An evaluation of the relative robustness of techniques for ecological ordination

Characterization and analysis of dynamic changes of microbial community associated with grape decay during storage

The rot caused by pathogens during the storage of table grapes is an important factor that affects the development of the grape industry and food safety, and it cannot be ignored. The development of innovative methods for pathogen control should be based on a comprehensive understanding of the overall microbial community changes that occur during grape storage. The study aims to investigate the relationship between the native microbiota (including beneficial, pathogenic and spoilage microorganisms) on grape surfaces and the development of disease during grape storage. In this study, the bacteria and fungi present on grape surfaces were analyzed during storage under room temperature conditions using high-throughput sequencing. During the storage of grapes at room temperature, observable diseases and a noticeable decrease in quality were observed at 8 days. Microbial community analysis showed that 4996 bacterial amplicon sequence variants (ASVs) and 488 fungal ASVs were determined. The bacterial richness exhibited an initial increase followed by a subsequent decrease. However, the diversity exhibited a distinct pattern of gradual decrease. The fungal richness and community diversity both exhibit a gradual decrease during the storage of grapes. Fungal β-diversity analysis showed that despite the absence of rot and the healthy state of grapes on the first and fourth days, the fungal β-diversity exhibited a significant difference. The analysis of changes in genera abundances suggested that Candidatus Profftella and Aspergillus exhibited dominance in the rotting grape at 16 days, which are the main pathogens that caused disease in the present study. The co-occurrence networks among the microbial showed that the Candidatus proftella genera has a positive correlation with Aspergillus niger, indicating that they work together to cause disease and promote growth in grapes. Predicting the function of bacterial communities found that the microorganisms associated with lipid metabolism at 4 days play an important role in the process of postharvest decay of grapes.

Connection between the gut microbiota of largemouth bass (Micropterus salmoides) and microbiota of the aquaponics system environment

The significant role played by the gut microbiota in fish growth, development, immunity, and overall health has been widely established. Nevertheless, there remains a lack of clarity regarding the interaction and origin between the environmental microbiota and the gut microbiota of aquaculture species within the aquaponics coupling system. Thus, we conducted an analysis of the gut microbiota of largemouth bass (Micropterus salmoides) obtained from an indoor enclosed circulating water aquaponics coupling system located in greenhouses in northern China. Additionally, we examined the microbiota of the fish pond water and tomato rhizosphere soil using high-throughput sequencing of the 16S rRNA gene. Our results demonstrated significant differences in the compositions of fish pond water, rhizosphere soil, and the gut microbiota of largemouth bass. Moreover, these compositions changed throughout the culture period. Approximately 11.99% of the bacterial composition in the gut microbiota of largemouth bass could be attributable to the rhizosphere soil microbiota, while 62.01% of the bacterial composition could be attributable to the fish pond water microbiota. However, the proportion of bacteria in the gut microbiota from the fish pond water microbiota remained respectively 40.90% and 56.15% in May and September, which increased markedly to 88.97% in July. Similarly, the proportion of bacteria in the pond water microbiota from the tomato rhizosphere soil microbiota were respectively 0% and 8.95% in samples collected in May and September, which increased markedly to 69.26% in July, and the proportion of bacteria in the gut microbiota from the tomato rhizosphere soil microbiota were respectively 0.07% and 0% in samples collected in May and September, which increased to 0.45% in July. The research results offer essential insights into the interactions and origins of environmental microbiota and gut microbiota in the aquaponics system of cultured fish. This knowledge could enhance green aquaponics practices for largemouth bass.

Negative legacy effects of past forest use on native plant diversity in semi-natural grasslands on ski slopes

Over the past century, grassland and forest ecosystems globally have been heavily influenced by land-use changes driven by diverse socioeconomic activities. Ski resorts are a modern land-use type associated with biodiversity loss in mountain ecosystems worldwide. Below the treeline, by contrast, some ski slopes have been shown to provide suboptimal semi-natural habitats for native grassland plants and animals, depending on specific construction and management practices. We compared environmental factors and grassland vegetation between two types of ski slopes in central Japan with different land-use histories: slopes constructed on old pastures (pasture slopes) and slopes constructed by clearing secondary forests or larch plantations established on abandoned pastures during the 1940s-1990s (forest slopes). We examined the effects of land-use history and machine grading as well as other environmental factors on ski slope vegetation, including total species richness and the richness of native, endangered, and exotic plants, using a total of 108 plots of 2 m × 10 m. Compared to pasture slopes, forest slopes exhibited significantly lower richness of native grassland species, including endangered species. Forest slopes were more graded than pasture slopes, resulting in lower native and higher exotic grassland species richness. A significantly lower duration of direct sunlight on forest slopes than on pasture slopes likely decreased endangered species richness. The lower species richness on forest slopes may be also caused by seed dispersal limitations. Our findings demonstrate that ski slopes have good potential to support numerous native grassland plant species, including endangered species, but this potential is significantly and negatively affected by forest use history and concomitant environmental changes. The conservation of semi-natural conditions on pasture slopes as habitats for native grassland species can be promoted through the maintenance of annual mowing practices, avoidance of machine grading, and wider ski courses.

Disturbance and vegetational structure in an urban forest of Indian Siwaliks: an ecological assessment

Urban forests face multiple human-mediated pressures leading to compromised ecosystem structure and functioning. Therefore, understanding ecosystem structure in response to ongoing pressures is crucial for sustaining ecological integrity and human well-being. We aim to assess the disturbance and its effects on the vegetation structure of urban forests in Chandigarh using a combination of remote sensing techniques and vegetation surveys. The disturbance was evaluated as a change in NDVI (Normalised Difference Vegetation Index) from 2001 to 2021 by applying the BFAST (Breaks For Additive Season and Trend) algorithm to the MODIS satellite imagery data. A vegetation survey was conducted to compare the species composition, taxonomic and phylogenetic diversity as measures of forest vegetational structure. While signals of disturbance were evident, the changes in vegetation structure were not well established from our study. Further, this analysis indicated no significant differences in vegetation composition due to disturbance (F1,12 = 0.91, p = 0.575). However, the phylogenetic diversity was substantially lower for disturbed plots than undisturbed plots, though the taxonomic diversity was similar among the disturbed and undisturbed plots. Our results confirmed that disturbance effects are more prominent on the phylogenetic than taxonomic diversity. These findings can be considered early signals of disturbance and its impact on the vegetation structure of urban forests and contribute to the knowledge base on urban ecosystems. Our study has implications for facilitating evidence-based decision-making and the development of sustainable management strategies for urban forest ecosystems.

Quorum-Sensing Signal DSF Inhibits the Proliferation of Intestinal Pathogenic Bacteria and Alleviates Inflammatory Response to Suppress DSS-Induced Colitis in Zebrafish

The imbalance of gut microbiota is an important factor leading to inflammatory bowel disease (IBD). Diffusible signal factor (DSF) is a novel quorum-sensing signal that regulates bacterial growth, metabolism, pathogenicity, and host immune response. This study aimed to explore the therapeutic effect and underlying mechanisms of DSF in a zebrafish colitis model induced by sodium dextran sulfate (DSS). The results showed that intake of DSF can significantly improve intestinal symptoms in the zebrafish colitis model, including ameliorating the shortening of the intestine, reducing the increase in the goblet cell number, and restoring intestinal pathological damage. DSF inhibited the upregulation of inflammation-related genes and promoted the expression of claudin1 and occludin1 to protect the tightness of intestinal tissue. The gut microbiome analysis demonstrated that DSF treatment helped the gut microbiota of the zebrafish colitis model recover to normal at the phylum and genus levels, especially in terms of pathogenic bacteria; DSF treatment downregulated the relative abundance of Aeromonas hydrophila and Staphylococcus aureus, and it was confirmed in microbiological experiments that DSF could effectively inhibit the colonization and infection of these two pathogens in the intestine. This study suggests that DSF can alleviate colitis by inhibiting the proliferation of intestinal pathogens and inflammatory responses in the intestine. Therefore, DSF has the potential to become a dietary supplement that assists in the antibiotic and nutritional treatment of IBD.

