Abundant Species Research Articles

#983 Identification of gut microbiome signatures associated with albuminuria in diabetes mellitus

Abstract Background and Aims Diabetes is a growing global problem with serious complications, including kidney impairment and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Recent research suggests a link between the gut microbiome, plasma metabolites and albuminuria development in diabetes patients, highlighting the need for further investigation using deep metagenomic sequencing. Method We investigated the relationship between 1002 gut microbial species, 1308 metabolites and albuminuria in 752 participants with diabetes from the Swedish CArdioPulmonary BioImage Study. To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods. Results Shannon diversity index was inversely associated with albuminuria after adjusting for confounding factors (Fig. 1). Our multivariable-adjusted models revealed seven metagenomic species that were associated with albuminuria (Fig. 2). Furthermore, employing a global metabolomics approach, we identified phenyl sulfate, among 98 annotated metabolites (Fig. 3), as linked to the species Clostridium sp. AT4 and Eggerthella lenta. Notably, phenyl sulfate is involved in tyrosine metabolism, and we also observed an association between the gut metabolic module of Tyrosine degradation II and albuminuria. Conclusion In the present study, we identified seven gut microbial species linked to albuminuria and established a connection between these species and phenyl sulfate, which previously has been associated with podocyte damage and the development of albuminuria. These findings provided additional evidence of the impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in patients with diabetes.

Culture-based diversity of endophytic fungi of three species of Ferula grown in Iran

A total of 1,348 endophytic fungal strains were isolated from Ferula ovina, F. galbaniflua, and F. persica. They included Eurotiales (16 species), Pleosporales (11 species), Botryosphaeriales (1 species), Cladosporiales (2 species), Helotiales (6 species), Hypocreales (31 species), Sordariales (7 species), Glomerellales (2 species), and Polyporales (1 species). F. ovina had the richest species composition of endophytic fungi, and the endophytic fungi were most abundant in their roots compared to shoots. Chao, Margalef, Shannon, Simpson, Berger–Parker, Menhinick, and Camargo indices showed that F. ovina roots had the most endophytic fungal species. The frequency distribution of fungal species isolated from Ferula spp. fell into the log-series model, and F. ovina roots had the highest Fisher alpha. The dominance indices showed that there are no dominant species in the endophytic fungal community isolated from Ferula spp., indicating community stability. Evenness values were 0.69, 0.90, 0.94, and 0.57 for endophytic fungi isolated from F. ovina roots, F. ovina shoots, F. galbaniflua roots, and F. persica roots, respectively, indicating a species distribution that tends toward evenness. The fungal species community isolated from each of F. ovina roots, F. ovina shoots, F. galbaniflua roots, and F. persica roots was a diverse species group originating from a homogeneous habitat. Their distribution followed a log-normal distribution, suggesting that the interactions of numerous independent environmental factors multiplicatively control species abundances. Principal component analysis showed that the highest species diversity and dominance were observed in the endophytic fungal community isolated from F. ovina and F. persica roots, respectively.

On finding of an abundant population of free-living stages of ergasilids (Copepoda, Cyclopoida) in the Lyutoga river of Southern Sakhalin

In the littoral zone of the oxbow of the Lyutoga River (Southern Sakhalin), which remains connected to the main channel, a high population density of parasitic copepods was found (103 ind./m2). Ergasilus briani Markewitsch, 1933, widely distributed in Eurasia, but not previously recorded in South Sakhalin and noted only for one water body in northwestern Sakhalin (Lake Sladkoe), demonstrated the highest population density (98 ind./m2). The abundance of the second species, Thersitina gasterostei (Pagenstecher, 1861) was significantly lower (5 ind./m2). T. gasterostei has previously been noted in South Sakhalin, but the present finding is the first for the Lyutoga River. The high abundance of free-living stages of ergasilids is presumably related to the reproductive peak and the hydrological nature of the collection site (littoral area with a slow current and strong overgrowing with macrophytes).

Engineering Biomimetic Protein Camouflage for Delivering Peptide/siRNA Nanocomplexes.

