has been established in several pathologies, it has not been widely studied in leishmaniasis. The Syrian hamster is the most advanced laboratory model for developing vaccines and new drugs against VL. In the study reported here, we explored the relationship between the intestinal microbiome and infection with L. infantum in this surrogate host.MethodsMale Syrian hamsters (120–140 g) were inoculated with 108 promastigotes of a canine-derived L. infantum strain or left as uninfected control animals. Infection was maintained for 19 weeks (endpoint) and monitored by an immunoglobulin G (IgG) enyzme-linked immunosorbent assay throughout the experiment. Individual faecal samples, obtained at weeks 16, 18 and 19 post-inoculation, were analysed to determine the 16S metagenomic composition (the operational taxonomic units [OTUs] of the intestinal microbiome and the comparison between groups were FDR (false discovery rate)-adjusted).ResultsLeishmania infantum infection elicited moderate clinical signs and lesions and a steady increase in specific anti-Leishmania serum IgG. The predominant phyla (Firmicutes + Bacteriodetes: > 90%), families (Muribaculaceae + Lachnospiraceae + Ruminococcaceae: 70–80%) and genera found in the uninfected hamsters showed no significant variations throughout the experiment. Leishmania infantum infection provoked a slightly higher—albeit non-significant—value for the Firmicutes/Bacteriodetes ratio but no notable differences were found in the relative abundance or diversity of phyla and families. The microbiome of the infected hamsters was enriched in CAG-352, whereas Lachnospiraceae UCG-004, the [Eubacterium] ventriosum group and Allobaculum were less abundant.ConclusionsThe lack of extensive significant differences between hamsters infected and uninfected with L. infantum in the higher taxa (phyla, families) and the scarce variation found, which was restricted to genera with a low relative abundance, suggest that there is no clear VL infection-intestinal microbiome axis in hamsters. Further studies are needed (chronic infections, co-abundance analyses, intestinal sampling, functional analysis) to confirm these findings and to determine more precisely the possible relationship between microbiome composition and VL infection.Graphical

Nantucket's Neglected Herbivores II: Diptera

Records of Diptera and their hymenopteran parasitoids are reported from a ten-year study of herbivorous insects of Nantucket Island, Massachusetts, USA, with a focus on searching for galls, leaf mines, and other characteristic feeding evidence on host plants. Our field observations and reared specimens are supplemented with herbarium records and Johnson's (1930) list of the insect fauna of Nantucket. Compared with Johnson's list of nine species of Agromyzidae, we identified 53 along with 15 others determined only to genus or higher taxa (a few of the latter could conceivably be conspecific with the former or with one another). We found 37 named species of Cecidomyiidae (including eight of the nine on Johnson's list), as well as 26 others that are undescribed or are currently unidentifiable for other reasons (a few of which could conceivably be conspecific with one of the identified species, or represent galls not actually caused by midges). A few rearings and collections of Anthomyiidae, Chloropidae, Ephydridae, Phoridae, Sphaeroceridae, and Tephritidae are reported, adding another seven species and two genera to Johnson's list. Cerodontha (Dizygomyza) edithae Eiseman and Lonsdale (Agromyzidae), an as yet undescribed species of Ophiomyia Braschnikov (Agromyzidae), Megaselia nantucketensis Eiseman and Hartop (Phoridae), and the cecidomyiid parasitoids Platygaster tephrosiae Buhl and Eiseman and P. vitisiellae Buhl and Eiseman (Hymenoptera: Platygastridae) are known only from specimens reared as part of this study, which also produced paratypes of Liriomyza pistilla Lonsdale (Agromyzidae). Noteworthy cecidomyiid records include the first known specimens of an undescribed Asphondylia Loew on Solidago sempervirens L. (Asteraceae), galls of an undetermined lasiopterid species on Tephrosia virginiana (L.) Pers. (Fabaceae) that have only been found on Nantucket, and previously unreported galls on Gaylussacia baccata (Wangenh.) K. Koch (Ericaceae), Ionactis linariifolia (L.) Greene (Asteraceae) (Dasineura Rondani sp.), Quercus prinoides Willd. (Fagaceae), Salix purpurea L. (Salicaceae), and Solidago latissimifolia Mill. (Asteraceae) (Asphondylia sp., Rhopalomyia Rübsaamen sp.).