Exploring Gut Microbiome Composition and Circulating Microbial DNA Fragments in Patients with Stage II/III Colorectal Cancer: A Comprehensive Analysis

BACKGROUND

Colorectal cancer (CRC) significantly contributes to cancer-related mortality, necessitating the exploration of prognostic factors beyond TNM staging. This study investigates the composition of the gut microbiome and microbial DNA fragments in stage II/III CRC.

METHODS

A cohort of 142 patients with stage II/III CRC and 91 healthy controls underwent comprehensive microbiome analysis. Fecal samples were collected for 16S rRNA sequencing, and blood samples were tested for the presence of microbial DNA fragments. De novo clustering analysis categorized individuals based on their microbial profiles. Alpha and beta diversity metrics were calculated, and taxonomic profiling was conducted.

RESULTS

Patients with CRC exhibited distinct microbial composition compared to controls. Beta diversity analysis confirmed CRC-specific microbial profiles. Taxonomic profiling revealed unique taxonomies in the patient cohort. De novo clustering separated individuals into distinct groups, with specific microbial DNA fragment detection associated with certain patient clusters.

CONCLUSIONS

The gut microbiota can differentiate patients with CRC from healthy individuals. Detecting microbial DNA fragments in the bloodstream may be linked to CRC prognosis. These findings suggest that the gut microbiome could serve as a prognostic factor in stage II/III CRC. Identifying specific microbial markers associated with CRC prognosis has potential clinical implications, including personalized treatment strategies and reduced healthcare costs. Further research is needed to validate these findings and uncover underlying mechanisms.

Conserved patterns and locomotor-related evolutionary constraints in the hominoid vertebral column

The evolution of the hominoid lineage is characterized by pervasive homoplasy, notably in regions such as the vertebral column, which plays a central role in body support and locomotion. Few isolated and fewer associated vertebrae are known for most fossil hominoid taxa, but identified specimens indicate potentially high levels of convergence in terms of both form and number. Homoplasy thus complicates attempts to identify the anatomy of the last common ancestor of hominins and other taxa and stymies reconstructions of evolutionary scenarios. One way to clarify the role of homoplasy is by investigating constraints via phenotypic integration, which assesses covariation among traits, shapes evolutionary pathways, and itself evolves in response to selection. We assessed phenotypic integration and evolvability across the subaxial (cervical, thoracic, lumbar, sacral) vertebral column of macaques (n = 96), gibbons (n = 77), chimpanzees (n = 92), and modern humans (n = 151). We found a mid-cervical cluster that may have shifted cranially in hominoids, a persistent thoracic cluster that is most marked in chimpanzees, and an expanded lumbosacral cluster in hominoids that is most expanded in gibbons. Our results highlight the highly conserved nature of the vertebral column. Taxa appear to exploit existing patterns of integration and ontogenetic processes to shift, expand, or reduce cluster boundaries. Gibbons appear to be the most highly derived taxon in our sample, possibly in response to their highly specialized locomotion.

Comparative analysis of Deinagkistrodon acutus venom from Taiwan and China utilizing chromatographic, electrophoretic, and bioinformatic approaches, along with ELISA employing a monospecific antivenom

Deinagkistrodon acutus is a medically important pitviper inhabiting mainly South China and Taiwan. The hemorrhagic effects of its envenoming are compatible to its venom, which is abundant in metalloproteases (svMPs) and C-type lectin-like proteins. In this study, we investigated geographic variations in the venom of D. acutus collected from Taiwan and four Mainland Chinese provinces: Fujian, Jiangxi, Anhui, and Hunan. The variations were assessed through high-performance liquid chromatography, non-metric multidimensional scaling analysis, gel electrophoresis, and enzyme-linked immunosorbent assay (ELISA) with a monospecific antivenom (DaMAV) generated against the Taiwanese D. acutus venom, and discussed based on venom-protein sequences in databases and literature related to D. acutus venom. Additionally, the cross-reactivity of DaMAV against Crotalus horridus and Calloselasma rhodostoma venoms was investigated. We noted differential abundances of D. acutus venom metalloproteases, C-type lectin-like proteins, and phospholipase A2, along with point mutations and selective expression of serine protease isoforms. The ELISA results revealed that the venom from Taiwan was more reactive toward Taiwanese DaMAV than the four Mainland Chinese venoms, consistent with chromatographic profile differences, whereas C. horridus venom presented moderate cross-reactivity with DaMAV. The observed immunoreactivities of these venom with DaMAV can be attributed to the high prevalence of their PIII-svMPs, which are the dominant antigens, and the conservation of PIII-svMP epitopes.

The loss of plant functional groups increased arthropod diversity in an alpine meadow on the Tibetan Plateau

Plant species loss, driven by global changes and human activities, can have cascading effects on other trophic levels, such as arthropods, and alter the multitrophic structure of ecosystems. While the relationship between plant diversity and arthropod communities has been well-documented, few studies have explored the effects of species composition variation or plant functional groups. In this study, we conducted a long-term plant removal experiment to investigate the impact of plant functional group loss (specifically targeting tall grasses and sedges, as well as tall or short forbs) on arthropod diversity and their functional groups. Our findings revealed that the removal of plant functional groups resulted in increased arthropod richness, abundance and the exponential of Shannon entropy, contrary to the commonly observed positive correlation between plant diversity and consumer diversity. Furthermore, the removal of different plant groups had varying impacts on arthropod trophic levels. The removal of forbs had a more pronounced impact on herbivores compared to graminoids, but this impact did not consistently cascade to higher-trophic arthropods. Notably, the removal of short forbs had a more significant impact on predators, as evidenced by the increased richness, abundance, the exponential of Shannon entropy, inverse Simpson index and inverse Berger-Parker index of carnivores and abundance of omnivores, likely attributable to distinct underlying mechanisms. Our results highlight the importance of plant species identity in shaping arthropod communities in alpine grasslands. This study emphasizes the crucial role of high plant species diversity in controlling arthropods in natural grasslands, particularly in the context of plant diversity loss caused by global changes and human activities.

Changes in quality characteristics based on protein oxidation and microbial action of ultra-high pressure-treated grass carp (Ctenopharyngodon idella) fillets during magnetic field storage

Ultra-high pressure (UHP) and magnetic field (MF) are emerging food preservation technologies, but the research on the effects of combined treatment (UHP-MF) on aquatic products quality is insufficient. Hence, we explored the effects of UHP-MF treatment on the protein properties, microbial action and quality characteristics of stored grass carp fillets. Results showed that 300 MPa UHP treatment combined with MF storage (UHP300-MF) delayed the protein oxidation of stored fillets by inhibiting the accumulation of protein radical and the formation of lipid pro-oxidation products, thus the quality (texture, color) deterioration caused by oxidation was deferred. Additionally, 16S rDNA bacteria flora analysis revealed that UHP300-MF treatment inhibited the flora activity and diversity of fillets, delayed the protein degradation and quality deterioration caused by microbial action. Overall, UHP300-MF treatment suppressed the lipid and protein oxidation as well as microbial action, retarded the quality deterioration, and prolonged the shelf life of stored fillets.

