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The Qinghai-Tibet Plateau (QTP) is an important cushion plant hotspot. However, the distribution of cushion plants on the QTP is unknown, as are the factors that drive cushion plant distribution, limiting our understanding of the evolution of cushion species in the region. In this study, we assessed spatial patterns of total cushion plant diversity (including taxonomic and phylogenetic) over the entire QTP and compared patterns of diversity of cushion plants with different typologies (i.e., compact vs. loose). We also examined how these patterns were related to climatic features. Our results indicate that the southern QTP hosts the highest total cushion plant richness, especially in the south-central Hengduan Mountains subregion. The total number of cushion species declines from south to north and from southeast to northwest. Compact cushion plants exhibit similar patterns as the total cushion plant richness, whereas loose cushion plants show random distribution. Cushion plant phylogenetic diversity showed a similar pattern as that of the total cushion plant richness. In addition, cushion plant phylogenetic community structure was clustered in the eastern and southwestern QTP, whereas random or overdispersed in other areas. Climatic features represented by annual energy and water trends, seasonality and extreme environmental factors, had significant effects on cushion plant diversity patterns but limited effects on the phylogenetic community structure, suggesting that climatic features indeed promote the formation of cushion plants. Because cushion plants play vital roles in alpine ecosystems, our findings not only promote our understanding of the evolution and formation of alpine cushion plant diversity but also provide an indispensable foundation for future studies on cushion plant functions and thus alpine ecosystem sustainability in the entire QTP region.

Gut dysbiosis, defined as pathogenic alterations in the distribution and abundance of different microbial species, is associated with neuropathic pain in a variety of clinical conditions, but this has not been explored in the context of neuropathy in people with HIV (PWH). We assessed gut microbial diversity and dysbiosis in PWH and people without HIV (PWoH), some of whom reported distal neuropathic pain (DNP). DNP was graded on a standardized, validated severity scale. The gut microbiome was characterized using 16S rRNA sequencing and diversity was assessed using phylogenetic tree construction. Songbird analysis (https://github.com/mortonjt/songbird) was used to produce a multinomial regression model predicting counts of specific microbial taxa through metadata covariate columns. Participants were 226 PWH and 101 PWoH, mean (SD) age 52.0 (13.5), 21.1% female, 54.7% men who have sex with men, 44.7% non-white. Among PWH, median (interquartile range, IQR) nadir and current CD4 were 174 (21, 302) and 618 (448, 822), respectively; 90% were virally suppressed on antiretroviral therapy. PWH and PWoH did not differ with respect to microbiome diversity as indexed by Faith's phylogenetic diversity (PD). More severe DNP was associated with lower alpha diversity as indexed by Faith's phylogenetic diversity in PWH (Spearman's ρ=.224, P=0.0007), but not in PWoH (Spearman's ρ=.032, P=.748). These relationships were not confounded by demographics or disease factors. In addition, the log-ratio of features identified at the genus level as Blautia to Lachnospira was statistically significantly higher in PWH with DNP than in PWH without DNP (t-test, P=1.01e-3). Furthermore, the log-ratio of Clostridium features to Lachnospira features also was higher in PWH with DNP than in those without (t-test, P=6.24e-5). Our results, in combination with previous findings in other neuropathic pain conditions, suggest that gut dysbiosis, particularly reductions in diversity and relative increases in the ratios of Blautia and Clostridium to Lachnospira, may contribute to prevalent DNP in PWH. Two candidate pathways for these associations, involving microbial pro-inflammatory components and microbially-produced anti-inflammatory short chain fatty acids, are discussed. Future studies might test interventions to re-establish a healthy gut microbiota and determine if this prevents or improves DNP. PERSPECTIVE: The association of neuropathic pain in people with HIV with reduced gut microbial diversity and dysbiosis raises the possibility that re-establishing a healthy gut microbiota might ameliorate neuropathic pain in HIV by reducing proinflammatory and increasing anti-inflammatory microbial products.

Bull’s eye rot, caused by Phlyctema vagabunda and Neofabraea species, is one of the most important postharvest diseases of apple. South Tyrol (northern Italy) is the largest continuous apple-producing area in Europe, with approximately 1 million tons being produced yearly and conserved in technologically advanced storage facilities for several months. Still, studies on the pathogen species causing postharvest bull’s eye rot of apple, as well as their diversity and biology, are lacking for this region. Therefore, the main purpose of the present work was to identify and characterize fungal isolates obtained from decayed apple fruit with symptoms of bull’s eye rot that were collected in 2018 and 2019 in different packinghouses in South Tyrol. Among more than 1,000 fungal isolates that were obtained, 419 could be assigned to the genera Phlyctema and/or Neofabraea based on rot symptoms on apple fruit and colony morphology on potato dextrose agar. A smaller subset of 101 representative isolates was further analyzed by DNA sequencing of the internal transcribed spacer region. Furthermore, partial segments of the β-tubulin gene, the translation elongation factor 1α gene, and the 16S mitochondrial ribosomal RNA gene were studied. The phylogenetic analyses, including sequences of reference species, showed that P. vagabunda is the dominant species associated with bull’s eye rot of apple in the study area, whereas Neofabraea kienholzii was found only on a small number of apple fruit samples. The combination of multilocus sequence data revealed 11 unique genotypes that belonged to P. vagabunda and four to N. kienholzii. To the best of our knowledge, this study is the first to report N. kienholzii as a postharvest pathogen of apple in Italy. Finally, a pathogenicity test demonstrated different degrees of virulence among selected isolates of P. vagabunda and N. kienholzii on the cultivar Golden Delicious. The present study emphasizes the importance of accurate species identification, because different species may vary in their biological and pathogenic characteristics, and consequently require distinct disease management strategies, both in the field and during the postharvest stages. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