Taxonomic review of the subfamily Hypenodinae (Lepidoptera: Erebidae) from Korea

The Hypenodinae are distributed only in the old world, including the temperate zone of eastern Asia. This study was conducted to review the subfamily Hypenodinae, in which the members have been placed under the different higher taxa. A total of 13 species including one new subspecies under 7 genera of two tribes are recognized from Korea in this study. Among them, one new subspecies, Micreremites pyraloides pyraloides ssp. n., is described as new to science and one species Hypenodes turfosalis Wocke, 1850 was treated to synonymize H. humidalis. Also, all available information, including distribution, images of adults, and genitalic structures, were provided.

Grand challenges in feather mite biology

In the 26 years since Gaud and Atyeo (1996) published their seminal work “Feather Mites of the World”, remarkable progress has been made in increasing the number of described feather mite species and host-mite records. Advances in molecular genetic methods are shedding light on relationships both among higher taxa and within species. Nevertheless, there are aspects of these research areas that need further study, as well as many other important areas of feather mite biology that have been almost unexplored since the works of V.B. Dubinin in the 1950’s (e.g., Dubinin, 1951). In this presentation I outline what I feel are desirable targets for future feather mite studies, some of which will be more challenging to achieve than others.

New perspectives on soil animal trophic ecology through the lens of C and N stable isotope ratios of oribatid mites

Knowledge of the trophic ecology of soil animals is important for understanding their high alpha diversity as well as their functional role in soil food webs and systems. In the last 20 years, the analysis of natural variations in stable isotope ratios (15N/14N, 13C/12C) has revolutionized our view on soil animal trophic ecology. Here, we review the state of the art of the trophic ecology of a highly abundant and diverse soil animal taxon, oribatid mites (Oribatida), investigated by stable isotope analyses. The review is based on 25 papers reporting stable isotope data of 292 oribatid mite taxa from 30 different sites. Four main findings emerged. (1) Oribatid mites cluster into six trophic groups, i.e. moss feeders, lichen feeders, primary decomposers, fungal feeders/secondary decomposers, predators/scavengers and marine algal feeders, plus one additional group, which incorporates CaCO3 in their cuticle for defence but still belongs to the fungal feeders/secondary decomposers group. (2) Of the 292 species studied 43.7% were classified as fungal feeders/secondary decomposers, 27.0% as primary decomposers and 15.7% as predators/scavengers, only few species include CaCO3 into their skeleton (6.1%), feed on lichens (4.9%), mosses (2.1%) or marine algae (0.7%). (3) In about one-third of the species studied the trophic niche was constant or varied little between sites or habitats, but in two-thirds of the species their trophic niche varied between habitats, with some species even shifting trophic levels, indicating trophic plasticity. (4) When aggregated at higher taxonomic level oribatid mite species clustered in only three instead of six trophic groups. This indicates that species within the same high level taxon often belong to different trophic groups, for example because feeding habits evolved convergently. Therefore, to accurately reflect the trophic ecology of oribatid mites their stable isotope signatures need to be analysed at species level. However, stable isotope analyses also have limitations, e.g. feeding on bacteria and fungi cannot be separated, and the same is true for feeding on ectomycorrhizal and arbuscular mycorrhizal fungi. Other methods such as fatty acid, amino acid and molecular gut content analyses as well as microbiome analyses may complement stable isotope studies and resolve oribatid mite trophic niche differentiation at a higher resolution. This will contribute to a better understanding of the local coexistence of large numbers of species in soil. Finally, we provide perspectives on how to integrate microarthropods into soil food webs using stable isotope and other methods allowing deeper insight into their trophic structure.

