Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

Maternal Sweeteners Intake Modulates Gut Microbiota and Exacerbates Learning and Memory Processes in Adult Male Offspring

Background: There is increasing evidence that gut microbiota in offspring is derived in part from maternal environment such as diet. Thus, sweeteners intake including caloric or non-caloric during perinatal period can induce gut dysbiosis and program the offspring to develop cognitive problems later in life.Objective: To determine the effect of maternal high-sweeteners intake during gestation and lactation on gut microbiota shifts in adult male offspring rats and the impact on cognitive dysfunction.Methods: Thirty-four male pups from dams fed standard diet (Control-C, n = 10), high-sucrose diet (HS-C, n = 11), high-honey diet (Ho-C, n = 8), and high-stevia diet (HSt-C, n = 5) were fed standard diet after weaning, and body weight and food intake were recorded once a week for 26 weeks. Learning and memory tests were performed at week 23 of life using the Barnes maze. Fecal samples from the breastfeeding and adulthood periods were collected and analyzed by sequencing the 16S rRNA V3-V4 region of gut microbiota.Results: Maternal high-sucrose and stevia diets programmed the male offspring, and changes in microbial diversity by Shannon index were observed after weaning (p < 0.01). Furthermore, maternal high-stevia diet programming lasted into adulthood. The increase of Firmicutes abundance and the decrease in phylum Bacteroidetes were significant in HS-C and HSt-C groups. This led to an increase in the Firmicutes/Bacteroidetes index, although only in HS-C group was statistically significant (p < 0.05). Of note, the downstream gram-negative Bacteroidales and the upregulation of the gram-positive Clostridiales abundance contribute to cognitive dysfunction.Conclusion: These results suggest that dams fed a high-sucrose and stevia diets during gestation and lactation favor a deficient memory performance in adult male offspring rats through shifts gut microbiota diversity and relative abundance at several taxa.

Microbial Community Shift and Role of Bacteria in Rapid Granulation By Using Diatomite

Aerobic granular sludge (AGS) technology is a promising biological method for modern wastewater treatment. However, granulation time have become a major issue for the application of AGS technology especially in low strength wastewater. Recent studies on granulation are focusing towards rapid start-up granulation process. Diatomite, a friable light-coloured sedimentary rock was introduces in this study to enhanced the granules formation. This study highlight the effect of diatomite towards the microbial community during the transformation of seed sludge until development of granules. DNA extraction and Metagenomic analysis was conducted with three samples (seed sludge, control AGS, AGS diatomite) to compare the microbial community. The microbial community analysis revealed the alpha diversity, phylum and class level, and the abundance of EPS producing bacteria of each bacteria samples respectively. Diatomite has a significant influence towards the microbial diversity (High Shannon index alpha diversity). Also, diatomite promotes the abundance of functional bacteria especially EPS producing bacteria, which seen as a crucial elements in granulation process.

Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

Unlike intracellular chromosome, extracellular DNA (eDNA) may accelerate the spreading of antibiotic resistance genes (ARGs) through natural transformation, but one of the core issues regarding to the taxonomic characterization of eDNA in the complex water environments is largely unknown. Hence, Illumina Miseq sequencing was used to identify the genotype of eDNA from wastewater (WW), river water (RW) and stormwater (SW) runoff. High-throughput qPCR targeting 384 genes was implemented to detect extracellular ARGs (eARGs) and mobile genetic elements (eMGEs). We obtained 2,708,291 high quality sequences from 66 eDNA samples. The SW exhibited the significant higher Shannon Index. Subsequently, we identified 34 core bacteria sources of eDNA widely distributed in the three water compartments. Among which, Pseudomonas, Flavobacterium, Limnohabitans, Burkholderiaceae_unclassified, Methylotenera and Acinetobacter were the most prevalent. A total of 302 eARGs and eMGEs were detected, suggesting that eDNA is an important antibiotic resistance reservoir. Among the 127 shared genes of the three groups, 15 core resistance genes were filtered, including IS6100, sul1 NEW, intI1, ISPps1-pseud, aac3-Via, qacH_351 and ISSm2-Xanthob. The Procrustes analysis and Variance Partitioning Analysis (VPA) demonstrated that core bacteria and MGEs were significantly correlated with eARGs. These results suggested that the occurrence and changes of eARGs in the water compartments may be largely attributed to the core microbiota and eMGEs.