To highlight the importance of the soil-root interface in bacterial root colonization, we performed 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform to characterize the bacterial endophytes of rice plants grown by two experiments – soil and hydroponic, considering their soil, solution, and endosphere compartments. We hypothesized that rice plants from both experiments would exhibit dissimilar endophytic bacterial communities. Alpha-diversity (richness (ASVs), Shannon index, Faith’s phylogenetic diversity, and Pielou’s evenness) for bacterial endophytes was lower in the soil experiment than in the hydroponic experiment. However, the rhizospheric soil exhibited higher microbial diversity and richness than the hydroponic solution after 6 weeks. Proteobacteria and Firmicutes were the most dominant phyla in both experiments, while several other bacterial taxa showed major differences at genus levels. A Venn diagram revealed that 5 overlapping bacterial genera were shared by the endosphere and rhizosphere/solution compartments of both experiments. Principal coordinate analysis (PCoA) based on weighted UniFrac distances showed a clear distinction between microbial communities of all sampled compartments. Furthermore, PERMANOVA results showed that the endophyte communities of both experiments differed significantly (p

The abstract is available here: https://uscholar.univie.ac.at/o:1588368

Roadside trees alter biotic and abiotic factors of plants diversity in an ecosystem. Rows of plants grow along the roadside due to the interplay between the arrival of propagule and seedling establishment, which depends on the road's specifications, land pattern, and road administration and protection practices. A field study was conducted to measure the roadside tree diversity in the city of Karachi (Pakistan). A total of 180 plots, divided into three primary road groups, were surveyed. The highest quantity of tree biomass per unit area was found on wide roads, followed by medium roads. On narrow roads, the least biomass was detected. A single species or a limited number of species dominated the tree community. Conocarpus erectus was the most dominant non-native species on all types of sidewalks or roadsides, followed by Guaiacum officinale. A total of 76 species (32 non-natives and 44 natives) that were selectively spread along the roadsides of the city were studied. There was a significant difference in phylogenetic diversity (PD), phylogenetic mean pairwise distance (MPD), and phylogenetic mean nearest taxon distance (MNTD) among wide, medium, and narrow roads. Management practices have a significant positive correlation with diversity indices. Our study identified patterns of diversity in roadside trees in Karachi. It provides the basis for future planning for plant protection, such as the protection of plant species, the maintenance of plant habitats, and the coordination of plant management in Karachi.

Wheat dwarf virus (WDV) has caused an epidemic in many cereal production areas of Turkey in recent years. There is no current literature data on this important virus in the country. This study presents the extensive molecular characterization of WDV isolates causing serious problems in the Central Anatolia Region between 2019 and 2020. Of the 51 locations, 44 locations (25 barley + 19 wheat) were found to be infected with WDV and 7 locations (1 barley + 6 wheat) were WDV-negative by PCR (Polymerase chain reaction). To differentiate the wheat- and barley-specific (WDV-W and WDV-B) forms of WDV, PCR tests were also performed. Eleven locations were identified as WDV-W, and 33 locations were identified as WDV-B. Although two Turkish isolates in WDV-B specific form have been reported in previous studies, isolates belonging to WDV-W specific form were identified for the first time by this study. Partial sequences of randomly selected 16 isolates (8 WDV-W and 8 WDV-B) were realized and deposited in GenBank. The phylogenetic tree was generated by the neighbor-joining method, and 16 isolates were clustered as follows: two isolates in WDV-A, six isolates in WDV-B, and eight isolates in WDV-E. To our knowledge, this study is the first report of B and E strains of WDV in Turkey. This is the first comprehensive study presenting both specific form prevalence and the strains of WDV in Turkey.

Bulk tank milk (BTM) is regularly used for surveillance on dairy farms for disease conditions such as mastitis and Johne's disease. In this study, we used 16S rRNA sequencing and bait-capture enrichment to characterize the microbiota and resistome of BTM, and investigate potential differences between the cream or pellet fractions. A total of 12 BTM samples were taken from 12 Prince Edward Island dairy farms, in Atlantic Canada, in duplicates. The DNA was analyzed by high-throughput sequencing of the 16S rRNA gene and a suite of antimicrobial resistance (AMR) genes. Target-capture enrichment of AMR genes was conducted before shotgun sequencing. The bioinformatics pipelines QIIME 2 and AMR++ were used for microbiota and resistome analysis, respectively. Differences between microbiotae were evaluated qualitatively with nonmetric multidimensional scaling and quantitatively with permutational ANOVA of UniFrac distances. A total of 47 phyla were present across the BTM samples. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the most abundant phyla. At the genus level, Corynebacterium, Acinetobacter, Lactobacillus, and Turicibacter were the most abundant. There was no significant difference in the Faith's phylogenetic diversity between the cream and pellet fraction. Faith's phylogenetic diversity differed marginally by stall type. There were 10,217 hits across 80 unique AMR genes, with tetracycline resistance being the most common class.

To investigate phylogenetic and phenotypic diversity of resident chickpea-nodulating rhizobia from Australian cropping soils. Eighty Mesorhizobium strains collected from across Australian cropping regions were analysed in a pot experiment to evaluate nodulation and symbiotic effectiveness (SE%) in chickpea plants. In vitro testing of these strains tolerant to specific stresses (pH, temperature, antibiotics, heavy metals and NaCl) was performed. In addition, phylogenetic analyses were carried out using16S-23S rRNA, atpD, recA, nodC and nifH. All strains were members of the genus Mesorhizobium based on phylogenies of 16-23S rRNA IGS and core genes. Strains with diverse 16S-23S rRNA IGS carried symbiosis genes that had high similarity to those in chickpea symbionts, suggesting the resident rhizobia in Australian soils may have acquired symbiotic traits from inoculant strains through horizontal gene transfer (HGT). Inoculation of chickpea revealed that variation in SE% among isolated strains was correlated with phylogenetic relatedness to the commercial inoculant strain Mesorhizobium ciceri CC1192. Strain A47 collected from Queensland gave the highest shoot biomass and two strains (A78 and A79) from Western Australia grew under acidic conditions (pH 4.4). In a field experiment, inoculation with four selected strains or strain CC1192 all increased shoot biomass compared with an uninoculated control; chickpea inoculated with strain A47 had the highest nodulation. Australian cropping soils contain resident chickpea rhizobial genotypes that are genetically and phenotypically diverse, with some genotypes having equal or superior SE compared with the inoculant strain CC1192. This study provides evidence to support HGT of symbiosis genes in Australian soils, and has identified strains adapted to different environmental conditions.