Integrated Analysis of the Intestinal Microbiota and Transcriptome of Fenneropenaeus chinensis Response to Low-Salinity Stress

Salinity is an important environmental stress factor in mariculture. Shrimp intestines harbor dense and diverse microbial communities that maintain host health and anti-pathogen capabilities under salinity stress. In this study, 16s amplicon and transcriptome sequencing were used to analyze the intestine of Fenneropenaeus chinensis under low-salinity stress (15 ppt). This study aimed to investigate the response mechanisms of the intestinal microbiota and gene expression to acute low-salinity stress. The intestinal tissues of F. chinensis were analyzed using 16S microbiota and transcriptome sequencing. The microbiota analysis demonstrated that the relative abundances of Photobacterium and Vibrio decreased significantly, whereas Shewanella, Pseudomonas, Lactobacillus, Ralstonia, Colwellia, Cohaesibacter, Fusibacter, and Lachnospiraceae_NK4A136_group became the predominant communities. Transcriptome sequencing identified numerous differentially expressed genes (DEGs). The DEGs were clustered into many Gene Ontology terms and further enriched in some immunity- or metabolism-related Kyoto Encyclopedia of Genes and Genomes pathways, including various types of N-glycan biosynthesis, amino acid sugar and nucleotide sugar metabolism, and lysosome and fatty acid metabolism. Correlation analysis between microbiota and DEGs showed that changes in Pseudomonas, Ralstonia, Colwellia, and Cohaesibacter were positively correlated with immune-related genes such as peritrophin-1-like and mucin-2-like, and negatively correlated with caspase-1-like genes. Low-salinity stress caused changes in intestinal microorganisms and their gene expression, with a close correlation between them.

Characterization of the Bacterial Profile from Natural and Laboratory Glossina Populations

Tsetse flies (Glossina spp.; Diptera: Glossinidae) are viviparous flies that feed on blood and are found exclusively in sub-Saharan Africa. They are the only cyclic vectors of African trypanosomes, responsible for human African trypanosomiasis (HAT) and animal African trypanosomiasis (AAT). In this study, we employed high throughput sequencing of the 16S rRNA gene to unravel the diversity of symbiotic bacteria in five wild and three laboratory populations of tsetse species (Glossina pallidipes, G. morsitans, G. swynnertoni, and G. austeni). The aim was to assess the dynamics of bacterial diversity both within each laboratory and wild population in relation to the developmental stage, insect age, gender, and location. Our results indicated that the bacterial communities associated with the four studied Glossina species were significantly influenced by their region of origin, with wild samples being more diverse compared to the laboratory samples. We also observed that the larval microbiota was significantly different than the adults. Furthermore, the sex and the species did not significantly influence the formation of the bacterial profile of the laboratory colonies once these populations were kept under the same rearing conditions. In addition, Wigglesworthia, Acinetobacter, and Sodalis were the most abundant bacterial genera in all the samples, while Wolbachia was significantly abundant in G. morsitans compared to the other studied species. The operational taxonomic unit (OTU) co-occurrence network for each location (VVBD insectary, Doma, Makao, and Msubugwe) indicated a high variability between G. pallidipes and the other species in terms of the number of mutual exclusion and copresence interactions. In particular, some bacterial genera, like Wigglesworthia and Sodalis, with high relative abundance, were also characterized by a high degree of interactions.

The Potential Hypoglycemic Competence of Low Molecular Weight Polysaccharides Obtained from Laminaria japonica

This study aimed to assess the hypoglycemic efficacy of low molecular weight polysaccharides fractions obtained from Laminaria japonica (LJOO) in a model of type 2 diabetes mellitus (T2DM) constructed using mice. Biochemical parameters were measured after 4 weeks of continuous gavage, and fasting blood glucose (FBG) concentrations were analyzed. Pathological changes in tissues were assessed. The intestinal contents were obtained for 16S rDNA high-throughput sequencing analysis and detection of short-chain fatty acids (SCFAs). LJOO lowered FBG and insulin concentrations. It altered the gut microbiota composition, as evidenced by enriched probiotic bacteria, along with an increase in the Bacteroidetes/Firmicutes ratio and a decrease in the population of harmful bacteria. LJOO stimulated the growth of SCFA-producing bacteria, thereby increasing cecal SCFAs levels. LJOO can potentially aid in alleviating T2DM and related gut microbiota dysbiosis. LJOO may be used as a food supplement for patients with T2DM.

Early-melting snowpatch plant communities are transitioning into novel states

Snowpatch plant community distribution and composition are strongly tied to the duration of long-lasting snow cover in alpine areas; they are vulnerable to global climatic changes that result in warmer temperatures and longer growing seasons. We used a revisitation study to quantify early-melting snowpatch floristic and functional diversity change in southern Australia, and document shrub size-class distributions over time to detect evidence for their encroachment into snowpatches, a key prediction with climatic change. Early-melting snowpatch vegetation has declined in areal extent, changed in species composition, and shrub and tussock grass cover has increased, but changes in functional trait diversity were less clear. Species gains, particularly by non-clonal species, accounted for most of the floristic change observed. Shrub recruitment was ongoing by most shrub species. Biotic differentiation is occurring; many early-melting snowpatches are transitioning to a novel state with changed composition and taller vegetation structure, but there is little evidence for species loss having occurred. Given enough time, however, the long-term loss of species is likely (i.e. biotic homogenisation) if taller shrubs outcompete short-statured snowpatch species. Our results provide evidence that this alpine ecosystem is forming a novel community with an uncertain future.

Postmortem Nasopharyngeal Microbiome Analysis of Zambian Infants With and Without Respiratory Syncytial Virus Disease: A Nested Case Control Study

BACKGROUND

Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis and lower respiratory tract infections in children in their first year of life, disproportionately affecting infants in developing countries. Previous studies have found that the nasopharyngeal (NP) microbiome of infants with RSV infection has specific characteristics that correlate with disease severity, including lower biodiversity, perturbations of the microbiota and differences in relative abundance. These studies have focused on infants seen in clinical or hospital settings, predominantly in developed countries.

METHODS

We conducted a nested case control study within a random sample of 50 deceased RSV+ infants with age at death ranging from 4 days to 6 months and 50 matched deceased RSV- infants who were all previously enrolled in the Zambia Pertussis and RSV Infant Mortality Estimation (ZPRIME) study. All infants died within the community or within 48 hours of facility admittance. As part of the ZPRIME study procedures, all decedents underwent one-time, postmortem NP sampling. The current analysis explored the differences between the NP microbiome profiles of RSV+ and RSV- decedents using the 16S ribosomal DNA sequencing.

RESULTS

We found that Moraxella was more abundant in the NP microbiome of RSV+ decedents than in the RSV- decedents. Additionally, Gemella and Staphylococcus were less abundant in RSV+ decedents than in the RSV- decedents.

CONCLUSIONS

These results support previously reported findings of the association between the NP microbiome and RSV and suggest that changes in the abundance of these microbes are likely specific to RSV and may correlate with mortality associated with the disease.

Use climatic space-for-time substitutions with care: Not only climate, but also local environment affect performance of the key forest species bilberry along elevation gradient

An urgent aim of ecology is to understand how key species relate to climatic and environmental variation, to better predict their prospects under future climate change. The abundant dwarf shrub bilberry (Vaccinium myrtillus L.) has caught particular interest due to its uphill expansion into alpine areas. Species' performance under changing climate has been widely studied using the climatic space-for-time approach along elevation gradients, but potentially confounding, local environmental variables that vary along elevation gradients have rarely been considered. In this study, performed in 10 sites along an elevation gradient (200-875 m) in W Norway, we recorded species composition and bilberry performance, both vegetative (ramet size and cover) and reproductive (berry and seed production) properties, over one to 4 years. We disentangled effects of local environmental variables and between-year, climatic variation (precipitation and temperature), and identified shared and unique contributions of these variables by variation partitioning. We found bilberry ramet size, cover and berry production to peak at intermediate elevations, whereas seed production increased upwards. The peaks were less pronounced in extreme (dry or cold) summers than in normal summers. Local environmental variables explained much variation in ramet size and cover, less in berry production, and showed no relation to seed production. Climatic variables explained more of the variation in berry and seed production than in ramet size and cover, with temperature relating to vegetative performance, and precipitation to reproductive performance. Bilberry's clonal growth and effective reproduction probably explain why the species persists in the forest and at the same time invades alpine areas. Our findings raise concerns of the appropriateness of the climatic space-for-time approach. We recommend including both climatic and local environmental variables in studies of variation along elevation gradients and conclude that variation partitioning can be a useful supplement to other methods for analysing variation in plant performance.