For cationic nanoparticles, the spontaneous nanoparticle-protein corona formation and aggregation in biofluids can trigger unexpected biological reactions. Herein, we present a biomimetic strategy for camouflaging the cationic peptide/siRNA nanocomplex (P/Si) with single or dual proteins, which exploits the unique properties of endogenous proteins and stabilizes the cationic P/Si complex for safe and targeted delivery. An in-depth study of the P/Si protein corona (P/Si-PC) formation and protein binding was conducted. The results provided insights into the biochemical and toxicological properties of cationic nanocomplexes and the rationales for engineering biomimetic protein camouflages. Based on this, the human serum albumin (HSA) and apolipoprotein AI (Apo-AI) ranked within the top 20 abundant protein species of P/Si-PC were selected to construct biomimetic HSA-dressed P/Si (P/Si@HSA) and dual protein (HSA and Apo-AI)-dressed P/Si (P/Si@HSA_Apo), given that the dual-protein camouflage plays complementary roles in efficient delivery. A branched cationic peptide (b-HKR) was tailored for siRNA delivery, and their nanocomplexes, including the cationic P/Si and biomimetic protein-dressed P/Si, were produced by a precise microfluidic technology. The biomimetic anionic protein camouflage greatly enhanced P/Si biostability and biocompatibility, which offers a reliable strategy for overcoming the limitation of applying cationic nanoparticles in biofluids and systemic delivery.

Circadian regulation of macromolecular complex turnover and proteome renewal.

Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.

Woody species diversity, structure and regeneration status of the church forests in West Gojjam Zone, Northwestern Ethiopia

Ethiopia's diverse ecology faces challenges from significant deforestation. Church forests are relatively protected although under pressure from agricultural expansion, grave house construction and climate related factors. The present study was aimed to assess the woody species composition, structure and regeneration status of church forests in the West Gojjam Zone. Twenty-six church forests were selected using stratified random sampling based on agroecology, elevation, forest size, and distance from population centers. A total of 175 main plots of 20 m × 20 m (400 m2) for trees, 875 subplots of 5 m × 5 m (25 m2) for saplings, and 875 subplots of 1 m × 1 m (1 m2) for seedlings were laid down. Diameter at breast height (DBH) was measured for woody plants with a DBH ≥2.5 cm and also height ≥ 2.5 m. Diversity and structural analysis of the woody species were carried out using appropriate tools. The regeneration status of the study forests was evaluated based on the number of seedlings, sapling and matured plants. A total of 111 woody species that belong to 95 genera and 51 families with 72 (64.86 %) trees, 23 (20.72 %) shrubs, 8 (7.2 %) shrubs/trees and 8 (7.2) lianas were identified. In the study sites, the woody plant species consist of 82.88 % indigenous, 15.32 % exotic, and 1.8 % endemic species. Fabaceae was the dominant family in West Gojjam zone church forests. The Shannon diversity ranged from 0.99 to 3.47, with an average of 2.55, and evenness varied from 0.5 to 0.96 (average 0.82). Species richness ranged from 7 to 45 with the average value of 23.81, and a total stem density of 5880 individuals per hectare. Additionally, 5923 saplings and 6136 seedlings per hectare were recorded. The most abundant species include Eucalyptus camaldulensis, Calpurnia aurea, and Juniperus procera. The average basal area was 29.268 m²/ha for the studied church forests, with Ficus vasta having the highest basal area. Juniperus procera and Rhus vulgaris exhibited the highest Importance Value index (IVI), while Premna schimperi, and Myrtus communis had the lowest IVI. The overall regeneration status of west Gojjam church forests was found to be good. Significant differences in woody species composition and diversity were observed between church forests. The study revealed the importance of church forests in the West Gojjam Zone for plant diversity conservation, revealing their resilience and potential for sustainable protection of forests despite the challenges like deforestation and climate change, and their potential for sustainable maintenance. As we have already seen, some of the church's forests were converted to agriculture as a source of income for the church. This practice is dangerous for the survival of the endemic plants in the church forests and leads to deforestation. Therefore, it is recommended to form an alternative source of income for the church.