The loss of a particular species from a community may have different effects on its functioning, depending on the presence or absence of functionally similar or phylogenetically close species in that community (redundancy). Redundancy is thus defined as the fraction of species diversity not expressed by functional or phylogenetic diversity. We assessed functional and phylogenetic alpha- and beta-redundancy in helminth and flea assemblages of two species of South African rodents, Rhabdomys dilectus and Rhabdomys pumilio, using community uniqueness as the inverse indicator of redundancy. We asked whether patterns of functional and phylogenetic alpha- and beta-uniqueness differed between (i) parasite groups (endo- versus ectoparasites), (ii) host species within parasite groups, and (iii) biomes within host species. We found differences between the two hosts in the functional and phylogenetic alpha-uniqueness (but not beta-uniqueness) of flea, but not helminth, assemblages. Significant correlations between the alpha-uniqueness of parasite assemblages and the total parasite prevalence were found only for phylogenetic uniqueness and only in helminths. Pairwise site-by-site dissimilarities in uniqueness (beta-uniqueness) and pairwise dissimilarity in prevalence were significantly associated (positively) in helminths but not in fleas. A between-biome difference in functional (but not phylogenetic) alpha-uniqueness was found in both helminth and flea assemblages harboured by R. pumilio. We conclude that the resilience of parasite assemblages in terms of the effect on hosts depends not only on their transmission strategy but also on traits of host species and environmental factors.

Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.

Host phylogenetic relatedness and ecological similarity are thought to contribute to parasite community assembly and infection rates. However, recent landscape level anthropogenic changes may disrupt host-parasite systems by impacting functional and phylogenetic diversity of host communities. We examined whether changes in host functional and phylogenetic diversity, forest cover, and minimum temperature influence the prevalence, diversity, and distributions of avian haemosporidian parasites (genera Haemoproteus and Plasmodium) across 18 avian communities in the Atlantic Forest. To explore spatial patterns in avian haemosporidian prevalence and taxonomic and phylogenetic diversity, we surveyed 2241 individuals belonging to 233 avian species across a deforestation gradient. Mean prevalence and parasite diversity varied considerably across avian communities and parasites responded differently to host attributes and anthropogenic changes. Avian malaria prevalence (termed herein as an infection caused by Plasmodium parasites) was higher in deforested sites, and both Plasmodium prevalence and taxonomic diversity were negatively related to host functional diversity. Increased diversity of avian hosts increased local taxonomic diversity of Plasmodium lineages but decreased phylogenetic diversity of this parasite genus. Temperature and host phylogenetic diversity did not influence prevalence and diversity of haemosporidian parasites. Variation in the diversity of avian host traits that promote parasite encounter and vector exposure (host functional diversity) partially explained the variation in avian malaria prevalence and diversity. Recent anthropogenic landscape transformation (reduced proportion of native forest cover) had a major influence on avian malaria occurrence across the Atlantic Forest. This suggests that, for Plasmodium, host phylogenetic diversity was not a biotic filter to parasite transmission as prevalence was largely explained by host ecological attributes and recent anthropogenic factors. Our results demonstrate that, similar to human malaria and other vector-transmitted pathogens, prevalence of avian malaria parasites will likely increase with deforestation.

There is growing interest in the study of avian endoparasite communities, and metabarcoding is a promising approach to complement more conventional or targeted methods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme, with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed this challenge by comparing different primer sets across 16 samples from 5 bird species. Samples consisted of blood, feces, and controlled mixes with known proportions of bird and nematode DNA. Illumina sequencing revealed that a 28S primer set used in combination with a custom blocking primer allowed detection of various plasmodiid parasites and filarioid nematodes in the blood, coccidia in the feces, as well as two potentially pathogenic fungal groups. When tested on the controlled DNA mixes, these primers also increased the proportion of nematode DNA by over an order of magnitude. An 18S primer set, originally designed to exclude metazoan sequences, was the most effective at reducing the relative number of avian DNA sequences and was the only one to detect Trypanosoma in the blood. Expectedly, however, it did not allow nematode detection and also failed to detect avian malaria parasites. This study shows that a 28S set including a blocking primer allows detection of several major and very diverse bird parasite clades, while reliable amplification of all major parasite groups may require a combination of markers. It helps clarify options for bird parasite metabarcoding, according to priorities in terms of the endoparasite clades and the ecological questions researchers wish to focus on., Parasites of birds are extremely diverse, spanning no less than four different kingdoms (Chromista, Protozoa, Metazoa and Fungi). Our understanding of these communities and their fascinating interactions could benefit from metabarcoding approaches. This report provides a side‐by‐side comparison of different metabarcoding options for a broad description of avian eukaryotic endoparasite communities.

Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.

Freshwater biodiversity is currently under multiple threats. Conservation of freshwater fish biodiversity needs to be prioritized because natural conservation resources are always limited.Samples were collected at 24 sites in the Min River, the largest basin in southeastern China. Taxonomic, functional, and phylogenetic diversity were analyzed. Biodiversity vulnerability was measured by removing one species each time out of the community with replacement.Results suggested that hotspots for taxonomic and phylogenetic diversity were located at two impounded sites, while for functional diversity were those sites with no upstream dams. Little congruence was observed between taxonomic, functional, and phylogenetic diversity. Fragmentation of river network connectivity caused by dams was a significant factor affecting the biodiversity patterns. Beta turnover was the driving component for beta diversity, indicating that biodiversity dissimilarity along the river was mostly explained by environmental sorting. Fifteen out of 16 species that contributed the most to different facets of biodiversity were mostly endemic, either they had distinctive functional traits or they were the most prevalent species. Sites with the highest diversity vulnerability were characterized by these distinctive species. Functional diversity was more vulnerable to species loss comparing with the other two biodiversity facets.Prioritizing those biodiversity hotspots, sites with extreme functional vulnerability, and those distinctive endemic species which contributed the most to biodiversity vulnerability is suggested in the Min River. The study found evidence that congruence among different facets of biodiversity is hard to achieve, and functional diversity is the most vulnerable in a freshwater system fragmented by intensive dam constructions. This work will help to develop systematic conservation planning from the perspective of different biodiversity facets., Fish functional diversity is more vulnerable than taxonomic and phylogenetic diversity in a freshwater riverine system segmented by an intensive distribution of dams.

