Predominant Phyla Research Articles

Exploration of Bacterial Community Structure Profiling and Functional Characteristics in the Vermicomposting of Wasted Sludge and Kitchen Waste

Nowadays, the enormously growing amount of kitchen waste and wasted sludge has greatly received global attention. Vermicomposting has been represented as an eco-friendly and sustainable alternative for organic waste management. This study utilized kitchen waste generated by the university canteen and excess sludge from municipal wastewater treatment to collaboratively realize waste to resource through vermicomposting with a composting control. The results indicated that the treatment utilizing an equal mass ratio of wasted sludge and kitchen waste (T3) exhibited the greatest reduction in total organic carbon and the highest increase in total nitrogen. Furthermore, the predominant phyla observed were Proteobacteria, Actinobacteriota, Bacteroidetes, and Firmicutes. Functional prediction analysis demonstrated higher relative abundances of β-glucosidase (ascF) and 6-phospho-β-glucosidase (bglA, celF) in the vermicomposting, suggesting that the earthworms essentially enhanced the cellulose degradation. More importantly, the co-occurrence network analysis demonstrated that the vermicomposting showed a stronger interaction between Gordonia and other bacteria, thereby enhancing its ability to degrade macromolecular compounds. In general, the vermicomposting can smoothly and remarkably stabilize the kitchen waste, assisted by excess sludge and sawdust.

Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits

The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.

Spatiotemporal Distribution of nirS-Type Denitrifiers in Cascade Reservoir Sediments of the Qinghai Plateau

Compared to single damming, the impact of cascade damming on nitrogen-related microorganisms in river ecosystems exhibits greater complexity. However, there is still a lack of research on the response of denitrifiers to the construction of cascade reservoirs. A study was conducted on 10 cascade reservoirs in the upper reaches of the Yellow River to investigate the impact of cascade reservoir construction on nirS-type denitrifying bacteria in sediments. Sediment samples were collected in May (dry season) and August (wet season) of 2023. The spatiotemporal characteristics of the nirS-type denitrifying bacterial community and gene abundance were analyzed using Illumina high-throughput sequencing and real-time fluorescence quantification PCR (qPCR). Redundancy analysis (RDA) and variation partitioning (VP) were utilized to assess the impact of environmental factors on these communities. The results showed the following: (1) Proteobacteria was the predominant phylum of nirS-type denitrifying bacteria in cascade reservoir sediments. At the genus level, unclassified Proteobacteria (69.51–95.64%) showed the highest relative abundance, followed by Paracoccus, Rhodanobacter, and Pseudomonas, indicating that unclassified Proteobacteria may dominate denitrification in these reservoir sediments. (2) The α and β diversity indices of nirS-type denitrifying bacteria were higher in the dry season than in the wet season, and also higher in young reservoirs compared to old reservoirs (p < 0.05). (3) Temporally, the abundance of the nirS gene was significantly higher in the wet season (12.71 × 107 copies/g dry sediment) compared to the dry season (66.35 × 105 copies/g dry sediment). Spatially, the abundance of the nirS gene was higher in the central region, while relatively lower at both ends. (4) RDA and VP analysis indicated that the community structure and abundance of nirS-type denitrifying bacteria were significantly influenced by the total nitrogen in sediments (19.31%) and water temperature (14.13%). Spearman correlation analysis showed that organic carbon significantly affected the diversity of nirS-type denitrifying bacteria (p < 0.05). The results contribute to a better understanding of the nitrogen-related microbial community in cascade reservoir sediments of the Yellow River, providing a scientific basis for reservoir management.

Comparative analysis of intestinal flora community composition and diversity of Anas platyrhynchos and Anser fabalis in the Yellow River Delta

Abstract The Yellow River Delta wetland is a habitat for wintering waterfowl, where mallard (Anas platyrhynchos) and tundra bean goose (Anser fabalis) are commonly observed. Although the intestinal flora plays a pivotal role in maintaining host health and promoting nutrient absorption, it remains unclear whether the same overwintering habitat and challenging feeding conditions specifically affect the composition and diversity of intestinal flora in both species. Here, high-throughput sequencing was used to compare the intestinal bacterial communities of mallard and tundra bean goose from the same region. There was no significant difference in alpha diversity and beta diversity between the two species. Firmicutes and Proteobacteria were the two predominant phyla, accounting for more than 50.00% of the total. They enhanced the nutrient absorption and metabolic efficiency during overwintering. Catellicoccus was the most dominant genus in the intestinal flora of tundra bean goose, accounting for 33.91%, whereas Clostridium sensu stricto 1 was the most dominant genus in mallard, accounting for 7.34%. This difference is considered to be related to the feeding habits of these two species. No significant differences in the structure and diversity of intestinal bacterial communities were observed between mallard and tundra bean goose, and the similarity of intestinal flora between them was high. This study deepens our understanding of the intestinal flora of two coexisting species with different dietary preferences in the Yellow River Delta. It also lays the foundation for waterfowl disease prevention in this area, carrying significant scientific and practical implications for biodiversity and ecosystem conservation.

