Individual Taxa Research Articles

Latitudinal gradients and ocean fronts strongly influence protist communities in the southern Pacific Ocean.

Protist communities in the southern Pacific Ocean make a major contribution to global biogeochemical cycling, but remain understudied due to their remote location. We therefore have limited understanding of how large-scale physical gradients (e.g. temperature) and mesoscale oceanographic features (e.g. fronts) influence microeukaryote diversity in this region. We performed a high-resolution examination of protist communities along a latitudinal transect (>3000km) at 150°W in the central southern Pacific Ocean that encompassed major frontal regions, including the sub-tropical front (STF), the sub-Antarctic front (SAF), and the polar front (PF). We identified distinct microbial communities along the transect that were primarily delineated by the positions of the STF and PF. Some taxa were not constricted by these environmental boundaries and were able to span frontal regions, such as the colonial haptophyte Phaeocystis. Our findings also support the presence of a Latitudinal Diversity Gradient (LDG) of decreasing diversity of the protist community with increasing latitude, although some individual taxa, notably the diatoms, do not adhere to this rule. Our findings show that oceanographic features and large-scale physical gradients have important impacts on marine protist communities in the southern Pacific Ocean that are likely to strongly influence their response to future environmental change.

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

BackgroundLifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remain less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called “vanishing microbiomes” potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations.ResultsHere, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the USA within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain sources.ConclusionOur findings demonstrate that by studying populations within Nepal, we can isolate an important role of lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.CnT2gR8wWnMkEju1223Bx6Video

The impact of microplastics on lake communities: A mesocosm study

Plastics are pervasive pollutants that are being produced at an increasing rate to meet consumer demands. After entering the environment, plastics can break down, creating smaller fragments, including secondary microplastics. Microplastic contamination in lakes has been recorded worldwide, and the ingestion of microplastics has been documented in zooplankton, macroinvertebrates, and fish. Microplastic ingestion and exposure can cause varying deleterious effects on these organism groups, but the impact of realistic microplastic concentrations on whole freshwater food webs requires further study. We addressed these knowledge gaps by conducting an 8-week experiment factorially crossing microplastic addition at a concentration of 1.5 particles/L with a fish predator (perch, Perca fluviatilus) presence in 1200-L outdoor mesocosms. Microplastic exposure had time-varying effects on zooplankton abundance, with a lower abundance of zooplankton in plastic treatments at the end of the experiment. Although microplastics had no impact on total macroinvertebrate abundance, there were effects on individual taxa. In the presence of microplastics, the cased caddisfly Triplectides spp. had a significantly lower abundance, which may have led to an increase in the snail Gyraulus spp. in week eight. Across the benthic and pelagic invertebrate communities, there were near-significant compositional differences between control and plastic treatments. These findings indicate that microplastic exposure may negatively impact freshwater invertebrate communities, even at low, field-realistic concentrations representative of the densities currently found in lakes.

No association between the early-life gut microbiota and childhood body mass index and body composition.

The gut microbiota has been implicated in adult obesity, but the causality is still unclear. It has been hypothesized that an obesity-prone gut microbiota can be established in infancy, but only few studies have examined the early-life gut microbiota in relation to obesity in childhood, and no consistent associations have been reported. Here, we examine the association between the early-life gut microbiota and body mass index (BMI) development and body composition throughout childhood. Gut microbiota from stool were collected from 700 children in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) cohort at ages of 1week, 1month, 1 year, 4 years, and 6 years and analyzed by 16S rRNA gene sequencing. Outcomes included BMI World Health Organization (WHO) Z scores (zBMI), overweight (zBMI>1.04) and obesity (zBMI>1.64) (0-10 years), and adiposity rebound and body composition from dual-energy X-ray absorptiometry at 6 years. The early-life gut microbiota diversity, overall composition, and individual taxon abundances in unsupervised and supervised models were not consistently associated with either current or later BMI Z scores, overweight, obesity, adiposity rebound, or body composition in childhood. In a deeply characterized longitudinal birth cohort, we did not observe any consistent associations between the early-life gut microbiota and BMI or risk of obesity in later childhood. While this does not conclusively rule out a relationship, it suggests that if such associations exist, they may be more complex and potentially influenced by factors emerging later in life, including lifestyle changes. COPSAC is funded by private and public research funds (all listed on www.copsac.com).