Paleoclimate changes and ecosystem responses of the Bulgarian Black Sea zone during the last 26000 years

Multi-proxy analysis (spore-pollen, dinoflagellate cysts, other non-pollen palynomorphs (NPPs), radiocarbon dating and lithology) was performed on marine sediments from three new cores retrieved during the two cruise expeditions on board the Research Vessel “Akademik” in 2009 and 2011. The Varna transect comprises three cores extending from the outer shelf, continental slope and deep-water zone. The record spans the last 26000 years (all ages obtained in this study are given in calendar years BP (cal. yrs BP)). The pollen record reveals the spreading of steppe vegetation dominated by Artemisia and Chenopodiaceae, suggesting cold and dry environments during the Late Pleniglacial – Oldest Dryas (25903–15612 cal. yrs BP). Stands of Pinus and Quercus reflect warming/humidity increase during the melting pulses (19.2–14.5 cal. ka BP) and the Late Glacial interstadials Bølling and Allerød. The Younger Dryas (13257–11788 cal. yrs BP) coldest and driest environments are clearly demonstrated by the maximum relative abundance of Artemisia and Chenopodiaceae. During the Early Holocene (Preboreal and Boreal chronozones, 11788–8004 cal. yrs BP), Quercus appeared as a pioneer species and, along with other temperate deciduous arboreal taxa, formed open deciduous forests as a response to the increased temperature. The rapid expansion of these taxa indicates that they survived in Glacial refugia in the coastal mountains. During the Atlantic chronozone (8004–5483 cal. yrs BP), optimal climate conditions (high humidity and increased mean annual temperatures) stimulated the establishment of species-rich mixed temperate deciduous forests. During the Subboreal chronozone (5483–2837 cal. yrs BP), Carpinus betulus and Fagus expanded simultaneously and became more important components of mixed oak forests and probably also formed separate communities. During the Subatlantic chronozone (2837 cal. yrs BP to pre-industrial time), climate-driven changes (an increase of humidity and a cooling of the climate) appear to be the main drivers of the specific vegetation succession expressed by increased abundance of Alnus, Fraxinus excelsior and Salix along with lianas, suggesting formation of flooded riparian forests (so called ‘Longoz’) lining the river valleys along the Black Sea coast. The first indicators of farming and other human activities have been recorded since 7074 cal. yrs BP. The dinoflagellate cyst (dinocyst) assemblages have been analysed to assess the changes in the Black Sea environment over the last 26000 years in terms of fluctuation in paleoproduction and surface water conditions related to changes in climate, freshwater input and Mediterranean water intrusion. Two major dinocyst assemblages were distinguished: one dominated by stenohaline freshwater/brackish-water species and a successive one dominated by euryhaline marine species. The changes in the composition of the assemblages occurred at 7668 cal. yrs BP. The abrupt decrease of stenohaline freshwater/brackish-water species Pyxidinopsis psilata and Spiniferites cruciformis was followed upwards by a gradual increase in euryhaline marine species, such as Lingulodinium machaerophorum, Spiniferites belerius, S. bentorii and acritarch Cymatiosphaera globulosa. The first occurrence of euryhaline marine species took place synchronously with the onset of sapropel deposition. Modern marine conditions were established after 6417 cal yrs BP when an abundance of Mediterranean-related species, such as Operculodinium centrocarpum and Spiniferites mirabilis, along with other heterotrophic species, occurred. After the stable cold and dry environment during the Last Glacial Maximum, the phytoplankton record of core AKAD 11-17 shows that Pediastrum boryanum var. boryanum has a cyclical abundance associated with the deposition of four red-brown clay layers between 19.2 and 14.5 cal. ka BP. This event is associated with the major melting phase of European Ice drained by the Danube and Dnieper Rivers in response to climate warming observed after the end of the Last Glacial Maximum. During the Early Holocene, P. psilata, characterised by a preference to warmer temperatures, demonstrates its ecological optimum for growth concerning SST reaching maximum relative abundance of 94% between 11072 and 8638 cal. yrs BP. This maximum was interrupted by an abrupt significant short-term decrease in the relative abundance of P. psilata centred between 8500 and 8300 cal. yrs BP reflecting cold conditions similar to those of Younger Dryas. This finding, also confirmed by the rapid significant decrease of arboreal pollen, particularly of Quercus in the same studied core, is considered a regional expression of the well-known ‘8.2 ka cold event’ which is commonly linked to a meltwater-related perturbation of the Atlantic Meridional Overturning Circulation (AMOC) and associated collapse of oceanic northward heat transport. Our fossil pollen and dinocyst data confirm that the high amplitude temperature anomaly associated with ‘the 8.2 ka cold event’ may have also occurred in south-eastern Europe, at lower latitudes of the western Black Sea coastal area, most probably due to atmospheric transition and/or river discharge.