Diet composition of wild columbiform birds: next-generation sequencing of plant and metazoan DNA in faecal samples

Accurate knowledge of a species' diets is fundamental to understand their ecological requirements. Next-generation sequencing technology has become a powerful and non-invasive tool for diet reconstruction through DNA metabarcoding. Here, we applied those methods on faecal samples of Common Woodpigeons Columba palumbus, European Turtle Doves Streptopelia turtur, and Stock Doves C. oenas to investigate their dietary composition. By applying primer pairs targeting both the ITS2 region of plant nuclear DNA and the mitochondrial COI region of metazoan DNA, we provide a complete picture of the food ingested and estimate the dietary overlap between the columbiform species during the breeding season. Animal DNA was present very rarely, and a diverse range of plants from the class Spermatopsida dominated the diet, with Asteraceae, Brassicaceae, Cucurbitaceae, Fabaceae, and Poaceae as the most frequently represented families. Generally, we detected a variability between species but also amongst individual samples. Plant species already known from previous studies, mainly visual analyses, could be confirmed for our individuals sampled in Germany and the Netherlands. Our molecular approach revealed new plant taxa, e.g. plants of the families Malvaceae for Woodpigeons, Lythraceae for Turtle Doves, and Pinaceae for Stock Doves, not found in previous studies using visual analyses. Although most of the plant species observed were of wild origin, the majority of cultivated plants found were present in higher frequencies of occurrence, suggesting that cultivated food items likely constitute an important part of the diet of the studied species. For Turtle Doves, a comparison with previous studies suggested regional differences, and that food items (historically) considered as important part of their diet, such as Fumitory Fumaria sp. and Chickweed Stellaria media, were missing in our samples. This indicates that regional variations as well as historic and current data on diet should be considered to plan tailored seed mixtures, which are currently proposed as an important management measure for conservation of the rapidly declining Turtle Dove.

Diel, seasonal and vertical changes in the abundance, biomass and community structure of pelagic polychaetes at the subtropical station S1 in the western North Pacific: comparison with the results from the subarctic station K2

Information on pelagic polychaete community structure in the western North Pacific is available for the subarctic region (Station K2) but not for the subtropical region. Hence, we analyzed day-night vertically stratified samples collected in eight layers within the first 1000 m of the water column during four seasons in 1 year, using the same sampling method as St. K2, at the subtropical region (Station S1). At St. S1, 27 species of pelagic polychaetes belonging to 13 genera and six families were identified. The annual mean abundance was 35.0 ind. 1000 m-3 and the biomass was 17.3 mg WW 1000 m-3. At St. S1, the numbers of genera and species were higher and the annual mean abundance and biomasses were much lower than St. K2. The pelagic polychaetes often peaked in the mesopelagic layer at St. K2, with the carnivores and particle feeders peaking in the epipelagic and mesopelagic layers, respectively. At St.S1, the carnivorous species predominated throughout the entire water column, and were most abundant in the epipelagic layer. Thus, In the western Pacific Ocean, the subarctic pelagic polychaete community structure changed vertically with feeding ecology. On the other hand, the subtropical community may be adapted to conditions of high irradiance and light transmission.

High Oxygen Shocking Reduces Postharvest Disease and Maintains Satisfying Quality in Fresh Goji Berries during Cold Storage by Affecting Fungi Community Composition

Fresh goji (Lycium barbarum L.) berries were treated with high-concentration (50% and 90%) oxygen shocking for 30 min and then stored at 0 ± 0.5 °C for 30 d. Decay, aerobic plate count, firmness, weight loss, total soluble solid (TSS), and titratable acidity (TA) were evaluated during storage. A total of 90% O₂ shocking more effectively reduced decay and maintained the weight loss and firmness of goji berries. Subsequently, changes in fungi communities were analyzed using high-throughput sequencing (HTS) in the 90% O₂-shocking and control groups. The results showed that 90% O₂ shocking retained the richness and diversity of fungi communities and the microbiome was related to the quality properties of the fruit. Thus, we inferred that high oxygen shocking inhibited the development of natural decay and maintained the satisfying quality of goji berries by affecting the fungi community composition, which reduced the growth of pathogenic fungi and harmful saprotrophic fungi in the genera, such as Filobasidium sp., Alternaria sp., and Cladosporium sp. We provide a new insight into the disease development and quality changes during the storage of postharvest goji berries.

No lukewarm diatom communities-the response of freshwater benthic diatoms to phosphorus in streams as basis for a new phosphorus diatom index (PDISE)

In the present study, we developed a new Swedish phosphorus diatom index (PDI_SE) to improve the poor fit of existing indices to match the needs of water managers to detect and mitigate eutrophication. We took advantage of a large amount of data (820 Swedish stream sites) collected in recent years. During our work, we found an unexpected bimodal response of the diatom assemblages to phosphorus. The taxa clustered either into an assemblage with a low or with a high site-specific averaged TP optimum (a calculated value comprised of the diatom taxa-specific optima). We could not find a characteristic diatom assemblage for sites with intermediate site-specific averaged TP optima. To our knowledge, this bimodal community response has not been shown earlier. The PDI_SE correlated more strongly than the currently used TDI to changes in TP concentrations. Thus, the PDI_SE should replace the TDI in the Swedish standard method. The modeled TP optima (expressed as categories) were different compared to the TDI for most of the taxa included in the index, indicating that the realized niche for these morphotaxa was different between Sweden and the UK where the TDI was developed originally. With a r² of 0.68, the correlation of the PDI_SE to TP is among the highest reported for other diatom nutrient indices globally; thus, we believe that it might be worth to test it for other bioregions with similar geography and climate.

Fossil berries reveal global radiation of the nightshade family by the early Cenozoic

Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.

Using Next-Generation Sequencing to Disentangle the Diet and Incidence of Intestinal Parasites of Falkland Flightless Steamer Duck Tachyeres brachypterus and Patagonian Crested Duck Lophonetta specularioides Sharing a South Atlantic Island

Species overlapping in habitat use can cohabit depending on how they exploit resources. To understand segregation in resource use, an exhaustive knowledge of the diet is required. We aimed to disentangle the diet composition of the Falkland Flightless Steamer Duck Tachyeres brachypterus and the Patagonian Crested Duck Lophonetta specularioides sharing a coastal environment. Using DNA extracted from scats and Illumina sequencing, we generated a list of molecular operational taxonomic units. Both ducks consumed a variety of invertebrates, frequently overlapping in the taxa consumed. However, only the Falkland Flightless Steamer Ducks consumed fish, which might be indicative of dietary specialization and inter-specific segregation in the restricted space that these birds share. Moreover, the female and male Falkland Flightless Steamer Ducks consumed different fish prey, with almost one-third of the fish taxa being consumed by females only and another similar number consumed by males only. This result might suggest a case of intra-specific competition, triggering sexual segregation. Additionally, we detected parasitic Platyelminthes (Cestoda and Trematoda), with different frequencies of occurrence, probably related to the different diet compositions of the ducks. This study provides the necessary baseline for future investigations of the ecological segregation of these ducks.

