Taxonomic Assignment Research Articles

Microbiome in the nasopharynx: Insights into the impact of COVID-19 severity

BackgroundThe respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome. MethodsWe conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages. ResultsThe microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of Lawsonella and Cutibacterium genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of Streptococcus, Actinomyces, Peptostreptococcus, Atopobium, Granulicatella, Mogibacterium, Veillonella, Prevotella_7, Rothia, Gemella, Alloprevotella, and Solobacterium genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of Staphylococcus, Corynebacterium, and Streptococcus. ConclusionsOur study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.

Palaeoscolecids from the Ludlow Series of Leintwardine, Herefordshire (UK): the latest occurrence of palaeoscolecids in the fossil record

AbstractThe documentation of cuticular micro‐ornament is vital for the taxonomic assignment of palaeoscolecids: vermiform lower Palaeozoic ecdysozoans interpreted as stem‐group priapulans or early diverging panarthropods. This is due to the absence of the character‐rich proboscis and tail hooks in palaeoscolecid material not from Burgess Shale‐type Konservat‐Lagerstätten. Here, the cuticular micro‐ornamentation of palaeoscolecids from the upper Silurian (Ludlow) fauna of Leintwardine (Herefordshire, England), is described using scanning electron microscopy and reflectance transformation imaging. This material is taxonomically unstable because it was included in an effective wastebasket genus (Protoscolex) long before these imaging techniques were developed. The Leintwardine material is shown to be most closely comparable to a palaeoscolecid from the Darriwilian (Middle Ordovician) of the Builth–Llandrindod inlier, Powys, Wales, and is transferred accordingly to Radnorscolex Botting et al. as Radnorscolex latus (Bather). The Leintwardine fauna represents the uppermost stratigraphic occurrence of palaeoscolecids, constrained to the Saetograptus leintwardinensis Zone (lower Ludfordian), and the comparatively sparse Silurian palaeoscolecid record is subsequently discussed. It is hypothesized that palaeoscolecids may have become extinct during the mid‐Ludfordian Lau Event, the onset of which is recorded in the biozone immediately above the Leintwardine fauna (Bohemograptus Zone). Finally, the British palaeoscolecid fauna is summarized, including a new record from the Dapingian (Middle Ordovician) of Carmarthenshire, South Wales.

A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).

Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated insitu temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.

Liberate the power of biodiversity literature as FAIR digital objects

Knowledge about biodiversity is largely embedded in a daily growing corpus of over 500 million pages of biodiversity literature that is not machine-actionable. It is thus not open to building a biodiversity knowledge graph, or facilitating the use of artificial intelligence tools. This hinders the completion of a much-needed taxonomic name reference system, prevents the discovery of the biotic interactions underpinning the prediction and understanding of global change trends and consequences, viral spillovers, annotation of genes with their respective phenotypes, and their citations in various domains dealing with biological species such as conservation, agriculture, medicine, life sciences and industry, necessary to achieve the objectives of the Green Deal and address the targets identified in the Global Biodiversity Framework. This Policy Brief highlights key actions that can liberate the scientific data published, exploit their use , promote an enhanced way to publish, and ultimately foster excellence and innovation in biodiversity science, monitoring and conservation.

Population dynamics and prey community of the invasive paper wasp Polistes chinensis (Hymenoptera: Vespidae) in a protected coastal habitat in New Zealand

AbstractThe Asian paper wasp (Polistes chinensis) is an invasive species in New Zealand and a voracious arthropod predator, incorporating a wide range of prey into its diet. We examined the colony survival and prey community composition of these wasps in a protected coastal habitat in New Zealand. Paper wasp colonies at this site were surveyed and monitored weekly over two summers. Our data showed that only ~20% of the monitored colonies each year survived until late summer, with high rates of colony mortality in late spring and early summer. We collected samples of wasp larval guts over a temporal gradient in one nesting season, and via DNA metabarcoding analysis, we identified the prey species consumed. The prey species most frequently identified in larval samples were endemic cicadas and several lepidopteran species. No native arthropod species of known conservation concern were identified in the analysis. However, 63% of the unique taxon sequences retrieved could not be identified by genus or species level, likely due to the absence of reference barcodes. These taxa may represent a group of understudied species, potentially highly endemic or localised. Our analysis indicates that these invasive wasps are opportunistic‐generalist predators with the potential to exert high predation pressure on native arthropods. P. chinensis may be preying on a range of understudied species, especially in remote, natural habitats across New Zealand. We recommend future studies continue to barcode native New Zealand arthropods in order to improve the taxonomic assignments of dietary studies.