Decoding the intestinal response to heat stress in Gymnocypris eckloni: Insights from a thorough analysis of microbiome and transcriptome

The Qinghai-Tibetan Plateau has exhibited heightened sensitivity to global warming than any other region. G. ekloni, an endemic fish of the Qinghai-Tibetan Plateau, holds ecological significance and is a key highland cold-water species in Chinese aquaculture. However, the warming of its habitat poses a significant threat to its survival. The intestine serves as the primary line of external immune defense. There are no reports available on alterations in the intestine of G. eckloni in response to varying levels of heat stress. In this study, G. ekloni was categorized into the optimum temperature culture group (CO, control group), the 22 °C heat stress culture group (HT-22) and the 28 °C heat stress culture group (HT-28).The adaptability of G. ekloni intestine to varying levels of heat stress was investigated through a comprehensive analysis involving tissue sections, blood biochemical indexes, sequencing of 16S and RNA-Seq. Tissue sections showed severe intestinal damage in the HT-28, characterized by mucosal layer necrosis, swelling of thrush cells, and erosion of villi. In the HT-28 group, the significantly increased plasma levels of inflammatory markers (DAO, LPS, IL-1β, IL-6, and TNF-α) also corroborated the substantial impairment of intestinal barrier function. Meanwhile, the RNA-Seq analysis revealed a significant upregulation of most genes in the HIF-1 signaling pathway. This suggests that the HIF-1 signaling pathway likely plays a crucial role in safeguarding the intestinal tract from injuries caused by extreme temperature stress.Intriguingly, there was very little change in the intestinal histological structure and no significant changes in biochemical indicators of stress and inflammation in the blood in the HT-22 group, and 16S amplification sequencing also revealed a greater abundance of intestinal microbial species in the HT-22 group. Through co-analysis with the up-regulated DEGs in HT-22, it was determined that the augmentation of intestinal flora taxa in the HT-22 group positively contributing to enhancing intestinal immunity and stabilizing intestinal barrier. This comprehensive histomorphological and multi-omics study showcased the resilience of G. ekloni intestine to environmental warming. The findings offer fundamental data for future research on the artificial culture of highland economic fishes, and their environmental adaptations.

Environmental factors modulate the distribution of elasmobranchs in southern Mozambique

Investigating the spatiotemporal ecology of elasmobranchs is an important precursor to their effective management. Understanding long-term patterns in the movement and habitat use of threatened species can improve management plans so that they yield increased conservation benefits. We investigated the spatiotemporal and environmental drivers that underpin the abundance and distribution of elasmobranchs around reef habitats in southern Mozambique to highlight reefs that are important (“hotspots”) to the regional elasmobranch community. Visual belt transects (n = 738), supported by video recordings, were completed on 16 reef sites off the coast of southern Mozambique from 2018 to 2022. Nine elasmobranch species were encountered annually (Carcharhinus amblyrhynchos, Triaenodon obesus, Stegostoma tigrinum, Neotrygon caeruleopunctata, Pateobatis jenkinsii, Taeniurops meyeni, Mobula kuhlii, Mobula alfredi, Mobula birostris) and 11 individual environmental and spatiotemporal parameters (horizontal water visibility, tidal range and state, moon illumination, temperature on the reef, cloud cover, time of day, day of the year, transect distance from shore, transect depth, and the region that the transect occurred in) were measured. All species, (bar P. jenkinsii) were significantly more abundant around certain reefs in the sampled region. Total counts for most species were highest in the austral summer however two species’ (M. birostris and S. tigrinum) were most abundant in the winter months. The tidal state, tidal range, and moon illumination correlated significantly with the numbers of each of the nine elasmobranch species. Non-Metric Multidimensional Scaling (NMDS) indicated that species’ responses to the measured parameters grouped taxonomically. Environmental influences resulted in strong seasonal patterns of reef use by large-bodied and pelagic elasmobranch species (e.g. manta rays). The measured environmental parameters also resulted in daily, monthly, and seasonal patterns of abundance of reef-resident stingray and shark species. Banning extraction of elasmobranch species around the reefs where they aggregate and reflecting species distributions within fisheries regulations may significantly benefit the regional elasmobranch community.

Evaluating the influence of marine protected areas on surf zone fish.