The “evolution” of the mitochondrial genome of the (<i>Phylloscopus borealis</i> sensu lato) occurs in its nuclear genome

Sequencing of a partial fragment of the ND5–cytb mithochondrial genes (1553 bp) and its nuclear copies was carried out to Phylloscopus borealis sensu lato, belonging to individual taxonomic groups from different parts of the range. It was shown that the majority of taxon-specific and unique mitochondrial substitutions in examinandus and xanthodryas forms were identical to those in nuclear copies of borealis mtDNA. Differences between mitochondrial haplotypes of examinandus and nuclear copies of mtDNA borealis were low (p = 0.02), at the same time the mtDNA genetic divergence in borealis–examinandus, borealis–xanthodryas and examinandus–xanthodryas significantly exceeded this value (p = 0.035, 0.044 and 0.046, respectively). A nuclear copy of the mitochondrial haplotype of the easternmost form of xanthodryas was first discovered in the nuclear genome of one borealis individual in the western part of the breeding range (Komi Republic). Alongside this, it was shown at the first time, the nuclear copies of xanthodryas mtDNA from Toyama Prefecture (Japan) were close to the mitochondrial haplotypes of borealis from Kytlym (Sverdlovsk region) (p = 0.018). Thus, the mutations emerging in the nuclear copies of mitochondrial genes are the source of most substitutions in the mitochondrial DNA of the studied forms. The origin of the mitochondrial haplotypes examinandus and xanthodryas from nuclear copies of mtDNA borealis and the close similarity of their nuclear genomes gives grounds to consider the mitogenomes of these forms as variants of the haplotype of the single species Ph. borealis sensu lato. With a high degree of probability, it can be argued that the divergence time of the haplotypes of the analyzed forms is significantly less than 2.5-3 million years, as previously assumed by a number of authors [Saitoh et al. 2010; Alström et al. 2011], and the “molecular clock” that do not take into account recombination events between the nuclear and mitochondrial genomes cannot be used in this case.

Best Practice for Publishing Environmental DNA (eDNA) Data According to FAIR Principles

Reversing global biodiversity loss will require transformational human actions and robust measurements of their effectiveness. Diversity assessment using environmental DNA (eDNA) has emerged as a cutting-edge technique with the potential to address the challenges of measuring biodiversity. Vast amounts of eDNA sequences and eDNA-based species detections are generated in scientific studies. These datasets are typically stored in a variety of different repositories in multiple formats, hindering their reuse (Berry et al. 2020). Ensuring the publication of eDNA data following the FAIR (Findable, Accessible, Interoperable, Reusable) principles (Wilkinson et al. 2016) would revolutionise environmental assessment, including monitoring of biodiversity, individual species, and interactions across extensive spatial and temporal scales, and generate critical knowledge for evidence-based management. Archiving FAIR eDNA data requires standardising data formats and vocabularies, cyberinfrastructures, guidelines, data sharing policy, and collaboration among scientists and institutions. Some of these requirements are addressed by existing data standards and infrastructures, including Darwin Core (DwC) (Wieczorek et al. 2012), Minimum Information about any (x) Sequence (MIxS) (Yilmaz et al. 2011), the Global Biodiversity Information Facility (GBIF) network, and International Nucleotide Sequence Database Collaboration (INSDC) partners (Arita et al. 2020). However, multiple challenges remain and FAIR data practices have yet to be established among the eDNA community. This is partly because critical attributes unique to eDNA data are not adequately accommodated by existing standards. For example, monitoring contamination and excluding non-target taxa, and the parameters used for quality filtering and species detection vary greatly between studies, depending on the study scopes and the associated financial and ecological costs of incorrectly inferring presence or absence. Making such information FAIR is needed for future studies reusing data and requiring high confidence levels in species detection and taxonomic assignment. Furthermore, the procedures of targeted-taxon detection approach (e.g., interpretations of quantitative polymerase chain reaction (qPCR) results in detecting the presence of DNA from individual taxa) have not yet been fully captured by existing standards. Increasing efforts have been made to establish minimum reporting requirements to validate eDNA study methods and data (Klymus et al. 2020, Thalinger et al. 2021). These requirements need further development to be translated into data standards and formats to enhance machine readability and reusability, and to support and guide the eDNA community, so that they are effectively utilised. In this talk, we share our best practice guide for formatting and publishing eDNA data, developed by an international multidisciplinary working-group comprising eDNA researchers, journal editors, and biodiversity and omics data scientists. We identified required data types, formats and metadata checklists through reviewing and integrating existing data standards, devising subject-specific vocabularies, and introducing additional terms to accommodate the distinctive properties of eDNA data. Implementing the FAIR eDNA data best practice guide, offers a pivotal step towards standardising and enhancing the publication and re-use of eDNA data.