Biodiversity of orb-web spiders (family: araneidae) of buner valley, Pakistan

The present research was carried out to explore the spider fauna of Buner valley with taxonomic study from February 2018 to January 2019. For this purpose samples were collected, four times at each month from 4 tehsils: Daggar, Gagra, Mandan and Totalai. Two methods were used, hand picking and sweep net for collection of samples. During day and night, three habitats, arid area, agriculture land and building area were search for collection. A total of 534 samples of spider were collected from four sampling sites, in which 379 were belonging to family Araniedae. After confirmation, the identified species were belonging to 8 genera (Neoscona, Argiope, Cyclosa, Araneus, Cyrtophora, Larinia, Erivoxia and Poltys) and 19 species. 18 of them were identified to specie level while a single specie to its generic level. The genus Neoscona was the dominant genus 26.31% having 5 species while the genus Argiope 21.05% is the second dominant having 4 species followed by Cyclosa 15.78% having 3 species followed by Cyrtophora and Araneus 10.52% having two species both. The Poltys and Larinia 5.26% are the rarest genera represent single-single specie both. Statistical analysis show that specie richness (D) = 5.77, Simpson index (1-D) = 0.87, Shannon index (H) = 2.33. Diversity of spiders was evenly distributed and calculated Evenness value was H/InS = 0.5408. There is also few atypical species and Fisher alpha estimate high value (Fisher α) = 4.42. Chao-1 estimated we have reported 22 species.

Genetic diversity of the Central European wild boar (Sus scrofa scrofa) population and domestic pig (Sus scrofa domesticus) breeds based on a microsatellite DNA locus

The results of studies of the genetic structure of the Central European wild boar (Sus scrofa scrofa) population and four breeds of domestic pigs (Duroc, Yorkshire, Large White and Landrace) bred in the Central Black Earth region of Russia are presented in this work. Based on 12 microsatellite loci, a significant ( p <0.05) decrease in the level of genetic variability in bred breeds was shown. The expected heterozygosity and Shannon index were as follows: in the wild boar, Ho = 0.763 ± 0.026, I = 1.717 ± 0.091; in the Duroc breed, Ho = 0.569 ± 0.068, I = 1.191 ± 0.157; in the Landrace, Ho = 0.618 ± 0.062, I = 1.201 ± 0.147; in the Large White, Ho = 0.680 ± 0.029, I = 1.362 ± 0.074; and in the Yorkshire, Ho = 0.642 ± 0.065, I = 1.287 ± 0.156. The results of checking genotypic Hardy–Weinberg equilibrium based on the G-test of maximum likelihood demonstrated that the overwhelming majority of loci in the wild boar population were in the state of said equilibrium. By contrast, in pig breed populations, some loci demonstrated a significant deviation from the indicated equilibrium. In addition, the Yorkshire, Large White, and Landrace populations had loci, for which the hypothesis of neutrality was reliably rejected based on the results of the Ewens–Watterson test. The revealed private alleles, characteristic of the wild boar and breeds, can later be used to identify them. The ordination of the centroids of different herds in the space of the first two principal coordinates based on the matrix of pairwise estimates of Nei’s genetic distances showed that the most distant populations are the Duroc and Boar breeds, and the most genetically close are the Yorkshire and Landrace breeds. The closest to the wild boar population was the Large White breed. The assessment of the effective size, carried out using the method based on the linkage disequilibrium and the molecular coancestry method, showed that in all studied groups, including the wild boar population, the effective size was less than 100 individuals. The low effective size of the wild boar population (Ne = 21.8, Neb = 4.0) is probably caused by the death and shooting of animals due to Pestis africana suum.

Distribution and abundance of dinoflagellates from the coastal waters of Karachi, Pakistan, northern part of the Arabian Sea

The present study reports on seasonal and spatial variations in diversity, distribution and abundance of dinoflegellates and indicates the presence of HAB species in Pakistan waters. A total of 179 taxa, recorded in this study from offshore and near-shore waters, belong to 41 genera in 26 families and 10 orders. The high species count (149 species) was recorded from Manora Island offshore station (MI-1) and 105 spp, 109 spp and 115 spp were encountered from the Mubarak village offshore station (MV-1), Manora near shore station (MI-2) and Mubarak Village near-shore station (MV-2) respectively. Tripos furca was the dominant and frequently occurring species (> 1 x103 to > 25 x103 cells L-1 from coastal and >1x 105 cells L-l from near-shore stations) in addition to less abundant Alexandrium catenella, Alexandrium sp., Alexandrium minutum, and Prorocentrum micans (>103 to 25x 103cells/L). Another 44 species occurred in relatively low numbers (<103 cell L-l). Seventy species were found throughout the study period at all four stations. High number of species in three genera (Tripos (38), Protoperidinium (34) and Prorocentrum (20) was recorded. Potently toxic (16 genera 43 species) and HAB related (19 genera and 30 species) dinoflagellate taxa were also recorded. The percent contribution of dinoflagellates in total phytoplankton population generally remained below 20% except for a few instances. Manora Island stations had comparatively higher Shannon index and equitability and slightly lower dominance index. The PCA plot showed strong positive correlation among chlorophyll-a concentration, dissolved oxygen, total number of phytoplankton and dinoflagellates.