Aim: Previous studies have found strikingly different geographical patterns of phylogenetic diversity of gymnosperms and angiosperms, which have been suggested to result, in part, from the greater age of the former. To assess the effects of clade age on phylogenetic structure, we assessed phylodiversity patterns of pteridophytes (lycophytes and ferns), which combine ancient and modern lineages, across China. Location: China. Time period: Present day. Taxon: Pteridophytes. Methods: We divided China into 66 regions and collated species lists of pteridophytes for each region. We then related taxonomic and phylogenetic diversity, and their related metrics, to six climatic variables for pteridophytes as a whole and for different evolutionary clades. We examined the effect of spatial autocorrelation among regional floras on the results. Results: We found that when all pteridophytes or ferns were considered, the patterns resembled those of gymnosperms, presumably reflecting the effects of several ancient global mass extinctions and the relict distribution of old families. In contrast, when we considered only the modern Polypodiales radiation, which accounts for three-quarters of current fern diversity and is about as old as the angiosperm radiation, we found a pattern similar to that of angiosperms. This pattern is consistent with the tropical niche conservatism hypothesis and suggests that both major groups of land plants have a broadly similar evolutionary trajectory, with most families originating in tropical conditions and few families adapting to cold and arid conditions. Main conclusions: Our study shows that the phylogenetic structures of more recently evolved and diversified clades of pteridophytes are fairly consistent with the tropical niche conservatism hypothesis, suggesting that the age of the taxon, its physiological adaptations and the global climatic changes that it experienced during its evolutionary history are reflected in the composition of current plant assemblages.

Methane oxidation rates and diversity of methane-oxidizing microorganisms were studied in the upper sediment layers of the Laptev Sea (methane seep area, Lena fore-delta, shelf, and upper slope not affected by seeps and river flow). The highest methane concentrations and methane oxidation rates (up to 1.16 µmol СН4 dm−3 day−1) were revealed at the seep stations. Carbon dioxide was the main product of methane oxidation at all stations. Sequencing of the 16S rRNA gene fragments revealed microorganisms of the class Gammaproteobacteria, order Methylococcales. Since the share of methanotrophs was high at the sites of constant gas seepage (up to 1.93% of the total read number), they could be detected by sequencing of the native samples. Phylogenetic diversity of methane-oxidizing bacteria was not high, and all detected microorganisms belonged to the Deep-Sea 1 cluster. On the phylogenetic tree, the sequences formed a cluster together with the genus Methyloprofundus. Members of the genera Methylomonas and Methylobacter related to methanotrophs inhabiting freshwater ecosystems were revealed in enrichments from the coastal stations sediment samples.

Antibiotic-resistant genes (ARGs) have been regarded as emerging contaminants that threaten public health worldwide. Poultry excreta, often used as a fertilizer in agriculture, are a major route for the proliferation and dissemination of ARGs in the environment. The aim of the present study was to assess the potential of dietary palygorskite (Plg) supplementation as nutritional manipulation for the modulation of microbial community structure and the attenuation of ARGs in the cecal contents of broilers fed with chlortetracycline (CTC). In total, 256 one-day-old, mixed-sex, broiler chicks were allocated randomly into a 2 × 2 factorial design of four treatments, which consisted of two levels of CTC (0 or 50 mg/kg) and Plg (0 or 10 g/kg). By employing in vivo feeding and slaughter experiments, after collecting the cecal contents and extracting the total genomic DNA, 16S rRNA V3-V4 hypervariable amplicon pyrosequencing and quantitative PCR-based approaches were used to address the impact of Plg on microbiota and the abundance of ARGs in broilers. The results showed that broilers given a diet supplemented with Plg had greater α-diversity indices including Chao1, phylogenetic diversity tree, and observed-species index calculations, when compared with those without Plg supplementation. Birds given a diet supplemented with Plg had fewer Firmicutes at the phylum level, but a greater abundance of Alistipes at the bacterial genus level. Dietary Plg counteracted the CTC-induced increased abundance of ARGs, among which tet(K) had a pronounced decrease, along with a similar decreased tendency for other measured ARGs and intI1. Overall, the results indicated that Plg supplementation caused pronounced changes in cecal microbial diversity and microbiota community composition of broilers, and effectively reduced ARGs, indicating that Plg supplementation is a potential alternative measure for the attenuation of ARGs in the cecal contents of broilers.

Exploring vegetation distribution spatial patterns facilitates understanding how biodiversity addresses the potential threat of future climate variability, especially for highly diverse and threatened tropical plant communities, but few empirical studies have been performed. Dacrydium pectinatum is a constructive and endangered species in the tropical mountain forests of Hainan Island, China. In this study, sixty‐eight 30 m × 30 m permanent plots of D. pectinatum were investigated, and species‐based and phylogenetic‐based methods were used to analyze the α‐ and β‐diversity pattern variation and its key drivers. Our study showed that species and phylogenetic α‐diversity patterns are different on a local scale. However, on a regional scale, the variations in the two α‐diversity patterns tend to converge, and they decrease with increasing elevation. The phylogenetic structure changes from overdispersion to convergence with increasing elevation. Soil (SOM, TP, AP), topography (EL, SL), and stand (CD) factors and α‐diversity showed close correlations. Species and phylogenetic β‐diversity have significant positive correlations with changing environmental distance and geographical distance; however, as a representative form of habitat heterogeneity, elevation distance has a greater impact on β‐diversity changes than geographical distance. In conclusion, the α‐ and β‐diversity patterns of the D. pectinatum community are mainly related to habitat filtering, especially in high‐elevation areas, and the colonization history of various regions also affects the formation of diversity patterns. Species‐based and phylogenetic‐based methods robustly demonstrated the key role of the habitat filtering hypothesis in community assembly. We believe that more plant diversity patterns need to be explored to understand the biodiversity formation mechanisms in tropical forests. We also recommend strengthening the construction and management of nature reserves to help address the biodiversity loss crisis in endangered tropical plant communities.