Marine protected areas (MPAs) globally serve conservation and fisheries management goals, generating positive effects in some marine ecosystems. Surf zones and sandy beaches, critical ecotones bridging land and sea, play a pivotal role in the life cycles of numerous fish species and serve as prime areas for subsistence and recreational fishing. Despite their significance, these areas remain understudied when evaluating the effects of MPAs. We compared surf zone fish assemblages inside and outside MPAs across 3 bioregions in California (USA). Using seines and baited remote underwater videos (BRUVs), we found differences in surf zone fish inside and outside MPAs in one region. Inside south region MPAs, we observed higher abundance (Tukey's honest significant difference [HSD]=0.83, p=0.0001) and richness (HSD=0.22, p=0.0001) in BRUVs and greater biomass (HSD=0.32, p=0.0002) in seine surveys compared with reference sites. Selected live-bearing, fished taxa were positively affected by MPAs. Elasmobranchs displayed greater abundance in BRUV surveys and higher biomass in seine surveys inside south region MPAs (HSD=0.35, p=0.0003 and HSD=0.23, p=0.008, respectively). Although we observed no overall MPA signal for Embiotocidae, abundances of juvenile and large adult barred surfperch (Amphistichus argenteus), the most abundant fished species, were higher inside MPAs (K-S test D=0.19, p<0.0001). Influence of habitat characteristics on MPA performance indicated surf zone width was positively associated with fish abundance and biomass but negatively associated with richness. The south region had the largest positive effect size on all MPA performance metrics. Our findings underscored the variability in species richness and composition across regions and survey methods that significantly affected differences observed inside and outside MPAs. A comprehensive assessment of MPA performance should consider specific taxa, their distribution, and the effects of habitat factors and geography.

Landscapes with higher crop diversity have lower aphid species richness but higher plant virus prevalence

Abstract Diversifying agricultural systems by growing more than one crop species in an area can decrease pest and disease pressure and increase crop yields. However, there is a lack of information on how crop diversity at larger spatial scales influences pest and disease pressure. Here, we investigated how landscape‐scale crop diversity affects aphid vector communities and prevalence of non‐persistently transmitted potato virus Y (PVY). To test the influence of landscape‐scale crop diversity on PVY prevalence and aphid communities, we conducted a field study during the 2020 and 2021 field seasons in the San Luis Valley, Colorado, where we quantified aphid communities and PVY incidence at multiple sites. We then determined the association between aphid species richness and abundance and PVY incidence with landscape variables (crop diversity metrics and percentage cover of crop species) within 1, 2 and 3 km buffers from study sites. Higher crop diversity (measured as Shannon Diversity Index) led to decreased aphid species richness at a 3 km buffer in the 2021 field season. We only detected a positive association between percentage of alfalfa crop cover and aphid species richness in 2020 and aphid abundance in 2021 within a 1 km buffer. Higher crop diversity led to increased PVY incidence at a 2 km buffer in 2021 and 3 km buffer in 2020 and 2021. At a 3 km buffer in 2021, we found a positive influence of crop species richness on PVY incidence and a negative influence of crop species evenness on PVY incidence. Also in 2021, we found a positive influence of percentage of potato (virus host) on PVY incidence and a negative influence of percentage of barley (virus non‐host) on PVY incidence. Synthesis and applications. In summary, we found that landscape‐scale crop diversity impacts plant virus prevalence at spatial scales of &gt;1 km. This suggests that potato growers could reduce PVY prevalence by geographically isolating potato fields from other potato or other PVY hosts. Crop diversity had a negative influence on aphid vector communities, so growers could reduce risk of virus spread by aphid vectors by using certified potato seed in a diversified landscape.

Incidence of fungal contamination in fresh ginseng samples and mycotoxigenic potential of representative fungal isolates.