Towards a Comprehensive DNA Barcode Library of Stenochironomus Kieffer, 1919 (Diptera: Chironomidae) from China

The adoption of DNA-based assessments for biodiversity monitoring has been on the rise. However, the effectiveness of DNA-based taxonomic assignments heavily relies on the availability and reliability of DNA barcode libraries. There is growing demand for a comprehensive understanding of aquatic biodiversity and the critical role of Chironomidae, specifically Stenochironomus in freshwater ecosystems. Therefore, our objective is to develop a reference barcode library for Stenochironomus in China. From 2016 to 2021, we collected Stenochironomus specimens in diverse Chinese landscapes using malaise traps, light traps, and sweep nets. These specimens were carefully preserved for DNA extraction and barcode sequencing. Our analysis unveiled 36 unique operational taxonomic units from 180 COI barcode sequences through a Neighbor-Joining tree and Automatic Barcode Gap Discovery program, highlighting a significant diversity within the Stenochironomus species. The findings emphasize the constraints of conventional morphological identification methods, especially for species with ambiguous morphologies. It also underscores the effectiveness of DNA barcoding in revealing hidden species diversity, known as cryptic species. Consequently, this study advocates for an integrated taxonomic approach, combining morphological and molecular data, to refine species identification and conservation strategies.

The Bezzi Diptera collection at the Museo di Storia Naturale di Milano: a list of the named genera and species, with their present status

Mario Bezzi’s collection of Diptera is probably the most important dedicated to this order of insects preserved in Italy and, in a scientific-historical view, one of the most important in the world. The aim of this work is to provide a complete list of the genera and species originally used by Bezzi and readable on the collection labels handwritten by Bezzi himself. A brief description of the collection and the methods used to acquire and check the names is given. The results obtained are discussed. Finally, a complete checklist of the taxonomic names found, and their current status is provided.

Novel Qnr Families as Conserved and Intrinsic Quinolone Resistance Determinants in Aeromonas spp.

The environment has been identified as an origin, reservoir, and transmission route of antibiotic resistance genes (ARGs). Among diverse environments, freshwater environments have been recognized as pivotal in the transmission of ARGs between opportunistic pathogens and autochthonous bacteria such as Aeromonas spp. In this study, five environmental strains of Aeromonas spp. exhibiting multidrug resistance (MDR) were selected for whole-genome sequencing to ascertain their taxonomic assignment at the species-level and to delineate their ARG repertoires. Analyses of their genomes revealed the presence of one protein almost identical to AhQnr (A. hydrophila Qnr protein) and four novel proteins similar to AhQnr. To scrutinize the classification and taxonomic distribution of these proteins, all Aeromonas genomes deposited in the NCBI RefSeq genome database (1,222 genomes) were investigated. This revealed that these Aeromonas Qnr (AQnr) proteins are conserved intrinsic resistance determinants of the genus, exhibiting species-specific diversity. Additionally, structure prediction and analysis of contribution to quinolone resistance by AQnr proteins of the isolates, confirmed their functionality as quinolone resistance determinants. Given the origin of mobile qnr genes from aquatic bacteria and the crucial role of Aeromonas spp. in ARG dissemination in aquatic environments, a thorough understanding and strict surveillance of AQnr families prior to the clinical emergence are imperative. In this study, using comparative genome analyses and functional characterization of AQnr proteins in the genus Aeromonas, novel Aeromonas ARGs requiring surveillance has suggested.

Fungi diversity in roots of Guarianthe skinneri in urban condition: velamen versus cortex

Objective: To Identify the endophytic fungal community of the G. skinneri root in urban populations, showing differences in composition between velamen and cortex to better understand the fungus-root interaction in these orchids.&#x0D; Design/Methodology/Approach: We collected tissues from velamen and root from five specimens of G. skinneri growing on urban trees in Tapachuala, Chiapas. We extracted DNA, PCR amplified the ITS marker, sequenced on the Illumina platform followed by diversity analyses and taxonomic assignment.&#x0D; Results: We detected 845 OTUs that were assigned to the Fungi kingdom. Velamen and cortex share 403 OTUs, 402 were found exclusively in velamen and 40 in cortex. Besides orchid mycorrhiza forming fungi, we detected other species (e.g Alternaria sp., Beauveria sp., Fusarium sp., Glomus sp. and Tricoderma sp.) that could be involved in root physiology during development and defense against pathogens and predators&#x0D; Study Limitations/Implications: Metagenomic studies provide substantial amounts of data that go beyond conventional studies. However, the information generated is still limited regarding the role of each endophyte.&#x0D; Findings/Conclusions: Despite these limitations, our work fills a knowledge gap because we detected endophytes that were previously unknown for G. skinneri, leading to new research questions about root-endophyte relationships.

Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool.

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modernized and completely rewritten user interface, together with numerous new features. A new dataset type has been introduced (colored/labeled ranges), greatly upgrading the functionality of the previous simple colored range annotation function. Additional annotation options have been implemented for several existing dataset types. Dataset template files now support simple assignment of annotations to multiple tree nodes through substring matching, including full regular expression support. Node metadata handling has been greatly extended with novel display and exporting options, and it can now be edited interactively or bulk updated through annotation files. Tree labels can be displayed using multiple simultaneous font styles, with precise positioning, sizing and styling of each individual label part. Various bulk label editing functions have been implemented, simplifying large scale changes of all tree node labels. iTOL's automatic taxonomy assignment functions now support trees based on the Genome Taxonomy Database (GTDB), in addition to the NCBI taxonomy. The functionality of the optional user account pages has been expanded, simplifying the management, navigation and sharing of projects and trees. iTOL currently handles more than one and a half million trees from >130000 individual user accounts.

Fungal Mycobiome of Mature Strawberry Fruits (Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts.

An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.

Genetics, geography, and subspecies status of American mink in Florida, with an emphasis on Neogale vison evergladensis

Historical records of American mink (Neogale vison) in Florida suggest they occur in four populations, each currently recognized as a separate subspecies. The Everglades mink (N. v. evergladensis) is a state-listed threatened subspecies, and the Atlantic salt marsh mink (N. v. lutensis) and Gulf salt marsh mink (N. v. halilimnetes) are both Species of Greatest Conservation Need, but support for their taxonomic status is limited. We acquired 62 samples of mink for genetic analysis using mtDNA and microsatellite data with the objective of assessing the subspecies status of mink in Florida with an emphasis on evergladensis. We also compared historical and current range estimates of mink subspecies in Florida using museum specimens, public sightings, and detection records from scientific studies. All estimates of FST were significant when evergladensis was paired with other subspecies and both assignment tests and the Principal Coordinate Analysis separated evergladensis from other subspecies. The single mtDNA haplotype from evergladensis was not found elsewhere in Florida but was present in a subspecies outside of Florida (vulgivaga). Genetic diversity was lowest in evergladensis and highest for vulgivaga from Louisiana. We found support for lutensis as a separate taxonomic unit and assignment tests found some support for the genetic distinctiveness of halilimnetes. Sample sizes limited analyses in halilimnetes and prevented any conclusions about the subspecies status of mink in the Panhandle. Based on current range estimates, mink from evergladensis, lutensis, and halilimnetes are geographically isolated from one another and supports the genetic analysis. Using a more modern definition of subspecies that includes genetics, distribution, and ecology, we conclude that the data supports multiple subspecies of mink in Florida.

Intervertebral disc microbiome in Modic changes: Lack of result replication underscores the need for a consensus in low-biomass microbiome analysis.

The emerging field of the disc microbiome challenges traditional views of disc sterility, which opens new avenues for novel clinical insights. However, the lack of methodological consensus in disc microbiome studies introduces discrepancies. The aims of this study were to (1) compare the disc microbiome of non-Modic (nonMC), Modic type 1 change (MC1), and MC2 discs to findings from prior disc microbiome studies, and (2) investigate if discrepancies to prior studies can be explained with bioinformatic variations. Sequencing of 16S rRNA in 70 discs (24 nonMC, 25 MC1, and 21 MC2) for microbiome profiling. The experimental setup included buffer contamination controls and was performed under aseptic conditions. Methodology and results were contrasted with previous disc microbiome studies. Critical bioinformatic steps that were different in our best-practice approach and previous disc microbiome studies (taxonomic lineage assignment, prevalence cut-off) were varied and their effect on results were compared. There was limited overlap of results with a previous study on MC disc microbiome. No bacterial genera were shared using the same bioinformatic parameters. Taxonomic lineage assignment using "amplicon sequencing variants" was more sensitive and detected 48 genera compared to 22 with "operational taxonomic units" (previous study). Increasing filter cut-off from 4% to 50% (previous study) reduced genera from 48 to 4 genera. Despite these differences, both studies observed dysbiosis with an increased abundance of gram-negative bacteria in MC discs as well as a lower beta-diversity. Cutibacterium was persistently detected in all groups independent of the bioinformatic approach, emphasizing its prevalence. There is dysbiosis in MC discs. Bioinformatic parameters impact results yet cannot explain the different findings from this and a previous study. Therefore, discrepancies are likely caused by different sample preparations or true biologic differences. Harmonized protocols are required to advance understanding of the disc microbiome and its clinical implications.