Missing the biodiversity for the bee: Natural land management strategies impact functional invertebrate diversity in commercial cranberry production

Abstract Simplification of agricultural environments is linked to declines in biodiversity. Improving the floral diversity within and around these areas may result in more robust and diverse ecosystems. We investigated how floral resource abundance, diversity, and species composition in a cranberry agricultural system correlated to the abundance and overall invertebrate diversity and to the abundance and diversity of specific invertebrate groups of agricultural importance (e.g. parasitoids, phytophagous taxa, pollinators and predators). This study focused on habitats immediately surrounding cranberry production and included grassy dikes under a managed system (‘dike’), and semi‐natural areas growing on the surrounding support land (‘semi‐natural’). Floral resource availability and diversity tended to be similar between habitats, while invertebrate richness, diversity and composition differed. As the availability of floral resources increased, invertebrate abundance increased but diversity decreased. Overall invertebrate community composition differed with the specific species and availability of floral resources. The habitat type and floral resource composition impacted some agriculturally important groups, as pollinator abundance was higher in the semi‐natural habitat, and parasitoid abundance varied with floral resource composition across both habitats. These results suggest that managing the structural and floral resource diversity associated with agroecosystems can help support local biodiversity. However, these systems may disproportionately benefit more common taxonomic groups. The difference in responses of individual taxonomic groups also highlights the potential tradeoffs of focusing on only a subset of biodiversity aspects.

Five-leaf generalizations of the D-statistic reveal the directionality of admixture

Abstract Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use 5 leaves to evaluate admixture. Among these, the DFOIL method, which tests allelic patterns on the “symmetric” tree S = (((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples are included because of the reliance on singleton patterns (such as BAAAA and ABAAA). Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the “asymmetric” tree A = ((((1,2),3),4),5) and the “quasisymmetric” tree Q = (((1,2),3),(4,5)), which can considerably supplement the “symmetric“ S = (((1,2),(3,4)),5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient polar bear samples from previous studies. Recently DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a more recent phase with predominant polar bear → brown bear directionality. Code and documentation available at https://github.com/KalleLeppala/Delta-statistics.

Growth rate as a link between microbial diversity and soil biogeochemistry.

Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation-some of the many ways in which organisms affect Earth's ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

Affective symptoms in pregnancy are associated with the vaginal microbiome

BackgroundComposition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Therefore, identifying sources of individual differences in the vaginal microbiome is of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual's experience of affective symptoms and stress exposure. MethodsData were based on a prospective longitudinal study of a medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34–40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community clusters (CC1–3) based on dissimilarity of vaginal microbiota composition. ResultsResults indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CC3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CC1–3 and individual taxa, including biosynthetic pathways for serotonin and dopamine. We did not find robust evidence linking symptom- and stress-related biomarkers and CCs. ConclusionsOur results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.