Wheat is a source of nutrients for around 40% world’s population and the second most important cereal crop in Kenya. However, Fusarium head blight (FHB) hinders sustainable sufficient production of the crop, causing both economic and health losses. With the emerging unfavorable climatic changes, effective disease management strategies and adequate seed system are necessary to meet the deficiency. Current information on prevalence of the causative pathogens in varieties of wheat genotypes is a critical prerequisite to such strategies. This study aimed at determining the prevalence of pathogenic Fusarium species in seeds of developed varieties of wheat genotypes in three major wheat-producing regions in Kenya. A total of 260 samples of 18 wheat genotypes from 123 farms were collected. Peptone pentachloronitrobenze agar was used for fungal isolation, while identification of Fusarium spp. was based on the gene encoding translation elongation factor 1-α (tef1-alpha) sequence analysis. Fusarium spp. isolated include Fusarium poae, F. tricinctum, F. heterosporum, F. culmorum, F. equiseti, Fusarium sp., F. verticillioides, and F. oxysporum. There was no significant difference in prevalence of Fusarium spp. pathogens among the three regions studied. Fusarium spp. diversity index for Nakuru was 2.008, Narok was 1.4603, and Uasin Gishu was 1.2337. Wheat produce from farm-saved seeds yielded 66.25% of the isolates, while the produce from certified commercial wheat seeds yielded 33.75% of the isolates. The significant finding of the study is that Fusarium spp. associated with mycotoxins that contaminate the wheat food chain seem to be flourishing in all the sampled wheat seed genotypes from the regions studied. Information on the prevalence and diversity of the pathogens on persistence of the disease in the crop is critical in advancing integrative FHB control measures.

The nitrogen-fixing symbiosis fixation between legumes and Rhizobium helps the plant to survive and to compete effectively on nitrogen poor soils. The soil environment attached to the root system is characterized by intense microbial activity. This work aimed to study the diversity of indigenous rhizobia living in the rhizosphere of forage pea in eastern and central Algeria. Bacteria were trapped in vitro from collected soils. They were isolated from nodules by direct isolation or by bacterial trapping, and tested for nodulation. Further characterization was carried out to identify the isolates. Ninety-four isolates were obtained. Thirty-four were rhizobial strains that could, with two exceptions, establish root-nodule symbioses with the host plant. Different profiles of susceptibility to rhizobiophages indicated that the majority of isolates were likely to be members of the Rhizobium leguminosarum group of species. The strains revealed diverse plasmid profiles, and diverse restriction patterns of cpn60 gene amplicons and on Southern blot analysis of nodABC genes. Sequences of 16S rRNA gene showed that all isolates exhibited 99.85% identity with R. leguminosarum sv. viciae USDA 2370T, R. laguerreae FB206T and R. anhuiense CCBAU 23252T. Analysis of cpn60 sequences revealed two groups. One of them clustered with ≤99% identity with R. laguerreae FB403. The second was clustered with ≤99% identity with R. laguerreae FB206T. Our findings suggest that the isolates may belong to the species R. laguerreae.

Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

The abundance of bacterioneuston and bacterioplankton and their taxonomic composition were determined with the fluorescence in situ hybridization (FISH) method in the harbor channel in Ustka. Among bacteria inhabiting the surface microlayer and subsurface water two phylogenetic groups dominated: Gammaproteobacteria and Cytophaga-Flavobacterium. The abundance of bacterial taxonomic groups in the water of the studied channel showed typical ranking, i.e., Gammaproteobacteria > Cytophaga-Flavobacterium > Marine alpha cluster > Pseudomonas > Vibrio. Total prokaryotic cell differed along the vertical and horizontal profiles. Similar taxonomic composition of bacterioneuston and bacterioplankton in both studied profiles were noted. All studied taxonomic groups occurred more often in the surface microlayer than subsurface water.

Parasites are strictly associated with their hosts and present a great diversity of life histories, often resulting in different diversity patterns than those observed in free-living species. However, ecological approaches have detected that, in some cases, mammal-associated helminths respond similarly to non-parasitic species in terms of diversity patterns. Using 2200 recorded interactions, we analysed the diversity patterns of helminths (Acanthocephala, Nematoda and Platyhelminthes) harbored by humans, wild and domestic mammals of Mexico, depending on latitude, host body mass and trophic guild (carnivore, herbivore, insectivore, omnivore), considering helminth richness and average taxonomic distinctness, and host phylogenetic diversity and phylogenetic clustering. Latitude was positively correlated with the average taxonomic distinctness encompassing the three parasite phyla and nematodes. Northern latitudes had less taxonomically related parasite assemblages. Host body mass had a significant negative relationship with the average taxonomic distinctness of acanthocephalans and the richness of helminths associated to wild hosts. The omnivore hosts had greater parasite richness, while insectivores had a less taxonomically related parasite assemblage and herbivores had a more heterogeneous parasite assemblage. Our results highlight the importance of incorporating different dimensions of diversity, such as average taxonomic distinctness and to consider the composition of parasite assemblages to better understand their diversity patterns., Graphical abstract Image 1, Highlights • Four diversity measures were used to describe diversity patterns of helminths. • Latitude was positively correlated with helminth average taxonomic distinctness. • Host body mass was negatively related with the helminth richness of wildlife hosts. • Helminth sets of omnivore hosts were richer in parasite species. • Helminth sets of insectivore hosts had a wider taxonomic breadth.

Biogeographic regions have been extensively used as reference units in macroecological studies and to prioritize biodiversity conservation efforts. However, classical bioregionalizations were delineated based on taxonomical similarity across space, and thus the importance of historical factors may have been underrated. This limitation may be particularly relevant for lineages with long and complex evolutionary histories, such as ferns. Here, we drew on an exhaustive distribution dataset including all fern species and subspecies of Europe (661 grid-cells of c. 110 × 110 km each), as well as a nearly complete molecular phylogeny to define fern phyloregions based on their phylogenetic relatedness. Also, we quantified the degree of specificity of individual phylogenetic clades to the phyloregions using a new index of geographical confinement based on phylogenetic diversity. Six distinct phyloregions were identified, with a primary divide between north-eastern and south-western Europe. Both phylogenetic beta diversity and clade specificity were overall low, supporting the idea that dispersal limitation is not a major driver of fern distribution. Yet, the phylogenetic specificity analysis revealed that ancient fern lineages show preference for northern latitudes, which explained the northeast to southwest split of the territory. More than 40 years after the only bioregionalization analysis for the European fern flora, our study provides a fresh regional delineation that takes into account the evolutionary history of the group. In addition to classical bioregionalization approaches, our phylogenetic specificity index allowed us to elucidate the identity of the clades that ultimately shaped the bioregions, which might otherwise had remained obscure.