Fresh ginseng is typically accompanied by soil after harvest, leading to contamination with harmful fungi during storage and distribution. In this study, we investigated the incidence of fungal contamination in fresh ginseng (5-6 years old) purchased from 22 different stores in Geumsan, Korea. The incidence of fungal contamination in the samples was 67.4-111.5%. Fusarium solani was the most abundant species in the head (38.5%) and fine root (19.3%) parts of the ginseng samples, whereas F. oxysporum was the most abundant in the main root (22.0%) part. We isolated Aspergillus, Fusarium and Penicillium spp. (total number of isolates: 395) from the ginseng samples, and 138 isolates were identified using phylogenetic analysis. Polymerase chain reaction-based screening of 65 mycotoxin-producing species revealed that two P. expansum isolates were positive for citrinin and/or patulin, and five F. oxysporum isolates were positive for fumonisin biosynthesis gene. One P. expansum isolate produced 738.0 mg kg-1 patulin, and the other produced 10.4 mg kg-1 citrinin and 12.0 mg kg-1 patulin on potato dextrose agar (PDA) medium. Among the 47 representative F. oxysporum isolates, 43 (91.5%) produced beauvericin (0.1-15.4 mg kg-1) and four of them (8.5%) produced enniatin B and enniatin B1 (0.1-1.8 mg kg-1) as well. However, none of these toxins was detected in fresh ginseng samples. Fusarium solani and F. oxysporum were the most abundant species in fresh ginseng samples. Most F. oxysporum (43) and P. expansum (2) strains isolated from fresh ginseng produced beauvericin and enniatins (B and B1), and patulin or citrinin, respectively, on PDA medium. This is the first report of the mycotoxigenic potential of P. expansum and F. oxysporum strains isolated from fresh ginseng. © 2024 Society of Chemical Industry.

Maize Kernel-Associated Metagenomes Reveal Potential Microbe–Microbe Interactions that Underlie Fusarium Ear Rot Disease

As an alternative to host resistance, transgenic expression of entomocidal and antimicrobial proteins from Bacillus thuringiensis ( Bt) in maize can mitigate Fusarium ear rot (FER). This study evaluated FER in Bt and conventional maize and the role of microbes in the kernel-associated metagenome using quantitative reduced representation sequencing. Our results revealed significant differences in FER severity across environments and varieties and between inoculation treatments. The lower FER scores of conventional maize Spectrum 6416 relative to other varieties highlighted resistant alleles in maize germplasm, whereas strong correlations indicated FER-induced yield loss. Mitigation of FER by transgenes was validated by about threefold enrichment of Fusarium verticillioides ( Fv) postinoculation compared with nonsignificant Fv enrichment in conventional maize. Although the major causal pathogen of FER, Fv, was the most abundant species in the metagenomes ( r = 0.41 to 0.49), a similar degree of correlation was observed between FER and several Fusarium spp. ( r = 0.2 to 0.56). The potential FER-suppressing properties of Talaromyces stipitatus and Ustilago maydis were indicated by negative correlations with FER ( r = –0.22 to –0.42), Fv, and some Fusarium spp. The more FER-resistant varieties consistently enriched for potential FER-suppressing Burkholderia cenocepacia (negatively correlated with Fv). This suggests host genetic background-dependent recruitment of beneficial microbes that suppress pathogens and that microbe–microbe interactions play a role in FER severity. Quantitative and species/strain-level metagenomic profiles hold promise for identifying robust disease-suppressing microbes and microbes that act in synergy with pathogens and for developing holobiont-aware breeding strategies that account for host–microbiome coevolution and host genotype, microbiome/metagenome, and environment interactions. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Dual RNA-seq in filarial nematodes and Wolbachia endosymbionts using RNase H based ribosomal RNA depletion.

Lymphatic filariasis is caused by parasitic nematodes and is a leading cause of disability worldwide. Many filarial worms contain the bacterium Wolbachia as an obligate endosymbiont. RNA sequencing is a common technique used to study their molecular relationships and to identify potential drug targets against the nematode and bacteria. Ribosomal RNA (rRNA) is the most abundant RNA species, accounting for 80-90% of the RNA in a sample. To reduce sequencing costs, it is necessary to remove ribosomal reads through poly-A enrichment or ribosomal depletion. Bacterial RNA does not contain a poly-A tail, making it difficult to sequence both the nematode and Wolbachia from the same library preparation using standard poly-A selection. Ribosomal depletion can utilize species-specific oligonucleotide probes to remove rRNA through pull-down or degradation methods. While species-specific probes are commercially available for many commonly studied model organisms, there are currently limited depletion options for filarial parasites. Here, we performed total RNA sequencing from Brugia malayi containing the Wolbachia symbiont (wBm) and designed ssDNA depletion probes against their rRNA sequences. We compared the total RNA library to poly-A enriched, Terminator 5'-Phosphate-Dependent Exonuclease treated, NEBNext Human/Bacteria rRNA depleted and our custom nematode probe depleted libraries. The custom nematode depletion library had the lowest percentage of ribosomal reads across all methods, with a 300-fold decrease in rRNA when compared to the total RNA library. The nematode depletion libraries also contained the highest percentage of Wolbachia mRNA reads, resulting in a 16-1,000-fold increase in bacterial reads compared to the other enrichment and depletion methods. Finally, we found that the Brugia malayi depletion probes can remove rRNA from the filarial worm Dirofilaria immitis and the majority of rRNA from the more distantly related free living nematode Caenorhabditis elegans. These custom filarial probes will allow for future dual RNA-seq experiments between nematodes and their bacterial symbionts from a single sequencing library.