Supplementing Glycerol to Inoculum Induces Changes in pH, SCFA Profiles and Microbiota Composition in In-Vitro Batch Fermentation

Glycerol was generally added to the inoculum as a cryoprotectant. However, it was also a suitable substrate for microbial fermentation, which may produce more SCFAs, thereby decreased pH of the fermentation broth. This study investigated the effect of supplementing glycerol to inoculum on in vitro fermentation and whether an enhanced buffer capacity of medium could maintain the pH stability during in vitro batch fermentation, subsequently improving the accuracy of short chain fatty acids (SCFAs) determination, especially propionate. Two ileal digesta were fermented by pig fecal inoculum with or without glycerol (served as anti-frozen inoculum or frozen inoculum) in standard buffer or enhanced buffer solution (served as normal or modified medium). Along with the fermentation, adding glycerol decreased the pH of fermentation broth (p < 0.05). However, modified medium could alleviate the pH decrement compared with normal medium (p < 0.05). The concentration of total propionic acid production was much higher than that of other SCFAs in anti-frozen inoculum fermentation at 24 and 36 h, thereby increasing the variation (SD) of net production of propionate. The α-diversity analysis showed that adding glycerol decreased Chao1 and Shannon index under normal medium fermentation (p < 0.05) compared to modified medium (p < 0.05) along with fermentation. PCoA showed that all groups were clustered differently (p < 0.01). Adding glycerol improved the relative abundances of Firmicutes, Anaerovibrio, unclassified_f_Selenomonadaceae, and decreased the relative abundance of Proteobacteria (p < 0.05). The relative abundances of Firmicutes, such as Lactobacillus, Blautia and Eubacterium_Ruminantium_group in modified medium with frozen inoculum fermentation were higher than (p < 0.05) those in normal medium at 36 h of incubation. These results showed that adding glycerol in inoculum changed the fermentation patterns, regardless of substrate and medium, and suggested fermentation using frozen inoculum with modified medium could maintain stability of pH, improve the accuracy of SCFA determination, as well as maintain a balanced microbial community.

Taxonomic structure of tissue endophytic bacterial microbiome in clonal apple rootstock grown on sod-podzolic soils with variant properties

The taxonomic structure of tissue endophytic bacterial microbiome was comparatively studied in microplants (undifferentiated explant callus tissues, passage 25) and 5-year clonal apple rootstocks 57-490 and 54-118 cultured from corresponding tissues (passage 1) on sod-podzolic soils with variant granulometry, chemical, physical and physicochemical properties. Proteobacteria (91.6 %) predominated in vitro tissues among other endophytic bacterial phyla in rootstock 57-490, while Proteobacteria (52.5 %) and Firmicutes (47.4 %) — in rootstock 54-118. The endophytic Firmicutes ratio vs. in vitro tissues decreases (0.7-2.0 %) in roots and more severely (0-0.2 %) in leaves. Endophytic Actinobacteriota are revealed in 11.7 % in roots of the study rootstock in heavy loam soil, whilst in medium loam their ratio drops to 2.74.1 % in roots and 0.1-0.2 % in leaves. The phylogenetic diversity indices estimation for main endophytic bacterial phyla in apple rootstock tissue recovers their essentially lower diversity and evenness in culture endosphere (Shannon index 0.42-1.00) vs. open soil roots (1.34-2.08). The leaves Shannon index is typically low (0.06-0.13) indicating poor diversity and evenness of the main endophytic bacterial phyla.

Effect of the Nanoparticle Exposures on the Tomato Bacterial Wilt Disease Control by Modulating the Rhizosphere Bacterial Community

Ralstonia Solanacearum is one of the most infectious soil-borne bacterial plant pathogens, causing tomato bacterial wilt (TBW). Nanotechnology is an emerging area of research, particularly the application of nanoparticles (NPs) as nanopesticides to manage plant disease is gaining attention nowadays. However, the interaction between NPs and rhizosphere bacterial communities remains largely elusive. This study indicated that metal NPs (CuO, ZnO, and FeO) reduced the incidence of bacterial wilt to varying degrees and affected the composition and structure of the rhizosphere bacterial community. The results revealed that the application of metal oxide NPs can improve the morphological and physiological parameters of TBW infected tomato plants. Among all, CuONPs amendments significantly increase the Chao1 and Shannon index. In the early stage (the second week), it significantly reduces the relative abundance of pathogens. However, the relative abundance of beneficial Streptomyces bacteria increased significantly, negatively correlated with the relative abundance of pathogenic bacteria. In addition, the nano-treatment group will enrich some potential beneficial bacteria such as species from Sphingomonadaceae, Rhizobiaceae, etc. In general, our research provides evidence and strategies for preventing and controlling soil-borne disease tomato bacterial wilt with metal oxide NPs.