Phylogenetic Diversity (PD) is increasingly recognised as a useful tool for prioritising species and regions for conservation effort. Increased availability of spatial and phylogenetic data for reptiles now facilitates their inclusion in phylogenetically-informed conservation prioritisation efforts. Geckos are a highly divergent and diverse clade that comprises almost 20% of global reptile diversity. Their global distribution is coincident with numerous anthropogenic threats, making them worthy of conservation prioritisation. Here, we combine phylogenetic, spatial distribution and extinction risk data for geckos with global human encroachment data to identify both regions and species representing irreplaceable gecko diversity at risk from human pressure. We show that high levels of irreplaceable gecko diversity are restricted to regions under intense human pressure, such as India, Sri Lanka and the Caribbean. There is a lack of extinction risk data for the western regions of Angola and Namibia, and yet these regions harbour high levels of irreplaceable diversity. At the species level, geckos display more unique PD than other lizards and snakes and are of greater conservation concern under our metric. The PD represented by Data Deficient geckos is at comparable risk to that of Endangered species. Finally, estimates of potential gecko diversity loss increase by up to 300% when species lacking extinction risk data are included. Our analyses show that many evolutionarily unique gecko species are poorly known and are at an increased risk of extinction. Targeted research is needed to elucidate the conservation status of these species and identify conservation priorities.

Xylan is one of the most abundant polysaccharides present in softwoods and hardwoods. Microbial xylanases mainly mediate its degradation. Xylanase has biotechnological potential with enormous demand in industries. The present study was initiated to investigate the diversity of culturable bacteria in mangrove sediments of Goa (India) and study the xylanase-coding gene in the isolated bacteria. Phylogenetic diversity was determined, in which proteobacteria was the dominant phylum (57%) with the abundance of Vibrio (36%) and Photobacterium (9%), while the second most abundant phylum Firmicutes (40%) was dominated by Bacillus (32%). Among all the culturable isolates screened for xylan degradation, the Bacillus genus was dominant (86%) xylan degrader. Bacillus isolates were further screened for the xylanase gene. The xylanase gene fragments of representative Bacillus were sequenced. All sequences matched to glycoside hydrolase (GH) family 10, thus, showing the dominance of GH10 xylanases in the mangroves regions of Goa (India). GH10 xylanases isolated from Bacillus sp. showed a broad pH optima ranged from pH 5.0 to 9.0 and temperature optima ranged from 50 to 60°C. These properties can be of potential interest for a variety of industrial processes where degradation of lignocelluloses is a crucial process.

Deep-sea sediments are now recognized as a home for rich and largely microbial community. Recently, it has been believed in an increasing number of studies that bacteria could be abundant in deep-sea sediments of many types; however, fungi in deep-sea sediments remain relatively unknown. The phylogenetic diversity and bioactivity of culturable deep-sea-derived fungi from Okinawa Trough sediments were investigated in traditional method combined with fungal identification of molecular biology in this study. A total of 76 isolates belonged to 15 fungal taxa were recovered in a harsh condition of low nutrient and low temperature, indicating that the fungal communities in deep-sea sediments from Okinawa Trough were relatively abundant and diversified. Aspergillus, Cladosporium, and Penicillium were the dominant fungal genera, while Mycosphaerella, Purpureocillium, and Schizophyllum were relatively rare in the deep-sea sediments from Okinawa Trough. Among the six genera recovered, Mycosphaerella was firstly recovered from deep-sea sediments in this study. Moreover, about 75% of the extracts from the 15 fungal representative isolates displayed distinct bioactivity against at least one indicator bacterium or marine macrofouler, emphasizing the potentials of these deep-sea-derived fungi from Okinawa Trough as producers of bioactive metabolites. Notably, isolates Cladosporium oxysporum SCSIO z001 and Penicillium citrinum SCSIO z049 displayed a wide spectrum of bioactivities, isolates Cladosporium cladosporioides SCSIO z015, Cladosporium sphaerospermum SCSIO z030, and Penicillium verruculosum SCSIO z007 exhibited a strong anti-bacterial-growth activity, and isolate Penicillium chrysogenum SCSIO z062 displayed a strong anti-larval-settlement activity. These results suggest that these isolates deserved further study as potential sources of novel bioactive metabolites.

Unicellular cyanobacteria constitute a substantial, ecologically important part of freshwater and marine microflora. Solitary, elongated cyanobacterial cells without apparent slime envelopes and dividing in a single plane perpendicular to the longitudinal axis were traditionally classified into the genus Synechococcus. The type species originates from a freshwater benthic habitat while a number of other Synechococcus-like species were described from diverse environments. Morphologically similar, unicellular populations of "Synechococcus" belong to the most abundant oxygen evolving prokaryotes inhabiting freshwater and oceanic picoplanktic communities. Other species from extreme thermal habitats were described from temperatures over 70 °C. Recent molecular analyses, particularly the 16S rRNA gene and other multi-locus gene based phylogenies of Synechococcus-like species reveal the polyphyly and phylogenetic diversity of such simple cyanobacteria emphasizing the necessity of their accurate polyphasic taxonomic re-classification. To better understand the phylogeny of different Synechococcus-like species, we constructed a genome-derived phylogenetic tree using 133 cyanobacterial and eubacterial genomes as well as a 16S rRNA gene phylogenetic tree. Both trees indicate existence of deep splits between individual Synechococcus lineages corresponding with indistinct ecological and cytomorphological differences. The generic units derived from the traditional concept of the genus Synechococcus based on the combined traits and markers must be defined and validly described. The comparative taxonomic classification of phylogenetic clusters corresponding to various morphotypes and genotypes similar to the genus Synechococcus (Cyanobium, Parasynechococcus, Picosynechococcus, Prochlorococcus, Thermosynechococcus, Thermostichus) are discussed in the article.