A Synoptic Review of the Cartilaginous Fishes (Chondrichthyes: Holocephali, Elasmobranchii) from the Upper Jurassic Konservat-Lagerstätten of Southern Germany: Taxonomy, Diversity, and Faunal Relationships

The Late Jurassic-Early Cretaceous (164-100 Ma) represents one of the main transitional periods in life history. Recent studies unveiled a complex scenario in which abiotic and biotic factors and drivers on regional and global scales due to the fragmentation of Pangaea resulted in dramatic faunal and ecological turnovers in terrestrial and marine environments. However, chondrichthyan faunas from this interval have received surprisingly little recognition. The presence of numerous entire skeletons of chondrichthyans preserved in several localities in southern Germany, often referred to as Konservat-Lagerstätten (e.g., Nusplingen and the Solnhofen Archipelago), provides a unique opportunity of to study the taxonomic composition of these assemblages, their ecological distributions and adaptations, and evolutionary histories in detail. However, even after 160 years of study, the current knowledge of southern Germany's Late Jurassic chondrichthyan diversity remains incomplete. Over the last 20 years, the systematic study and bulk sampling of southern Germany's Late Jurassic deposits significantly increased the number of known fossil chondrichthyan genera from the region (32 in the present study). In the present work, the fossil record, and the taxonomic composition of Late Jurassic chondrichthyans from southern Germany are reviewed and compared with several contemporaneous assemblages from other sites in Europe. Our results suggest, inter alia, that the Late Jurassic chondrichthyans displayed extended distributions within Europe. However, it nevertheless also is evident that the taxonomy of Late Jurassic chondrichthyans is in urgent need of revision.

Nest building in titmice Paridae: Selectivity in bryophyte use

In many bird species, reproductive success is dependent on nest quality. However, detailed data on nest composition are scarce, and quantitative analyses have generally used only rough categories, without species identification. Bryophytes dominate the nests of many passerine bird species, but little is known about whether birds have preferences for certain species. In this study, we determined the bryophyte species composition in nests of blue tits Cyanistes caeruleus and great tits Parus major in a forest near Oslo, Norway. We also sampled the abundance of the bryophyte species in plots on the forest floor surrounding a subset of the great tit nests. Blue tits and great tits both used 15 bryophyte species as nest materials, mainly the same pleurocarpous species but in different proportions. The tits preferred highly branched bryophyte species, i.e., Pleurozium schreberi, Rhytidiadelphus squarrosus, and Sanionia uncinata but avoided common forest floor bryophyte species that are sparsely branched. Great tits clearly collected bryophyte species selectively. We also found that bryophyte species content in great tit nests in the same nest box in different years was very similar. Our results also indicated that the great tits collected bryophyte nest materials close to their nests, mostly within 5 m, supporting the view that collecting nest materials is costly. We review several hypotheses to explain why the tits prefer certain species of bryophytes as nest materials. These include handling costs and their suitability as structural materials. We recommend field experiments to test specific hypotheses and to study whether preferences are heritable.

Characterization of the intestinal fungal microbiome in patients with hepatocellular carcinoma

OBJECTIVE

Gut mycobiota plays a crucial role in benign liver diseases; however, its correlation with hepatocellular carcinoma (HCC) remains elusive. This study aimed to elucidate fungal differences in patients with HCC-associated cirrhosis compared to cirrhotic patients without HCC and healthy controls.

METHODS

The 72 fecal samples from 34 HCC patients, 20 cirrhotic patients, and 18 healthy controls were collected and analyzed using ITS2 rDNA sequencing.

RESULTS

Our results revealed the presence of intestinal fungal dysbiosis with significant enrichment of opportunistic pathogenic fungi such as Malassezia, Malassezia sp., Candida, and C. albicans in HCC patients compared with healthy controls and cirrhosis patients. Alpha-diversity analysis demonstrated that patients with HCC and cirrhosis showed decreased fungal diversity compared to healthy controls. Beta diversity analysis indicated that the three groups exhibited significant segregated clustering. Besides, C. albicans was found to be significantly more abundant in the HCC patients with TNM stage III-IV than those with stage I-II, in contrast to the commensal organism S. cerevisiae. We also confirmed that the HCC patients were successfully classified with an area under the curve value of 0.906 based on the fecal fungal signature. Finally, our animal experiments confirm that aberrant colonization of the intestine by C. albicans and M. furfur can promote the development of HCC.

CONCLUSIONS

This study indicates that dysbiosis of the gut mycobiome might be involved in HCC development.

TRIAL REGISTRATION

ChiCTR, ChiCTR2100054537. Registered 19 December 2021, http://www.chictr.org.cn/edit.aspx?pid=144550&htm=4.

Alterations of gut mycobiota profiles in intrahepatic cholangiocarcinoma

Objective

Intrahepatic cholangiocarcinoma (ICC) is a silent liver malignancy with an increasing incidence. Gut mycobiota plays a crucial role in benign liver diseases; however, its correlation with ICC remains elusive. This study aimed to elucidate fungal differences in patients with ICC compared to healthy controls.

Methods

The 40 fecal samples from 23 ICC patients and 17 healthy controls were collected and analyzed using ITS2 rDNA sequencing. Obtaining the OTUs and combining effective grouping, we carried out the biodiversity and composition of the fungi, as well as FUNGuild functional annotation.

Results

Our results revealed the presence of intestinal fungal dysbiosis with significant enrichment of opportunistic pathogenic fungi such as Candida and C. albicans, and significant depletion of the beneficial fungus Saccharomyces cerevisiae in ICC patients compared with healthy controls. Alpha-diversity analysis demonstrated that patients with ICC showed decreased fungal diversity compared to healthy controls. Beta diversity analysis indicated that the two groups exhibited significant segregated clustering. Besides, C. albicans was found to be significantly more abundant in the ICC patients with TNM stage III-IV than those with stage I-II. The FUNGuild functional classification predicted that pathotrophs were the most abundant taxon in the ICC group, well above their abundance in healthy controls.

Conclusion

This study indicates that dysbiosis of the fecal mycobiome might be involved in ICC development. Further research into gut fungi may contribute to new therapeutic options for ICC patients.

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.

Canopy plant composition and structure of Cape subtropical dune thicket are predicted by the levels of fire exposure

Background

The subtropical dune thicket (hereafter "dune thicket") of the Cape Floristic Region experiences a wide range of fire exposure throughout the landscape, unlike other dry rainforest formations that rarely experience fire. We sought to determine how fire exposure influences species composition and the architectural composition of dune thicket.

Methods

We used multivariate analysis and diversity indices based on cover abundance of species to describe the species composition, architectural guild composition and structure of dune thicket sites subject to different levels of fire exposure, namely low (fire return interval of >100 years), moderate (fire return interval of 50-100 years), and high (fire return interval of 10-50 years).

Results

The diversity, cover abundance and architectural guild cover abundance of dune thicket canopy species were strongly influenced by the level of fire exposure such that each level was associated with a well-circumscribed vegetation unit. Dune thickets subject to low fire exposure comprises a floristically distinct, low forest characterized by shrubs with one-to-few upright stems (ca. 4-8 m tall) and a relatively small canopy spread (vertical growers). Of the 25 species in this unit, 40% were restricted to it. Dune thickets subject to moderate fire exposure had the highest abundance of lateral spreaders, which are multi-stemmed (ca. 3-6 m tall) species with a large canopy spread and lower stature than vertical growers. None of the 17 species found in this unit was restricted to it. Dune thickets subject to high fire exposure had the highest abundance of hedge-forming shrubs, these being low shrubs (ca. 0.6-1.4 m tall), with numerous shoots arising from an extensive system of below-ground stems. Of the 20 species in this unit, 40% were restricted to it. Multivariate analysis identified three floristic units corresponding to the three fire exposure regimes. Compositional structure, in terms of species and architectural guilds, was most distinctive for dune thickets subject to high and low fire exposure, while the dune thicket subject to moderate fire exposure showed greatest compositional overlap with the other units.

Conclusion

Fire exposure profoundly influenced the composition and structure of dune thicket canopy species in the Cape Floristic Region. In the prolonged absence of fire, the thicket is invaded by vertical-growing species that overtop and outcompete the multi-stemmed, laterally-spreading shrubs that dominate this community. Regular exposure to fire selects for traits that enable thicket species to rapidly compete for canopy cover post-fire via the prolific production of resprouts from basal buds below- and above-ground. The trade-off is that plant height is constrained, as proportionately more resources are allocated to below-ground biomass.