Systematic Study of Family Pholicidae (Cellar Spiders) from the District Hyderabad, Sindh, Pakistan

This study was carried out between 2017 and 2018; 150 spider specimens belonging to the family Pholicidae were collected from 04 different locations of District Hyderabad, viz, Talukas, Saddar, Latifabad, and Qasimabad. Taluka Latifabad was found the richest with 38.66% while least samples were collected from Saddar with 16.00%. Among 150 specimens, two genera were sorted out in genus Artema and Crossopriza. Total number specimen of Artema were 90, a new species also reported Artema hirabadi was also identified on the basis of taxonomical character, 60 specimen of genus Crossopriza and two new species namely C. tahirae, C. hyderabadi were identified to science. Beside this C. lyoni reported as new record from District Hyderabad. Most abundant species was Artema least found was Crossopriza. The spiders were collected from metropolitan city areas habituated in houses, stores, garages, etc. somewhere they form thin web while applying standard collected works proposed by entomologists and Arachnologists. The research work provides preliminary information knowledge about spider’s fauna.

Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas.

Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products' pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community.

High-voltage electrostatic field with 35 kV-15 min could reduce Pseudomonas spp. to maintain the quality of pork during −1 °C storage

This study evaluated the bacterial-reducing effects of different high voltage electrostatic field (HVEF) parameters (voltage 20,25,30,35 kV, time 5,10,15,20 min) on chilled pork, and studied the effects of HVEF bacterial-reducing treatment on the microbial number and the quality of pork during ice-temperature (−1 °C) storage. The results showed that HVEF of 35 kV-15 min was the best parameter, which made a 0.51 log CFU/g bacterial reduction. HVEF treatment reduced the number of Pseudomonas spp. by 0.50 log CFU/g, but no significant decrease was found in Brochothrix thermosphacta and lactobacilli. The abundance of Pseudomonas fragi (most abundant species in pork) significantly decreased after HVEF treatment, which may be the reason for the significant decrease of TVB-N and TBARS in HVEF group at the end of storage. During −1 °C storage, HVEF group exhibited better quality characteristics on shear force and cooking loss, which could effectively extend the shelf-life of chilled pork. Industrial relevanceHigh voltage electrostatic field (HVEF) is an emerging non-thermal inactivation technology. However, it is necessary to optimize the processing parameters based on the characteristics of the food. This study optimized the optimal processing parameters of HVEF for chilled pork and validated its contribution to maintaining the quality of pork during ice-temperature storage. These findings are of great significance for food processing, food preservation and the development of new refrigeration equipment.

Temporal changes in the composition of parasitoid assemblages associated with the invasive chestnut gall wasp

Abstract Invasive alien species pose a challenge to ecosystem stability and crop production, so understanding their interactions with the natural communities they invade is crucial to mitigate negative effects. The oriental chestnut gall wasp, Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae), is an invasive insect that attacks chestnut trees. It was first recorded in Spain in 2012 and is now presumably present in the majority of chestnut stands in the country. We assessed variation in the abundance of D. kuriphilus galls and the composition of their associated parasitoid community (Hymenoptera: Chalcidoidea) during a 4‐year period (2014–2017) in 12 sampling sites in Catalonia (Spain, northeastern Iberian Peninsula), and identified which species contributed most significantly to the control of D. kuriphilus. The results show that the abundance of individual parasitoid species varied during the study period and that the number of species increased year after year. There was also a transition in the parasitoid community composition across the years. Our data suggest that the joint action of the non‐native parasitoid Torymus sinensis Kamijo and the native T. notatus (Walker) (Hymenoptera: Chalcidoidea: Torymidae) led to the decline of D. kuriphilus until it was no longer considered a pest. Also, the observed pool of parasitoid species ended up being relatively homogeneous across sites over the years, which may be due to the high natural dispersal of these parasitoids (both by active flight and passive wind dispersal).