Background. This study is aimed at analyzing the changes in gut microorganism of patients with positive immune antibody-associated recurrent abortion using the 16s rRNA gene sequencing microbiome assay. Methods. The fecal samples from 20 recurrent abortion women with positive immune antibody (positive group) and 20 with negative immune antibody (negative group) were collected. After 16s rRNA gene sequencing, the obtained raw reads underwent quality filtering to obtain the clean tags and then classified into microbial genomes. All effective tags were clustered into operational taxonomic units (OTUs), and the representative sequence was selected for the annotation of taxonomic information, followed by alpha and beta diversity analyses. Results. A total of 43,116 OTUs were obtained in all 40 samples. Bacteroides had the highest relative abundance in the positive group. In the negative group, Bacteroides, Erysipelotrichaceae_UCG-003, Faecalibacterium, and Prevotella_9 had high relative abundance. Alpha diversity analysis results showed that the community richness, community diversity, and phylogenetic diversity in the positive group were higher than that in the negative group. Prevotella_9, Enterococcus, Megasphaera, and Anaerostipes presented significant differences between negative and positive groups. Conclusion. The present study for the first time investigated the gut microbiome involved in positive immune antibody-associated recurrent abortion via the 16s rRNA gene sequencing microbiome assay. The genera that were significantly differential between positive and negative groups may serve as therapeutic targets for positive immune antibody-associated recurrent abortion.

Nitrospira is the most diverse genus of nitrite-oxidizing bacteria, and its members are widely spread in various natural and engineered ecosystems. In this study, the phylogenetic diversity of Nitrospira and monthly changes of its abundance from Zhanjiang Bay were investigated. Phylogenetic analysis showed that among 58 OTUs with high abundance, 74% were not affiliated with any previously described Nitrospira species, revealing a previously unrecognized diversity of coastal Nitrospira. The abundances of both Nitrospira and Nitrospina exhibited a significantly monthly change. During most of the months, abundance of Nitrospina was greater than that of Nitrospira. In particle-attached communities, either abundance of Nitrospina or Nitrospira was highly correlated with that of ammonia-oxidizing archaea (AOA), whereas abundance of ammonia-oxidizing bacteria was only highly correlated with that of Nitrospina. In free-living communities, either abundance of Nitrospina or Nitrospira was correlated only with that of AOA. These results suggest that both Nitrospira and Nitrospina can be involved in nitrite oxidation by coupling with AOA, but Nitrospina may play a greater role than Nitrospira in this tropical bay.

Premise of research. Shared ancestry and convergent/parallel evolution are the two primary causes of morphologically similar species occurring in similar climatic niches. Alpine habitats harbor a u...

The Neotropical species Fomitiporia apiahyna was repeatedly shown to form a lineage with multiple sublineages that could correspond to different phylogenetic species, hence forming a highly diverse species complex. Due to their inconspicuous morphological features, species delimitation in this complex needs an integrative taxonomic perspective. In this study, we have performed multilocus molecular (ITS, ncLSU, TEF-1α, and RPB2) analyses in order to delimit the phylogenetic placement of specimens previously determined as F. apiahyna and to determine the phylogenetic diversity in term of clades that could be equated to species. Both morphological, ecological, and distribution data have been integrated to better delimit species boundaries. The F. apiahyna sensu lato lineage was shown to encompass four clades, corresponding to the four species: F. apiahyna sensu stricto, which is confirmed based on specimens originating from the type locality and here epitypified; F. nubicola sp. nov., proposed based on specimens found on Drimys angustifolia and Drimys sp., a relic plant species distributed exclusively in fragmented forests of high altitude areas in southern Brazil; F. conyana sp. nov., proposed from specimens previously suggested as the closest to F. apiahyna s.s.; and F. murrilli sp. nov., proposed based on specimens found on the locally exotic Eucalyptus sp. and another undefined angiosperm in southern Brazil. Additionally, Phellinus elegans emerged from the synonymy of F. apiahyna and the new combination Fomitiporia elegans is proposed. An identification key to the Neotropical species with pileate basidioma also is provided. Phylogenetically delimited species are strongly supported by ecological data, and in the case of F. conyana by clear-cut morphological data. It is expected that, with the redefinition of F. apiahyna s.s., other phylogenetic species will emerge in the near future.

Orthohantaviruses are negative-sense, single-stranded RNA viruses harbored by multiple small mammals. Dobrava-Belgrade virus (DOBV) and Puumala virus (PUUV) cause hemorrhagic fever with renal syndrome (HFRS) in Europe. In Poland, serological surveys have demonstrated antibodies against DOBV and PUUV in patients with HFRS. Molecular evidence of DOBV and PUUV has been found in Apodemus flavicollis and Myodes glareolus, respectively, in southeastern Poland, and Seewis virus (SWSV) has been reported in Sorex araneus in central Poland. However, data on the geographic distribution and phylogeny of orthohantaviruses are unavailable for other regions in Poland. To ascertain the prevalence and genetic diversity of orthohantaviruses in western and northern Poland, lung tissues from 106 small mammals were analyzed for the presence of orthohantavirus RNA. Dobrava-Belgrade virus and SWSV were detected in two of 42 (4.8%) Apodemus agrarius and in three of 10 (30%) S. araneus, respectively. Phylogenetic analyses of partial L- and S-segment sequences of DOBV indicated a shared genetic lineage with the Kurkino genotype from Slovakia, Russia, and Hungary, whereas the partial M segment of DOBV clustered with the Kurkino genotype from Germany. Phylogenetic relationships of the SWSV L and S segments showed a geographic lineage with SWSV strains from central Poland, Czech Republic, and Germany. In conclusion, the study provides an insight into the molecular prevalence, phylogenetic diversity, and evolutionary relationship of DOBV in A. agrarius and SWSV in S. araneus. This report increases awareness among physicians for HFRS outbreaks in western Poland.

The Early Cretaceous (145–100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66–56 Ma). Important aspects of the timing and geographical setting of angiosperm diversification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37–56 Myr) between the origin of families (stem age) and the diversification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the diversification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic diversity originated during the Cretaceous Terrestrial Revolution. A new study of the divergence time of angiosperm families shows that although most angiosperm families originated during the middle Cretaceous (~100–90 million years ago), the diversification of families into extant diversity was delayed until the Palaeocene (~66–56 million years ago), this time lag being geographically heterogeneous, and longer in tropical than in temperate and arid biomes.