Dietary supplementation with Cyberlindnera jadinii improved growth performance, serum biochemical Indices, antioxidant status, and intestinal health in growing raccoon dogs (Nyctereutes procyonoides)

This study was conducted to investigate whether different dietary Cyberlindnera jadinii levels affect growth performance, serum immunity, antioxidant capacity, and intestinal microbiota in growing raccoon dogs. Forty-five healthy male raccoon dogs were randomly assigned to three treatment groups, with 15 raccoon dogs per group. Each raccoon dog was housed in an individual cage. The raccoon dogs in the three groups were fed diets supplemented with Cyberlindnera jadinii at dosages of 0 (N group), 1 × 10⁹ (L group) and 5 × 10⁹ CFU/g (H group). A 7-day pretest period preceded a formal test period of 30 days. The results showed that Cyberlindnera jadinii in the L and H groups improved average daily gain (ADG) (P < 0.05) and decreased the ratio of feed to weight (F/G) (P < 0.05). Serum immunoglobulins A and G levels were increased in the L and H groups compared to the N group (P < 0.05). Cyberlindnera jadinii in the L and H groups increased serum superoxide dismutase activity (P < 0.05), and serum glutathione peroxidase activity was increased in the L group compared to the N group (P < 0.05). The relative abundance of Firmicutes and Actinobacteriota were increased, and the relative abundance of Bacteroidota was decreased in the L and H groups compared to the N group (P < 0.05). The relative abundance of Proteobacteria and Cyanobacteria was increased in the H group compared to the other two groups (P < 0.05). The ratio of Firmicutes to Bacteroidetes in the Cyberlindnera jadinii supplementation groups increased compared with the N group (P < 0.05). The relative abundance of Megasphaera and Bifidobacterium were increased, and the relative abundance of Prevotella was decreased in the L and H groups compared to the N group (P < 0.05). The relative abundance of Dialister was increased, while the relative abundance of Blautia was decreased in the H group compared to the other two groups (P < 0.05). The relative abundance of Agathobacter was decreased in the H group compared to the N group (P < 0.05). In conclusion, dietary supplementation with Cyberlindnera jadinii increased growth performance, serum immunity, antioxidant capacity, and improved intestinal microbiota in growing raccoon dogs. Cyberlindnera jadinii can therefore be used as a growth promoter in raccoon dogs.

Dietary Modulation of the Human Gut Microbiota and Metabolome with Flaxseed Preparations

Flaxseeds are typically consumed either as whole flaxseed, ground flaxseed, flaxseed oil, partially defatted flaxseed meal, or as a milk alternative. They are considered a rich source of vitamins, minerals, proteins and peptides, lipids, carbohydrates, lignans, and dietary fiber, which have shown hypolipidemic, antiatherogenic, anticholesterolemic, and anti-inflammatory property activity. Here, an in vitro batch culture model was used to investigate the influence of whole milled flaxseed and partially defatted milled flaxseed press cake on the gut microbiota and the liberation of flaxseed bioactives. Microbial communities were profiled using 16S rRNA gene-based high-throughput sequencing with targeted mass spectrometry measuring lignan, cyclolinopeptide, and bile acid content and HPLC for short-chain fatty acid profiles. Flaxseed supplementation decreased gut microbiota richness with Firmicutes, Proteobacteria, and Bacteroidetes becoming the predominant phyla. Secoisolariciresinol, enterodiol, and enterolactone were rapidly produced with acetic acid, butyric acid, and propionic acid being the predominant acids after 24 h of fermentation. The flaxseed press cake and whole flaxseed were equivalent in microbiota changes and functionality. However, press cake may be superior as a functional additive in a variety of foods in terms of consumer acceptance as it would be more resistant to oxidative changes.

Impact of host sex and age on the diversity of endoparasites and structure of individual-based host-parasite networks in nyalas (Tragelaphus angasii Angas) from three game reserves in KwaZulu-Natal province, South Africa

In recent years, numerous studies have examined the effect of host sex and age on the structure of parasite communities in several host taxa under various environmental conditions and in different geographic regions. However, the influence of such factors on the structure of host-parasite networks has received less attention, and remarkably few studies have been carried out on large terrestrial mammals. In this study, we investigated the effects of host age and sex on the parasite infra- and component communities of nyalas (Tragelaphus angasii) and on the structure of individual-based nyala-endoparasite networks. We also aimed to evaluate to what extent these effects vary spatially and if they are mediated by conservation management. Based on a data set of internal macroparasites of 74 nyalas from three game reserves in KwaZulu-Natal province, we found that host age strongly influenced parasite community structure as well as the structure of parasite-nyala networks, whereas host sex played a minor role. However, the effects of both host sex and age were mediated by environmental conditions and thus led to different patterns at the three localities. Our findings highlight that host-parasite communities from different localities should not be pooled when conducting host-parasite network and community studies as this may bias results and mask patterns that are typical for a given locality.

Limited decadal growth of mountain birch saplings has minor impact on surrounding tundra vegetation

Temperatures over the Arctic region are increasing at three times the rate of the global average. Consequently, Arctic vegetation is changing and trees are encroaching into the tundra. In this study, we examine the establishment and growth of mountain birch (Betula pubescens ssp. tortuosa), which forms the treeline in subarctic Europe, and its impact on community composition across the treeline ecotone nearby Abisko, Sweden. Birch advancement along elevational gradients was studied by comparing data collected in 2016 with data collected 10 and 15 years previously. Species identity, cover, and phylogenetic relatedness were used to assess the impact of birch encroachment on community composition. Our results show that birch occurrence above the treeline did not affect plant community composition, probably owing to the observed lack of significant growth due to herbivore browsing, nitrogen limitation, or a reduction in snow cover. Independent of birch performance, the tundra community structure shifted toward a novel community dissimilar from the forest plant community found below the treeline. Taken together, our findings are explained by species-specific responses to climate change, rather than by a linear forest advance. Future treeline advancements are likely more restricted than previously expected.

Interpopulational variation and ontogenetic shift in the venom composition of Lataste's viper (Vipera latastei, Boscá 1878) from northern Portugal

Lataste's viper (Vipera latastei) is a venomous European viper endemic to the Iberian Peninsula, recognised as medically important by the World Health Organization. To date, no comprehensive characterisation of this species' venom has been reported. Here, we analysed the venoms of juvenile and adult specimens of V. latastei from two environmentally different populations from northern Portugal. Using bottom-up venomics, we produced six venom proteomes (three per population) from vipers belonging to both age classes (i.e., two juveniles and four adults), and RP-HPLC profiles of 54 venoms collected from wild specimens. Venoms from juveniles and adults differed in their chromatographic profiles and relative abundances of their toxins, suggesting the occurrence of ontogenetic changes in venom composition. Specifically, snake venom metalloproteinase (SVMP) was the most abundant toxin family in juvenile venoms, while snake venom serine proteinases (SVSPs), phospholipases A₂ (PLA₂s), and C-type lectin-like (CTLs) proteins were the main toxins comprising adult venoms. The RP-HPLC venom profiles were found to vary significantly between the two sampled localities, indicating geographic variability. Furthermore, the presence/absence of certain peaks in the venom chromatographic profiles appeared to be significantly correlated also to factors like body size and sex of the vipers. Our findings show that V. latastei venom is a variable phenotype. The intraspecific differences we detected in its composition likely mirror changes in the feeding ecology of this species, taking place during different life stages and under different environmental pressures. SIGNIFICANCE: Lataste's viper (Vipera latastei) is a medically important viper endemic to the Iberian Peninsula, inhabiting different habitats and undergoing a marked ontogenetic dietary shift. In the current study, we report the first proteomic analysis of V. latastei venom from two environmentally different localities in northern Portugal. Our bottom-up venomic analyses show that snake venom serine proteinases (SVSPs), phospholipases A2 (PLA2s), and C-type lectin-like (CTLs) proteins are the major components of adult V. latastei venom. The comparative analysis of young and adult venoms suggests the occurrence of ontogenetic shift in toxin abundances, with snake venom metalloproteinases (SVMPs) being the predominant toxins in juvenile venoms. Moreover, geographic venom variation between the two studied populations is also detected, with our statistical analyses suggesting that factors like body size and sex of the vipers are possibly at play in its determination. Our work represents the first assessment of the composition of V. latastei venom, and the first step towards a better understanding of the drivers behind its variability.