Process stability in anaerobic Digestion: Unveiling microbial signatures of full-scale reactor performance

Anaerobic digestion is responding to the growing demand for sustainability by exploring alternatives for methane production through renewable processes. The target is to implement stable production systems at industrial scale that can accommodate heterogeneous feedstocks with seasonal or intermittent availability. In this study, we investigated the microbiomes of six full-scale biogas plant digesters, operated under continuous production with distinct feedstock and varying operating parameters, by monitoring multiple time points over an 18-month period. This time-course experiment analyzed 114 Metagenome-Assembled Genomes alongside physico-chemical assessments to identify common and plant-specific indicators for operational management. Results identify a Limnochordia and a Dysgonomonadaceae bacteria, as well as Candidatus Methanoculleus thermohydrogenotrophicum, as widespread and potentially desirable components of the microbiota for resilient digestion of varying waste, including the peculiar olive pomace. The abundance of individual taxonomic groups and their reconstructed metabolic pathways aligned with the availability of their fermentation substrates, finding a prevalence of beta-oxidizing bacteria with lipid-rich olive pomace. Monitoring through perturbation events revealed possible causative and remediative microbiological factors, in particular Methanosarcina flavescens and Candidatus Syntrophosphaera thermopropionivorans could contribute to restoration of reactor performance. This work showcases relationships between digester operation and its microbiome, supporting microbial monitoring as a tool to increase biogas production efficiency.

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized.

Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called 'vanishing microbiomes' potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. Our findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.

FloraVeg.EU — An online database of European vegetation, habitats and flora

AbstractThis article describes FloraVeg.EU, a new online database with open‐access information on European vegetation units (phytosociological syntaxa), vegetated habitats, and plant taxa. It consists of three modules. (1) The Vegetation module includes 149 phytosociological classes, 378 orders and 1305 alliances of an updated version of the EuroVegChecklist modified based on the decisions of the European Vegetation Classification Committee. Vegetation units dominated by vascular plants are characterized by country‐based distribution maps and data on the dominant life forms, phenology, soil properties, relationships to vegetation regions, elevational vegetation belts and azonal habitats, successional status, and degree of naturalness. A list of diagnostic taxa is also provided for each class. (2) The Habitats module includes vascular‐plant‐dominated terrestrial, freshwater, and marine habitat types from the first to the third or fourth highest hierarchical levels of the EUNIS classification. Of these, 249 vegetated habitats are characterized by a brief description, a point‐based distribution map, diagnostic, constant, and dominant taxa, and a list of the corresponding alliances. (3) The Species module provides information on 37 characteristics of European vascular plant species and some infrageneric or infraspecific taxa, including functional traits (habitus and growth type, leaf, flower, fruit and seed traits, and trophic mode), taxon origin (native vs alien), and ecological information (environmental relationships, Ellenberg‐type indicator values, disturbance indicator values, and relationships to vegetation units and habitat types). Values for at least three variables are available for 36,404 species. Individual taxa, vegetation units, and habitats in these three modules are illustrated by more than 34,000 photographs. The Download section of FloraVeg.EU provides open‐access data sets in a spreadsheet format that can be used for analyses. FloraVeg.EU is a new resource with easily accessible data that can be used for research in vegetation science, ecology, and biogeography, as well as for education and conservation applications.

Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries

Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.

Intersection of the microbiome and immune metabolism in lupus.

Systemic lupus erythematosus is a complex autoimmune disease resulting from a dysregulation of the immune system that involves gut dysbiosis and an altered host cellular metabolism. This review highlights novel insights and expands on the interactions between the gut microbiome and the host immune metabolism in lupus. Pathobionts, invasive pathogens, and even commensal microbes, when in dysbiosis, can all trigger and modulate immune responses through metabolic reprogramming. Changes in the microbiota's global composition or individual taxa may trigger a cascade of metabolic changes in immune cells that may, in turn, reprogram their functions. Factors contributing to dysbiosis include changes in intestinal hypoxia, competition for glucose, and limited availability of essential nutrients, such as tryptophan and metal ions, all of which can be driven by host metabolism changes. Conversely, the accumulation of some host metabolites, such as itaconate, succinate, and free fatty acids, could further influence the microbial composition and immune responses. Overall, mounting evidence supports a bidirectional relationship between host immunometabolism and the microbiota in lupus pathogenesis.

Advanced age worsens respiratory function and pulmonary inflammation after burn injury and this correlates with changes in the fecal microbiome in mice.