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

The capacity of some yeasts to extract energy from single sugars, generating CO2 and ethanol (=fermentation), even in the presence of oxygen, is known as the Crabtree effect. This phenomenon represents an important adaptation as it allowed the utilization of the ecological niche given by modern fruits, an abundant source of food that emerged in the terrestrial environment in the Cretaceous. However, identifying the evolutionary events that triggered fermentative capacity in Crabtree‐positive species is challenging, as microorganisms do not leave fossil evidence. Thus, key innovations should be inferred based only on traits measured under culture conditions. Here, we reanalyzed data from a common garden experiment where several proxies of fermentative capacity were recorded in Crabtree‐positive and Crabtree‐negative species, representing yeast phylogenetic diversity. In particular, we applied the “lasso‐OU” algorithm which detects points of adaptive shifts, using traits that are proxies of fermentative performance. We tested whether multiple events or a single event explains the actual fermentative capacity of yeasts. According to the lasso‐OU procedure, evolutionary changes in the three proxies of fermentative capacity that we considered (i.e., glycerol production, ethanol yield, and respiratory quotient) are consistent with a single evolutionary episode (a whole‐genomic duplication, WGD), instead of a series of small genomic rearrangements. Thus, the WGD appears as the key event behind the diversification of fermentative yeasts, which by increasing gene dosage, and maximized their capacity of energy extraction for exploiting the new ecological niche provided by single sugars., Whole‐genomic duplication and fermentative capacity in yeast evolution.

Summary Microalgae as a biofuel source are of great interest. Bacterial phycosphere inhabitants of algal cultures are hypothesized to contribute to productivity. In this study, the bacterial composition of the Chlorella sorokiniana phycosphere was determined over several production cycles in different growing seasons by 16S rRNA gene sequencing and identification. The diversity of the phycosphere increased with time during each individual reactor run, based on Faith’s phylogenetic diversity metric versus days post‐inoculation (R = 0.66, P, Microalgae can be efficiently cultivated to produce biomass suitable for conversion to liquid biofuels. Long term experiments conducted over multiple growing seasons in the arid Southwest region of the United States revealed significant associations between algal productivity and the bacterial members of the culture phycospheres. These species offer targets for improving algal biomass yields in mass cultivation.

TwoBifidobacteriumstrains, i.e., 2176BTand 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic andd-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (includinghsp60,rpoB,dnaJ,dnaG andclpC genes) and the core genome revealed that bifidobacterial strains 2176BTand 2177BTexhibit close phylogenetic relatedness toBifidobacterium felsineumDSM 103139TandBifidobacterium bifidumLMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognizedBifidobacteriumspecies. Thus,Bifidobacterium cebidarumsp. nov. (2176BT=LMG 31469T=CCUG 73785T) andBifidobacterium leontopithecisp. nov. (2177BT=LMG 31471T=CCUG 73786Tare proposed as novelBifidobacteriumspecies.

Highly biodiversity communities have been shown to better resist plant invasions through complementarity effects. Species richness (SR) is a widely used biodiversity metric but lacks explanatory power when there are only a few species. Communities with low SR can have a wide variety of phylogenetic diversities (PD), which might allow for a better prediction of invasibility. We assessed the effect of diversity reduction of a wetland community assemblage typical of the Beijing area on biotic resistance to invasion of the exotic weed Alternanthera philoxeroides and compared the reduction in SR and PD in predicting community invasibility. The eight studied resident species performed similarly when grown alone and when grown in eight-species communities together with the invasive A. philoxeroides. Variation partitioning showed that PD contributed more to variation in both A. philoxeroides traits and community indicators than SR. All A. philoxeroides traits and community indicators, except for evenness index, showed a linear relationship with PD. However, only stem length of A. philoxeroides differed between the one- and two-species treatments, and the diversity index of the communities differed between the one- and two-species treatments and between the one- and four-species treatments. Our results showed that in natural or semi-natural wetlands with relatively low SR, PD may be a better predictor of invasibility than SR. When designing management strategies for mitigating A. philoxeroides invasion, deliberately raising PD is expected to be more efficient than simply increasing species number.

Although lupin anthracnose caused by Colletotrichum lupini is a significant threat for spring and winter lupin crops, it has been poorly studied so far. This study aimed at characterizing the (i) phylogenetic, (ii) morphological, and (iii) physiological diversity of collected isolates from anthracnose-affected lupins. The genetic identification of representative isolates (n = 71) revealed that they were all C. lupini species, further confirming that lupin anthracnose is caused by this species. However, multilocus sequencing on these isolates and 16 additional reference strains of C. lupini revealed a separation into two distinct genetic groups, both of them characterized by a very low genetic diversity. The diversity of morphological characteristics of a selected subset of C. lupini isolates was further evaluated. To the best of our knowledge, microsclerotia production observed for some isolates has never been reported so far within the Colletotrichum acutatum species complex. Finally, the modeling of growth responses of a subset of C. lupini strains revealed the capacity of some strains to grow in vitro at 5°C. This ability was also evidenced in planta, because C. lupini DNA was detectable in plants from 14 days postinoculation at 5°C onward, whereas symptoms began to appear a week later, although at a very low level. Since lupin crops are planted during winter or early spring, growth studies in vitro and in planta demonstrated the capability of the species to grow at temperatures ranging from 5 to 30°C, with an optimum close to 25°C. In this study, C. lupini-specific primers were also designed for real-time quantitative PCR on fungal DNA and allowed the detection of C. lupini in asymptomatic field samples. These results open perspectives to detect earlier and limit the development of this pathogen in lupin crops.

Bacterial blight (Xanthomonas arboricola pv. corylina (Xac)) of hazelnut (Corylus avellana L.) was described first in Oregon in 1915 and is now recognized as a damaging disease of young hazelnut trees worldwide. Thousands of hectares of new hazelnut cultivars that are resistant to eastern filbert blight (Anisogramma anomala) are being planted in the Willamette Valley of Oregon, where 99% of the US hazelnut crop is grown. Reports of bacterial blight on young hazelnut trees have increased but information about the causal pathogen is limited. Isolates were recovered from tissues with bacterial blight symptoms that were then characterized for their ability to grow on semi-selective media, their nutrient utilization profiles using Biolog GN2, quinate metabolism, copper tolerance, hypersensitive response on tobacco, and pathogenicity on hazelnut. Additionally, isolates were identified with a duplex PCR assay (ftsX and qumA), 16S rRNA sequence, and multi-locus sequence analysis (MLSA) using rpoD and gyrB. Pathogenic isolates were identified as Xac using morphological, biochemical, molecular, and host assays. Using MLSA, Xac isolates from Oregon separated into two clades, one clade with the type strain and a second clade previously described using isolates from Europe. The phylogenetic diversity of Xac observed in other countries also is present in Oregon.