Pediococcus acidilactici Strain Alleviates Gluten-Induced Food Allergy and Regulates Gut Microbiota in Mice

Wheat flour, the most important source of food globally, is also one of the most common causative agents of food allergy. Wheat gluten protein, which accounts for 80% of the total wheat protein, is a major determinant of important wheat-related disorders. In this study, the effects of Pediococcus acidilactici XZ31 against gluten-induced allergy were investigated in a mouse model. The oral administration of P. acidilactici XZ31 attenuated clinical and intestinal allergic responses in allergic mice. Further results showed that P. acidilactici XZ31 regulated Th1/Th2 immune balance toward Th1 polarization, which subsequently induced a reduction in gluten-specific IgE production. We also found that P. acidilactici XZ31 modulated gut microbiota homeostasis by balancing the Firmicutes/Bacteroidetes ratio and increasing bacterial diversity and the abundance of butyrate-producing bacteria. Specifically, the abundance of Firmicutes and Erysipelotrichaceae is positively correlated with concentrations of gluten-specific IgE and may act as a fecal biomarker for diagnosis. The evidence for the role of P. acidilactici XZ31 in alleviating gluten-induced allergic responses sheds light on the application of P. acidilactici XZ31 in treating wheat allergy.

Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM2.5 by African dust incursions to the Mediterranean atmosphere

PM_2.5 atmospheric samples were regularly collected between January 2013 and March 2015 at a central location of Eastern Mediterranean (Island of Crete) during African dust events (DES) and periods of absence of such episodes as controls (CS). The elemental composition and microbiome DES and CS were thoroughly investigated. Fifty-six major and trace elements were determined by inductively coupled plasma-mass spectrometry. Relative mass abundances (RMA) of major crustal elements and lanthanoids were higher in DES than in CS. Conversely in CS, RMAs were higher for most anthropogenic transition metals. Lanthanum-to-other lanthanoids concentration ratios for DES approached the corresponding reference values for continental crust and several African dust source regions, while in CS they exceeded these values. USEPA's UNMIX receptor model, applied in all PM_2.5 samples, established that African dust is the dominant contributing source (by 80%) followed by road dust/fuel oil emissions (17%) in the receptor area. Potential source contribution function (PSCF) identified dust hotspots in Tunisia, Libya and Egypt. The application of 16S rRNA gene amplicon sequencing revealed high variation of bacterial composition and diversity between DES and CS samples. Proteobacteria, Actinobacteria and Bacteroides were the most dominant in both DES and CS samples, representing ~88% of the total bacterial diversity. Cutibacterium, Tumebacillus and Sphingomonas dominated the CS samples, while Rhizobium and Brevundimonas were the most prevalent genera in DES. Mutual exclusion/co-occurrence network analysis indicated that Sphingomonas and Chryseobacterium exhibited the highest degrees of mutual exclusion in CS, while in DES the corresponding species were Brevundimonas, Delftia, Rubellimicrobium, Flavobacterium, Blastococcus, and Pseudarthrobacter. Some of these microorganisms are emerging global opportunistic pathogens and an increase in human exposure to them as a result of environmental changes, is inevitable.

A contemporary survey of bumble bee diversity across the state of California

Bumble bees (genus Bombus) are important pollinators with more than 260 species found worldwide, many of which are in decline. Twenty-five species occur in California with the highest species abundance and diversity found in coastal, northern, and montane regions. No recent studies have examined California bumble bee diversity across large spatial scales nor explored contemporary community composition patterns across the state. To fill these gaps, we collected 1740 bumble bee individuals, representing 17 species from 17 sites (~100 bees per site) in California, using an assemblage monitoring framework. This framework is intended to provide an accurate estimate of relative abundance of more common species without negatively impacting populations through overcollection. Our sites were distributed across six ecoregions, with an emphasis on those that historically hosted high bumble bee diversity. We compared bumble bee composition among these sites to provide a snapshot of California bumble bee biodiversity in a single year. Overall, the assemblage monitoring framework that we employed successfully captured estimated relative abundance of species for most sites, but not all. This shortcoming suggests that bumble bee biodiversity monitoring in California might require multiple monitoring approaches, including greater depth of sampling in some regions, given the variable patterns in bumble bee abundance and richness throughout the state. Our study sheds light on the current status of bumble bee diversity in California, identifies some areas where greater sampling effort and conservation action should be focused in the future, and performs the first assessment of an assembly monitoring framework for bumble bee communities in the state.

Simulating selection and evolution at the community level using common garden data

A key issue in evolutionary biology is whether selection acting at levels higher than the individual can cause evolutionary change. If it can, then conceptual and empirical studies must consider how selection operates at multiple levels of biological organization. Here, we test the hypothesis that estimates of broad-sense community heritability, H C 2 , can be used to predict the evolutionary response by community-level phenotypes when community-level selection is imposed. Using an approach informed by classic quantitative genetics, we made three predictions. First, when we imposed community-level selection, we expected a significant change in the average phenotype of arthropod communities associated with individual tree genotypes [we imposed selection by favoring high and low NMDS (nonmetric multidimensional scaling) scores that reflected differences in arthropod species richness, abundance and composition]. Second, we expected H C 2 to predict the magnitude of the community-level response. Third, we expected no significant change in average NMDS scores with community-level selection imposed at random. We tested these hypotheses using three years of common garden data for 102 species comprising the arthropod communities, associated with nine clonally replicated Populus angustifolia genotypes. Each of our predictions were met. We conclude that estimates of H C 2 account for the resemblance among communities sharing common ancestry, the persistence of community composition over time, and the outcome of selection when it occurs at the community level. Our results provide a means for exploring how this process leads to large-scale community evolutionary change, and they identify the circumstances in which selection may routinely act at the community level.

Interannual climate variability mediates changes in carbon and nitrogen pools caused by annual grass invasion in a semiarid shrubland

Exotic plant invasions alter ecosystem properties and threaten ecosystem functions globally. Interannual climate variability (ICV) influences both plant community composition (PCC) and soil properties, and interactions between ICV and PCC may influence nitrogen (N) and carbon (C) pools. We asked how ICV and non-native annual grass invasion covary to influence soil and plant N and C in a semiarid shrubland undergoing widespread ecosystem transformation due to invasions and altered fire regimes. We sampled four progressive stages of annual grass invasion at 20 sites across a large (25,000 km² ) landscape for plant community composition, plant tissue N and C, and soil total N and C in 2013 and 2016, which followed 2 years of dry and wet conditions, respectively. Multivariate analyses and ANOVAs showed that in invasion stages where native shrub and perennial grass and forb communities were replaced by annual grass-dominated communities, the ecosystem lost more soil N and C in wet years. Path analysis showed that high water availability led to higher herbaceous cover in all invasion stages. In stages with native shrubs and perennial grasses, higher perennial grass cover was associated with increased soil C and N, while in annual-dominated stages, higher annual grass cover was associated with losses of soil C and N. Also, soil total C and C:N ratios were more homogeneous in annual-dominated invasion stages as indicated by within-site standard deviations. Loss of native shrubs and perennial grasses and forbs coupled with annual grass invasion may lead to long-term declines in soil N and C and hamper restoration efforts. Restoration strategies that use innovative techniques and novel species to address increasing temperatures and ICV and emphasize maintaining plant community structure-shrubs, grasses, and forbs-will allow sagebrush ecosystems to maintain C sequestration, soil fertility, and soil heterogeneity.