Cutaneous burn injury in the elderly is associated with poor clinical outcomes and increased pulmonary-related complications. We and others have shown that burn injury triggers a cascade of inflammatory mediators which increase gut permeability and dysbiosis of the fecal microbiota and this is more dramatic in the aged. Since cross-talk between intestinal microbes and the lung, termed the "gut-lung axis," impacts immunity and homeostasis in the airway, we hypothesized that the increased intestinal dysbiosis in age and burn injury may contribute to excessive pulmonary inflammation and poor prognosis after injury. To explore this hypothesis, we used a clinically relevant murine model of burn injury in which young and aged mice are subjected to a 12% total body surface area dorsal scald burn or sham injury. 24 hours after injury, lung function was assessed and lungs and feces were collected for analysis of inflammatory mediators and fecal microbial species. The results show that, when compared to younger mice, burn injury in aged mice triggers a decline in respiratory function and exacerbates pulmonary inflammation. In addition to heightened levels of the neutrophil recruiting chemokine CXCL1, aged mice displayed a profound increase in the pro-inflammatory protein, calprotectin, in the lung after burn injury. Comparison of the fecal microbiome and inflammatory markers in the lung revealed unique, age-dependent, correlation patterns between individual taxa and pulmonary inflammation. Taken together, these findings suggest that the post-burn dysbiosis of the gut flora in aged mice may contribute to the changes in pulmonary inflammatory profiles.

Assessing phenotypic variation and plasticity of endemic gastropods from thermal water refugia using complex morphometric techniques: A case study of Lake Pețea melanopsids.

Understanding the underlying reasons for phenotypic plasticity and resulting morphological disparity is one of the key topics of evolutionary research. The phenotypic plasticity of extant and fossil melanopsids has been widely documented. Yet millennial-resolution, well-dated records from small aquatic habitats harboring endemics are scarce. The thermal spring-fed Lake Pețea is an ice age refugia harboring a unique endemic warm-water fauna. Subfossil melanopsids display incredible morphological variability from smooth to keeled, elongated to ribbed, shouldered forms. Numerous morphotypes have been considered as individual taxa with a fluent succession from the smooth elongated to the ribbed, shouldered types. This study presents an extensive morphometric analysis of subfossil melanopsids (ca. 3500 specimens) derived from stratified samples with an independent chronology. The aim was to separate morphotypes for investigations of temporal morphological disparity. Our results challenge the widely accepted hypothesis that proposes the evolution of shouldered, compressed, ribbed shells through a two-step process from smooth elongated spindle-shaped shells. Instead, it suggests that the subfossil shells belong to two distinct taxa present throughout the available stratigraphic data. The main components of shape variation, shape globularity, and shell coiling seem allometry-related. Ribs, striation, and keels appear randomly. High-spired spindle-shaped forms were considered to represent specimens of Microcolpia daudebartii hazayi. Bulkier low-spired and shouldered specimens represent phenotypes of Mi. parreyssii parreyssii. The collective and random distribution of morphotypes from the early stages of the lake's history also refutes the idea of a continuous transformation of the elongated forms into compressed, shouldered ones. Rather points to multiple events and environmental stimuli triggering development. Melanopsids appear in Late Glacial horizons, with Theodoxus prevostianus preferring temperatures above 23°C which may indicate the subordinate presence of hot water microhabitats in cooler waters.

Microbiome dynamics during malting of barley grains infested by Fusarium graminearum strains

AbstractBarley grain harvested for malting poses an interesting case study for the impacts of plant‐associated microbiomes because the conditions created during malting favour continued vigorous microbial activity after grain harvest. Suppression of pathogens is among the key functions performed by microbiomes, and it would be beneficial if we could harness this function. Over a 3‐year field trial, we micro‐malted barley that had been experimentally infested with each of seven different strains of the fungal pathogen Fusarium graminearum, and profiled bacterial microbiomes at key stages in the malting process (grain, post‐steeping, post‐germination and final dried malt). The greatest impacts on bacterial microbiomes were observed to be from the year and stage of malting, with comparatively fewer impacts of barley cultivar or pathogen strain. Relatively limited impacts of the presence and strain identity of fungal pathogen on the bacterial microbiome of malting barley probably reflects the colonization by other fungi, as our inoculation took place under field conditions with supplemental irrigation. Both community level shifts and significant responses by individual taxa were evident. Microbiome characteristics or the relative abundances of specific bacterial taxa helped to explain pathogen biomass, mycotoxin production and beer gushing. Manipulative experiments will be required to test hypotheses suggested by these microbiome profiles.