Density data for Lake Erie benthic invertebrate assemblages from 1930 to 2019.

Benthic invertebrates are important trophic links in food webs and useful bioindicators of environmental conditions, but long-term benthic organism abundance data across broad geographic areas are rare and historic datasets are often not readily accessible. This dataset provides densities of benthic macroinvertebrates collected from 1930 to 2019 during surveys in Lake Erie, a Laurentian Great Lake. The surveys were funded by the governments of the United States and Canada to investigate the status and changes in the benthic community. From the total of 21 lake-wide and basin-wide benthic surveys conducted in Lake Erie from 1929 to 2019, we were able to acquire data for 17 surveys, including species-level data for 10 surveys and data by higher taxonomic groups for seven surveys. Our amassed Lake Erie dataset includes data from 11 surveys (including five with species-level data) conducted in the western basin in 1930-2019, seven surveys (six with species-level data) in the central basin, and eight surveys (seven with species-level data) in the eastern basin (1973-2019). This Lake Erie dataset represents the most extensive temporal dataset of benthic invertebrates available for any of the Laurentian Great Lakes. Benthic samples were collected using Ponar or Shipek bottom dredges and taxa densities were calculated as individuals per square meter using the area of the dredge. Density data are provided for taxa in the Annelida, Arthropoda, Mollusca, Cnidaria, Nemertea, and Platyhelminthes phyla. Current taxonomy was used for most groups but, in a few cases, older taxonomic names were used for consistency with historical data. Analysis of this dataset indicates that eutrophication, water quality improvement, and dreissenid introduction were the major drivers of changes in the benthic community in the western basin, while hypoxia was a major factor in the central basin, and dreissenid introduction was the most important driver in the eastern basin. Considering the rarity of high taxonomic resolution long-term benthic data for lake ecosystems, this dataset could be useful to explore broader aspects of ecological theory, including effects of eutrophication, hypoxia, invasive species, and other factors on community organization, phylogenetic and functional diversity, and spatial and temporal scales of variation in community structure. In addition, the dataset could be useful for studies on individual species, including abundance and distribution, species co-occurrence, and how the patterns of dominance and rarity change over space and time. Use of this dataset for academic or educational purposes is encouraged as long as this data paper is properly cited.

Comparing modern identification methods for wild bees: Metabarcoding and image-based morphological taxonomic assignment.

With the decline of bee populations worldwide, studies determining current wild bee distributions and diversity are increasingly important. Wild bee identification is often completed by experienced taxonomists or by genetic analysis. The current study was designed to compare two methods of identification including: (1) morphological identification by experienced taxonomists using images of field-collected wild bees and (2) genetic analysis of composite bee legs (multiple taxa) using metabarcoding. Bees were collected from conservation grasslands in eastern Iowa in summer 2019 and identified to the lowest taxonomic unit using both methods. Sanger sequencing of individual wild bee legs was used as a positive control for metabarcoding. Morphological identification of bees using images resulted in 36 unique taxa among 22 genera, and >80% of Bombus specimens were identified to species. Metabarcoding was limited to genus-level assignments among 18 genera but resolved some morphologically similar genera. Metabarcoding did not consistently detect all genera in the composite samples, including kleptoparasitic bees. Sanger sequencing showed similar presence or absence detection results as metabarcoding but provided species-level identifications for cryptic species (i.e., Lasioglossum). Genus-specific detections were more frequent with morphological identification than metabarcoding, but certain genera such as Ceratina and Halictus were identified equally well with metabarcoding and morphology. Genera with proportionately less tissue in a composite sample were less likely to be detected using metabarcoding. Image-based methods were limited by image quality and visible morphological features, while genetic methods were limited by databases, primers, and amplification at target loci. This study shows how an image-based identification method compares with genetic techniques, and how in combination, the methods provide valuable genus- and species-level information for wild bees while preserving tissue for other analyses. These methods could be improved and transferred to a field setting to advance our understanding of wild bee distributions and to expedite conservation research.

The fecal bacterial microbiota is not useful for discriminating between lymphoplasmacytic enteritis and low-grade intestinal T-cell lymphoma in cats nor for predicting therapeutic response.