PaleoWood: A machine learning approach for determining the affinity of Paleozoic gymnosperm woods

Fossil plant remains are commonly found in fragments in the sediment, thus complicating the reconstruction and classification of fossil plants into a higher taxonomic group. Particularly for stem anatomy, some described features repeat among the proposed lineages due to environmental pressures that induce anatomical convergence. Other characteristics cannot always be seen because of the fossil's state of preservation, as often happens with the bark and the arrangement of axes and leaves. Given these difficulties, we developed PaleoWood, an unprecedented affinity classifier for Paleozoic gymnosperm woods based on 16 variables collected from 42 consistent genera that have the central core, primary xylem, and secondary xylem described. Similarities among samples were analyzed by principal coordinates, and models were trained through logistic regression, linear discriminant, and k-nearest neighbors algorithms. Models' performance was estimated by cross-validation and testing of the affinity of 20 previously known samples. Results agreed with some hypotheses previously discussed in the literature, such as the linkage of Eristophyton, Megaloxylon, and Tetrastichia with Lyginopteridales. Some other predictions were interpreted to be a result of convergent evolution or the models' limitations, especially those predictions relating to the samples of simple protostele or pycnoxylic pteridosperms (but these models are not definitive and may be improved as new data are collected). Therefore, they could assist in future comparisons and discussions about the taxonomy, evolution, and paleobotanical affinities of the basal seed plants, especially for the woods from Gondwana, in which affinities are obscure for several genera.

Seasonal Patterns of Phytoplankton Taxon Richness in Lakes: Effects of Temperature, Turnover and Abundance

Species richness is a key ecological characteristic that influences numerous ecosystem functions. Here we analyse the patterns and possible causes of phytoplankton taxon richness in seasonal datasets from twenty contrasting lakes in the English Lake District over six years and near-weekly datasets over 33years from Windermere. Taxon richness was lowest in winter and highest in summer or autumn in all of the lakes. Observed richness was very similar to richness estimated from coverage and sampling effort, implying that it closely reflected true seasonal patterns. Summer populations were dominated by Chlorophyta and functional groups X1, F, N and P (sensu Reynolds). In Windermere, weekly taxon richness was strongly positively correlated with surface water temperature, as was the number of functional groups and the number of taxa per functional group. Turnover in richness of taxa and functional groups were positively correlated and both were related to surface temperature. This suggests that high taxon richness in summer is linked to higher water temperature, promoting a turnover in richness of taxa and functional groups in these lakes. However, since the number of taxa per unit concentration of chlorophyll a decreased with increasing concentration of chlorophyll a, competition might occur when abundance is high.

When Specimens Become Environmental Traits: Automating data extraction in aerobiology

The identity of a biological specimen can be considered the most basic type of trait: the species (or higher taxon) the specimen belongs to, one of the three most fundamental data elements (along with location and time) that configure the primary biodiversity data record whose quantification may underpin biological monitoring programs. A general image containing specimens (for example, a photo from a surveillance camera), where individual organisms are to be identified, is akin to an image of a single organism where traits are to be recognized: the individual, often distinct organisms in the image, become the traits of the image. In many cases, automated segmentation and classification/identification and counting of individuals captured within general images containing multiple organisms is most desirable—provided precision and recall exceed a reasonable threshold: that which minimizes the false-positive error rate, as compared to human identification in images. When this occurs, quantitative monitoring data are amenable to good automation, saving much time and human effort. One particularly well-suited case is that of airborne pollen and spore monitoring, hitherto done manually in most of the world. However, systems are being developed that can recognize atmospheric pollen content from images. Two main approaches are possible: either fully automated systems, or recognition from captured field images. In both cases, some instance of artificial intelligence, most often a convolutional neural network, is tasked with the recognition of pollen and spore types, after proper training, from microscopic images. Several problems exist for the wider adoption of such approaches. Among them, the workflow order of segmentation and identification, the portability of the neural network training for different locations, the differences in performance for distinct particle types, and the generation and archival of images: field images vs. individual (segmented) detected specimens, which call for wholly different approaches to metadata. In this presentation we review the general outlook of automated airborne pollen and spore monitoring data, and compare performance data in some specific deep learning settings and workflows, based on actual monitoring work, training and tests with real images.