Dysbiotic tumor microbiota associates with head and neck squamous cell carcinoma outcomes

BACKGROUND

The need for an effective tool to predict prognosis of head and neck squamous cell carcinoma (HNSCC) patients is critical and unmet. Microbiota has recently been found involved in tumor progression and response to immunotherapy. However, the association of microbiota with the prognosis of HNSCC patients remains obscure. This study aims to investigate the association between tumor microbiota and outcomes of HNSCC patients.

METHODS

A retrospective study including 129 primary tumors of HNSCC was conducted. Using 16S rRNA sequencing, the profile and the composition of tumor microbiota were measured and their associations with overall survival (OS) and disease free survival (DFS) were examined.

RESULTS

We observed a reduced richness and enriched abundances of genera Schlegelella and Methyloversatilis in tumor microbiota of HNSCC patients with poor prognosis. However, a richer tumor microbiota with greater abundances of genera Bacillus, and Lactobacillus and Sphingomonas was characterized in the patients with favorable prognosis.The ratio of these differentially abundant taxa, microbial dysbiosis index (MDI), was significantly associated with OS (hazard ratio [HR], 4.67, 95% confidence interval [CI], 2.51 to 8.69,P < 0.001) and DFS (HR, 2.89; 95% CI, 1.74 to 4.80, P < 0.001) independently of age, tumor size, lymph node metastasis, differentiation and p16 status. The risk score of multivariate Cox regression exhibited an excellent performance for estimating three-year OS (AUC of 0.826). We also found a richer tumor microbiota was correlated with moderate peritumoral inflammatory infiltration.

CONCLUSION

These results indicate that tumor microbiota associates with outcomes of HNSCC patients.

The effects of different coculture patterns with salt-tolerant yeast strains on the microbial community and metabolites of soy sauce moromi

In this study, the contributions of three strains and different coculture patterns to microbial community diversity and metabolites in the high-salt liquid-state fermentation (HLF) soy sauce moromi were investigated. A comparison of two strains of Zygosaccharomyces rouxii showed that strain QH-25 had a stronger ability to contribute metabolites, including both nonvolatile and volatile types, to the moromi than strain QH-1, except for volatile acids and ketones. Of the various fortification patterns tested, the content of metabolites was significantly increased by inoculating Z. rouxii QH-25 prior to C. versatilis, especially the content of volatiles, including ketones, esters, phenols, and alcohols, which increased 1.61-fold compared with those in the control sample; the contents of these components were increased 3.07-, 1.91-, 1.36-, and 1.22-fold, respectively. In particular, characteristic components such as ethyl octanoate, 4-hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone (HEMF), 4-ethyl-2-methoxy-phenol (4-EG), and 3-methyl-1-butanol were increased 3.99-, 3.29-, 1.63-, and 0.70-fold, respectively. Redundancy analysis (RDA) showed that Staphylococcus, Zygosaccharomyces, and Candida were positively correlated with the unique components described above. In addition, the nodes of the interaction network between Zygosaccharomyces and Candida were increased, and the positive correlation of Zygosaccharomyces with Staphylococcus was enhanced by inoculating Z. rouxii prior to C. versatilis. These results suggested that the unique flavor of soy sauce was closely related to the metabolic characteristics of strains affiliated with Z. rouxii, whether cultured singly or cocultured with C. versatilis. This study also provided a reference method for determining the differences in community structure and metabolites between traditional techniques and modern processes for soy sauce fermentation.

Dynamic Microbial Shifts and Signatures of Long-Term Remission in Allergic Rhinitis After an Herbal Formula Treatment

A mixed Chinese herbal formula, Xiao-Qing-Long-Decoction (XQLD), may contribute to sustained remission in allergic rhinitis (AR), but it is unknown which factors determine such long-term effect. Here, we aimed to identify bacterial signatures associated with sustained remission. To this end, samples from AR patients at four different times were analyzed to compare the dynamic bacterial community and structure shifts. Diversity indices Chao1 showed significant difference across different time (p<0.05), and the Kruskal-Wallis test identified that Dialister (OTU_31), Roseburia (OTU_36), Bacteroides (OTU_22), Bacteroides (OTU_2040), and Prevotella_9 (OTU_5) were the significant differential bacterial taxa (p<0.05). These distinctive genera were significantly associated with the change of AR clinical indices and the predicted functional pathways such as PPAR signaling pathway, peroxisome, and citrate cycle (TCA cycle) (p<0.05), indicating that they may be important bacterial signatures involving in the sustained remission in AR (p<0.05). Besides, lower Firmicutes/Bacteroidetes (F/B) ratio at 6 months follow-up may also contribute to the long-term remission of AR. No seriously adverse events and safety concerns were observed in this study. In conclusion, XQLD is a meaningful, long-term efficient and safe medication for AR treatment. The underlying mechanisms of sustained remission in AR after XQLD treatment may be associated with the dynamic alteration of featured gut bacteria taxa.

Compound Probiotics Improve Body Growth Performance by Enhancing Intestinal Development of Broilers with Subclinical Necrotic Enteritis

The aim of this study is to explore whether or not the combined application of BS15 and H2 is capable to have a more effective control effect on SNE in broilers. A total of 240 1-day-old female chickens were randomly divided into 5 groups: (a) basal diet in negative control group (NC group); (b) basal diet + SNE infection (coccidiosis vaccine + CP) (PC group); (c) basal diet + SNE infection + H2 pre-treatment (BT group); (d) basal diet + SNE infection + BS15 pre-treatment (LT group); and (e) basal diet + SNE infection + H2 pre-treatment + BS15 pre-treatment (MT group). The results showed the MT group had the most positive effect on inhibiting the negative effect of growth performance at 42 days of age. In the detection of the NC, PC, and MT group indicators at 28 days of age, we found that MT group significantly promoted ileum tissue development of broilers, and the ileum of broilers in the MT group formed a flora structure different from NC and PC, although it was found that the MT group had no effect on the butyrate level in the cecum, but it could affect the serum immune level, such as significantly reducing the level of pro-inflammatory cytokine IL-8 and increasing the content of immunoglobulin IgM and IgG. In conclusion, the composite preparation of Lactobacillus johnsonii BS15 and Bacillus licheniformis H2 could effectively improve the growth performance against SNE broilers, which is possibly caused by the improvement of the immune levels, the reduction of inflammation levels, and the promotion of the intestinal development.

Pulse grazing by reindeer (Rangifer tarandus) can increase the phylogenetic diversity of vascular plant communities in the Fennoscandian tundra

Herbivore grazing is an important determinant of plant community assemblages. Thus, it is essential to understand its impact to direct conservation efforts in regions where herbivores are managed. While the impacts of reindeer (Rangifer tarandus) grazing on plant biodiversity and community composition in the Fennoscandian tundra are well studied, the impact of reindeer grazing on phylogenetic community structure is not. We used data from a multiyear quasi-experimental study in northern Fennoscandia to analyze the effect of reindeer grazing on plant community diversity including its phylogenetic structure. Our study design used a permanent fence constructed in the 1960s and temporary fences constructed along the permanent fence to expose plant communities to three different grazing regimes: light (almost never grazed), pulse (grazed every other year), and press (chronic grazing for over 40 years). Similar to previous studies on low productivity ecosystems in this region, the species richness and evenness of plant communities with pulse and press grazing did not differ from communities with light grazing. Also consistent with previous studies in this region, we observed a transition from shrub-dominated communities with light grazing to graminoid-dominated communities with pulse and press grazing. Interestingly, communities with pulse, but not press, grazing were more phylogenetically dispersed than communities with light grazing. If grazing pulses can increase the phylogenetic diversity of plant communities, our result suggests changes in reindeer management allowing for pulses of grazing to increase phylogenetic diversity of plant communities.