PSII-19 Fecal microbiota composition of weaned piglets under mixed management and poor housing conditions fed diets increased in threonine, methionine and tryptophan

Abstract This study evaluated the effects of increased dietary Thr, Met and Trp supplementation on fecal microbiota composition of weaned piglets raised under contrasting sanitary conditions [(GOOD SC) or under mixed management and poor housing conditions (MM+POOR SC)] during the nursery phase. A total of 144 entire male piglets [body weight (BW) = 6.33 ± 0.91 kg] from a high sanitary status (HSS) farm were randomly housed following a 2×2 factorial arrangement regarding BW blocks. Factorial arrangement was composed of two contrasting SC (GOOD or MM+POOR) and two diets [control, with nutritional requirements according to NRC (2012); or supplemented with Thr:Lys, Met+Cys:Lys and Trp:Lys 20% more than the control]. In total, 12 pens with three piglets each were used for treatment. On d -2, the 144 HSS piglets were allocated to one of two facilities under contrasting SCs. Also on d -2, to mimic a mixed management in the MM+POOR SC, 48 entire male piglets, from a commercial farm with low sanitary status (LSS), were randomly allocated by two piglets per pen into the same pens where the three HSS piglets were. On d 0, the two LSS piglets were removed from the HSS pens and allocated as sentinels into the remaining pens (four/pen) located between pens with HSS piglets. The MM+POOR SC had a weekly cleaning routine only to remove the manure located under the slatted floor, while in the GOOD SC, a daily cleaning routine and a high level of biosecurity protocol were adopted. One fecal sample per pen was collected on d 0, 21 and 42. The V4 region of the bacterial 16S rRNA gene was amplified from each fecal sample to evaluate ecological changes into bacterial communities and taxonomy. Mean relative abundance for each family/genus/species (taxon) across groups were depicted as a heatmap using the log2 transformed relative abundance of the most dominant taxa based on a 2% cutoff and network analysis of clusters of co-occurrences of the most relevant taxa (Figure 1). Overall, fecal microbiome analyses revealed no differences (P >0.05) in bacterial community composition and individual taxon abundances at the bacterial genus level across treatments over time. The alpha- and beta-diversity analysis showed no diet or SC differences (P >0.05). Additional community structure analysis based on co-occurrence network mapping revealed the absence of major temporal changes in architecture or keystone nodes (taxa) for HSS animals housed in either GOOD or MM+POOR SCs, despite the AA+ supplementation. The analysis revealed no specific taxon or taxa that were preferentially enriched or diminished over time (P > 0.05). According to our results, the microbial fecal composition of weaned piglets under GOOD or MM+POOR SCs measured using 16S rRNA sequencing analysis was stable including the major central taxa with no Thr, Met and Trp supplementation effect.

25 years of the Natura Sloveniae journal

The article presents the history of the journal Natura Sloveniae over the 25 years, from 1999–2023, of its publication. The main aim of the journal is highlighted, as well as a brief analysis of the number of contributions and authors, the taxonomic groups covered in the articles, including an overview of the citation success of the articles published in the journal. In 25 years, 286 articles by 320 authors have been published in the journal. Over the years, the geographical scope of published articles has expanded from Slovenia to SE and Central Europe. A brief statistical analysis of the published articles shows the highest popularity of articles presenting species lists or new records for Slovenia. A considerable share of the contributions are focused on individual taxa, mostly insects, including butterflies and dragonflies. In its 25th year of publication, the journal, which is jointly published by the Biotechnical Faculty at University of Ljubljana and the National Institute of Biology, is switching to the digital submission and review system of the University of Ljubljana Press. In this year, a third, thematic issue is being published for the first time. After a quarter of a century of continuous publication, the journal occupies an important niche among Slovenian scientific biological journals and continues its mission to publish original scientific contributions in the field of biogeographical, biodiversity and ecological research in Central and Southeastern Europe and to encourage young authors to publish their field observations.