Quantifying controls on the occurrence of nonmarine fossils

Abstract Although numerous studies have described differential preservation of nonmarine fossils in channel and floodplain facies, quantitative comparisons are lacking. We present measurements of the probability of occurrence of plant, mollusk, and vertebrate fossils in the Campanian Judith River Formation of north-central Montana, USA. The data reveal little difference in the probability of occurrence among higher taxa in channel and floodplain facies, except for plants, which have a higher probability in floodplain deposits. This surprising result supports more recent models in which many organisms are buried initially in floodplain deposits, but those deposits are subsequently exhumed by migrating rivers, and finally buried in those channels. Comparisons across systems tracts revealed intriguing patterns in which plants have a higher probability of occurrence in high-accommodation systems tracts in channel and floodplain deposits, and vertebrates have a higher probability of occurrence in channels of the low-accommodation systems tract. These results confirm that sequence-stratigraphic architecture should be considered in interpretations of the nonmarine fossil record. This probability of occurrence method has promise for many other comparisons of fossilization potential.

The species-level microbiota of healthy eyes revealed by the integration of metataxonomics with culturomics and genome analysis

ObjectivesTo characterize the healthy ocular surface microbiota at the species level, including cultured and uncultured taxa.MethodsWe integrated the metataxonomic method with culturomics and genome sequencing analysis of selected isolated strains to better illustrate the taxonomic structure of the ocular surface microbiota. The metataxonomics used the full-length 16S rRNA gene sequences and the operational phylogenetic unit strategy, which can precisely identify the cultured and uncultured or potentially new taxa to species level based on the phylogenetic tree constructed.ResultsWe detected 1,731 operational phylogenetic units (OPUs) in 196 healthy eyes from 128 people, affiliated to 796 cultured species, 784 potentially new species, and 151 potentially new higher taxa. The microbiota for each eye had 49.17 ± 35.66 OPUs. Of the 796 cultured species, 170 (21.36%) had previously caused clinical infections. Based on where they were initially isolated, the ocular surface microbiota mainly came from human body sites (34.55%), the environment (36.93%), plants (9.05%), animals (4.90%), and others; 428 strains were isolated from 20 eyes, affiliated to 42 species, and had come from the environment (33.33%) and the skin (16.67%). Of these, 47.62% had previously caused clinical infections. Genome analysis of 73 isolators revealed that 68.5% of them carried antibiotic resistance genes. The most frequently isolated genera, namely Staphylococcus, Streptococcus, and Moraxella, had an average of 5.30, four, and three resistance genes per strain, respectively.DiscussionThe study found that the ocular surface microbiota mainly came from the environment, plants, animals, food, and human body sites such as the skin, oral cavity, upper respiratory tract, etc. No core member of ocular surface microbiota was detected at the species level. The human eyes were invaded and colonized by bacteria from the exposed environment, some of which were capable of causing infections in humans and carried antibiotic resistance genes. Preventive measures should be developed to protect our eyes from danger.