PHREEQ C Modelling Tool Application to Determine the Effect of Anions on Speciation of Selected Metals in Water Systems within Kajiado North Constituency in Kenya

Heavy metals and anions in water pose a significant risk to living organisms, including humans, and must therefore be carefully monitored. There are numerous approaches and methods of analysis to choose from. Using the PHREEQ C chemical modeling technique, this study looked at the effect of certain anions on the speciation of selected metals in the water environment of Kajiado North. Twenty-five sampling points were used in the study, which covered five Kajiado North election wards. Samples were taken twice during the dry and rainy seasons, in November 2019 and March 2020. Using standard methods, physicochemical characteristics were analyzed, concentrations of selected heavy metals using the (ICP- OES) 7000 series, and selected anions using a multi parameter photometer, their concentration values compared to the specified maximum contaminant level and speciation analysis done using the Computer-based technique PHREEQ C. The range observed for pH, temperature, electrical conductivity, sulphate, chloride, fluoride, nitrate and carbonates was 7.43- 9.30, 23.0 -28.0oC, 335-1265μS/cm, 4.54-361.41mgL-1, 5.19-184.6 mgL-1, 0.01-2.90 mgL-1, 0.1-8.6 mgL-1, and 3.18-55.19 mgL-1 respectively. The range observed for heavy metals was 0.06-1.08 mgL-1 , 0.00 -0.05082 mgL-1, 0.01-0.02597 mgL-1, 0.01-0.01610 mgL-1, 0.00 -0.0327 mgL-1, 0.00-42.7842 mgL-1, and below detection limit, for Fe, Mn, Cu, Zn, Pb, Mg, and Cd respectively. The findings revealed that Cd, Zn, Cu, Cl-, NO2-, and eElectrical cconductivity concentrations were below the WHO levels. At certain sampling points, however, SO42-, F-, Pb, Fe, and Mn were above WHO limits. In some water systems, traces of SO42-, F-, Cu, Fe, Cd, and Mn were found to pose significant health risks, according to PHREEQ C speciation analysis. Anion concentrations, pH, temperature, and metal concentrations are all important variables in modeling. Metals formed anion complexes and the total abundance of metal species was classified at the highest levels as Fe(OH)3, PbCO3, Zn(CO3)2, Cu(CO3)2, Mn+2, MgF-, and Mg+2. At a water system temperature of 25oC without anions, it was found to have the highest chemical species. CuCO3, CuNO3, and CuOH+ complexes are also formed at low pH. Based on the data for different metal species at different pH values, the bioavailability of metal species definitely depends on pH.

Enhanced Fenton performance of wet-mechanochemically synthesized FeS2/Biochar: The multiple synergistic effect derived from mutual element doping

FeS2-biochar composites have been considered as promising heterogeneous Fenton materials for pollutants removal. However, the chemical synthesis of element-doped FeS2-biochar composite with superior performance and the comprehensive investigation for its underlying multiple synergistic mechanism remain a difficult endeavor. Herein, a novel FeS2/Biochar nanocomposite with mutual element doping was firstly synthesized by facile wet-mechanochemical method using iron, sulfur and bamboo-biochar for efficient organic pollutant (sulfamonomethoxine, SMM) removal. Experiment and DFT calculation results revealed that multiple synergistic effect between FeS2 and biochar derived from newly formed Fe-C and C-S-C bonds induced the abundant reactive oxygen species (ROS) and excellent electron transfer capacity. Fe-C sites facilitated the H2O2 adsorption and populated O-O bond in H2O2 for its barrierless dissociation into •OH via forming bridging C-Fe-O-O-Fe bond. Oxygen vacancy, C-S-C and Fe-C bonds, persistent free radicals (PFRs) accelerated the generation and transformation of ROS, which resulted in dominating free radical (•OH, •O2–, •SO4-) and auxiliary non-radical (1O2) pathway. Meanwhile, Fe3+/Fe2+ redox-cycle was expedited by electron donor/shuttle (S22-, BC, •O2–, C-S-C and Fe-C bonds). All these specialties contributed to the superior performance of FeS2/Biochar Fenton system for SMM removal at wide pH range (3–11) with negligible Fe release. Completely SMM (50 mg/L) removal was achieved within 20 min for 8 successive reuses. This work emphasized the concept of building mutual element doping on molecular level in enhancing FeS2-Biochar synergy towards efficient environmental remediation.