To evaluate the fecal bacterial microbiota at the time of diagnosis (T0) and after 1 month of therapy (T1) in cats diagnosed with lymphoplasmacytic enteritis (LPE) or cats with low-grade intestinal T-cell lymphoma (LGITL) and to compare these findings with those of healthy cats. 5 healthy cats, 13 cats with LPE, and 7 cats with LGITL were prospectively enrolled between June 2020 and June 2021. Fecal samples were collected at T0 and T1, and DNA was extracted for 16S ribosomal amplicon sequencing. Alpha diversity and beta diversity were computed. The taxonomic assignment was performed using sequences from the Silva v138 formatted reference database. Differential abundant taxa were selected in each taxonomic level, with the P value adjusted < .05, as the cut-off. No significant differences in alpha and beta diversity were found either at T0 or T1 between healthy and diseased cats or between cats with LPE and LGITL. Beta-diversity analysis showed an increase in the Fusobacteriaceae family in cats with LGITL at T0, compared to cats with LPE. Regardless of histological diagnosis, several microbiota differences were found at T0 based on serum cobalamin levels. Fecal samples were successfully used to characterize the bacteriome of the intestinal tract in cats by 16S rRNA gene sequencing. However, results highlighted that the metagenomic evaluation was not useful to discriminate between LPE and LGITL nor to predict the therapeutic response in this study population.

Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities.

The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ13Ccol and δ15N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.

A Review and Analysis of Rangeland and Wildland Soil Health

Soil health is focused on intensively managed (IM) soils (often farmed soils), by-passing extensively managed (EM) soils (range lands, deserts, shrub lands, tundra). High economic value products are generated by IM systems. Many EM lands are of cultural, recreational, scenic, or scientific value. However, and despite the fact that they provide forage for domestic and wild animals, they are not always of high economic value. IM and EM soils are evaluated on the same health scales. The contention herein is all soils formed under soil state conditions under the absence of human interventions are inherently healthy. But a given soil has dynamic properties that determine its management as IM or EM. An EM sagebrush steppe soil may be deemed unhealthy as a result of low organic matter and short growing season. An IM grassland steppe soil is healthy as a result of high organic matter and a long growing season. The sagebrush soil, however, provides habitat for culturally important sage grouse. The grassland soil may provide, when plowed, habitat for economically important soybeans. Soil taxonomies can be used to establish inherent health of undisturbed soils. Determining a soil’s dynamic nature is a different construct. Here, four different sets of EM soils were evaluated to showcase their diversity, evaluate levels of health and display their often-unconventional dynamic characteristics. An argument is made that a soil’s health, an inherent condition, is not the same as its dynamic condition (potential to produce goods and services). Soil health changes are usually slowly driven by soil state factors but can be dramatically changed by humans. Otherwise, soil health can be viewed as a near constant ecosystem attribute. The dynamic nature of soils change according to needs placed by humans. EM soils may be healthy but lack attention since their dynamic nature is not traditional and often of low economic value. Evaluation of soil health and dynamic value on EM lands is often exacerbated by information absence. Strategies to circumvent this include sampling design, reference sites and standardized ways of EM soil health determination. A case is made that baselines of soil health can be taken from soil surveys, taxonomic names, and soil data from map units, where such information exists. Certified supplementary information is ambiguously available, but may be crucial. Outdoor living laboratories that feature inherent soil health and dynamic soil alternatives may help circumvent information voids.

Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms

Genitourinary syndrome of menopause (GSM) is the leading cause of vaginal symptoms in breast cancer survivors treated with aromatase inhibitors. However, there are currently no effective treatment options available for women with a history of breast cancer. Recent research has established that changes in the vaginal microbiome may be linked to GSM. Most studies have assessed the microbiome without accounting for the estrogen status. It remains unknown whether the vaginal microbiome differ among patients with a low estrogenic state with and without vulvovaginal symptoms. To address such research questions, our study compares the vaginal microbiomes among breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms. A total of 50 breast cancer survivors treated with aromatase inhibitors were recruited, among whom 25 had vulvovaginal symptoms and 25 had no vulvovaginal symptoms. Vaginal swabs were collected. DNA extraction, followed by sequencing of the V3–V4 regions of the 16S ribosomal RNA gene, were performed. Differential abundance analysis was conducted by linear discriminant analysis effect size. Taxonomy assignment, alpha diversity and beta diversity were examined. The relative abundance of genus Sneathia and genus Gardnerella was significantly increased in vulvovaginal symptoms group with no differences in bacterial diversity and richness.

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters

BackgroundAerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake.ResultsAAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment.ConclusionsOur findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and their consideration in further ecological models.