Extended Taxonomic Curation: Moving beyond species lists to linking species data

Taxonomy is at the center of modern biodiversity science. No species can be systematically studied until it is defined, and no observation can be linked to related data without a taxonomic label. However, taxonomy is also a science in constant flux—even well-studied groups like Mammalia have fluctuated by >25% in recognized species in the last decade (Burgin et al. 2018, MDD 2022a, MDD 2022b). As a result, there are calls to create a “global list of accepted species” to increase taxonomic stability, particularly for policy decisions in biodiversity conservation and management (Garnett et al. 2020). The counterargument notes that forcing definitional consensus is likely to further inequities, and that a pluralistic, coordinated approach to taxonomy can be achieved with innovative cyberinfrastructure designs and services (Sterner et al. 2020, Franz and Sterner 2018). Here, we propose that digitally “extended” taxonomic curation can play new and innovative roles in linking observational data to alternative taxonomic concepts; and enabling fit-for-use taxonomy to inform policy decisions. linking observational data to alternative taxonomic concepts; and enabling fit-for-use taxonomy to inform policy decisions. Taxonomic curators (TCs) have traditionally limited their activities to making lists of accepted species and higher taxa. However, most of today's biodiversity questions require observational data (e.g., specimen occurrences) that are taxonomically coherent, not just name lists, and for those linked data to be digitally available in public databases. If the collective activities of TCs can be effectively unified across distributed networks, they might facilitate the transition to Extended Specimen Networks of taxonomically coherent biodiversity data, a core goal of current research initiatives (e.g., Lendemer et al. (2020)). Beyond lists of species names is the domain of what names mean in practice (i.e., taxonomic concepts), which often differs by author (Fig. 1). Here we argue that curating the various lines of evidence that represent taxonomic concepts—what we call Species Meaning Artifacts (SMArts)—is a promising strategy for keeping track of how species splits and lumps will affect observational data records in the Global Biodiversity Information Facility (GBIF) or National Center for Biotechnology Information (NCBI). Instead of labeling records by a static name, records can be digitally associated with SMArt evidence from alternative taxonomies (e.g., geographic range maps before/after a species split). Networks of TCs curating digital SMArts will enable 'taxonomically intelligent' data aggregation (Bisby 2000), a long-pursued goal in biodiversity data science that, once realized, promises to enable investigations ranging from viral spillover to biodiversity loss (Upham et al. 2021).

Benthic species assemblages change through a freshwater cavern-type cenote in the Yucatán Peninsula, Mexico

We studied benthic assemblages through X-Batún, a continental freshwater cenote and its associated submerged cave located in San Antonio Mulix (Yucatán, Mexico). Using cave diving techniques, we collected sediment samples at four zones of the system. We extracted and counted individuals of benthic species in three replicates of 5 grams of wet sediment at each site. The biological composition was integrated by 15 species from eight higher taxonomic groups. Non-metric multidimensional scaling distinguished four assemblages that coincided with surface, open water, cavern and cave zones. ANOSIM test revealed significant differences between the assemblages. In the deeper zones of the cenote characterized by twilight and total darkness, Ostracoda and Gastropoda show the highest diversity and abundance, with practical absence in surface sediments. This pattern may suggest ecological interactions with chemosynthetic bacterial activity. Surface shows an assemblage typical of epigean environments. Environmental variables along the cenote varied little from the upper layers to bottom. Linear correlation and detrended canonical analysis revealed that light is the main driver of benthic species assemblages. Temperature, pH, and dissolved oxygen exert higher influence at individual biological benthic assemblage in X-Batún.

The reality of higher taxa and the question of intermediate forms.

Emphasis is placed on the fact that forms intermediate between closely related species of diverse genera are well known, that there are far fewer such examples between closely related genera, and almost none between families and higher taxa. The simplest explanation is that species to species level links, evolved in a microevolutionary manner, between families and higher taxa, occur under conditions of very small population size, high endemicity, and very rapidly, i.e., quantum evolution. The nature of community evolution indicates that most species level transitional forms will occur within ecological-evolutionary units, whereas almost none will occur during the adaptive radiations characterizing the initial phase of many ecological-evolutionary units. The phyletic evolution so characteristic of community evolution is gradualistic in those cases where an environmentally uniform set of samples is available. Finally, when discussing intermediate taxa it is important to state at what taxonomic level, i.e., is the form intermediate al tbe specific, generic, familial or ordinal level.