Archaeal community from the Northern Hangzhou Bay to the East China Sea: biogeography, ecological processes, and functional potential

IntroductionArchaeal communities play a crucial role in marine ecosystems, yet our understanding of their ecological and functional traits remains incomplete. This study focuses on northern Hangzhou Bay to fill gaps in knowledge regarding the biogeography and functionality of archaeal groups.MethodsWe utilized a high-throughput sequencing dataset based on the 16S rRNA gene to characterize the archaeal community, aiming to identify biogeographic patterns and assess the influence of environmental factors on community structure.ResultsThe predominant phyla identified were Woesearchaeota, Thaumarchaeota, Euryarchaeota, and Crenarchaeota. Archaeal community structure in sediments showed a geographical pattern along the environmental gradient, influenced by factors such as salinity, ammonium, total phosphorus, pH, and total nitrogen content. Network analysis revealed nonrandom co-occurrence patterns, with associations changing along the salinity gradient. Additionally, this study directly proved the existence of dispersal limitation in this strongly connected marine ecological system through null model analyses. Variation in the archaeal community was attributed to both environmental constraints and stochastic processes due to dispersal limitation. Furthermore, our results revealed that the key biogeochemical functions of the archaeal community also exhibited a clear salinity gradient, the functional differences appear to be influenced by salinity, and the critical roles of archaeal diversity were highlighted.DiscussionAll these findings enhance our understanding of microbial ecology and element transformation in estuarine environments. The highlighted roles of archaeal diversity and the influence of environmental factors on community structure and function underscore the complexity of marine microbial ecosystems.

Sex-Dependent Rhizosphere Microbial Dynamics and Function in Idesia polycarpa through Floral and Fruit Development

Male Idesia polycarpa, which display distinct morphological and physiological traits, exhibit greater adaptability to stressful environments than females. However, the connection between this adaptability and rhizosphere processes remains unclear. Here, we investigate the differences in root bacterial community structures between male and female plants at different developmental stages, identifying bacterial strains associated with plant sex through functional predictions. This study aims to inform the optimal allocation of male and female plants during cultivation and provide a theoretical basis for sex identification and breeding. Samples from seven-year-old male and female plants were collected during the flowering (May) and fruit ripening (October) stages. Rhizosphere nutrient content and bacterial diversity were analyzed using Illumina high-throughput sequencing technology. The results demonstrate that total nitrogen (TN), total carbon (TC), and available potassium (AK) varied between sexes at different times. No significant differences between male and female plants were observed in the Shannon, Simpson, and Chao1 indexes during the flowering period. However, the Chao1 and Shannon indexes were significantly higher at fruit maturity in male rather than female plants. The predominant phyla of rhizosphere bacteria were Pseudomonadota, Acidobacteriota, and Actinomycetes. Interestingly, from flowering to fruit ripening, the dominant phyla in both male and female plants shifted from Actinomycetes to Pseudomonadota. A significant correlation was observed between pH and AK and rhizosphere bacteria (p < 0.05), with metabolism being the main functional difference. This study provides preliminary insights into the functional predictions and analyses of bacteria associated with Idesia polycarpa. The above findings lay the groundwork for further investigation into the sex-specific differences in microbial flora across different developmental stages, elucidating the mechanisms underlying flora changes and offering theoretical support for the high-quality management of Idesia polycarpa.

The source and dissemination of ARGs in pristine environments: elucidating the role of migratory birds in the Arctic

Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.

Temporal dynamics of protist communities and environmental factors in the horizontal flow-polyculture pond aquaculture model of Sinonovacula constricta

The horizontal flow (HF)–polyculture pond (PP) model has emerged as a new aquaculture model that has attracted considerable attention. The growth of Sinonovacula constricta in the HF is highly dependent on phytoplankton in the PP; however, the current understanding of the basic microbes in the HF-PP model research remains insufficient. To address this knowledge gap, we analyzed the temporal dynamics of protist communities in water and sediment samples obtained from the HF and PP in this study. In addition, we measured the temporal variations in physicochemical factors in these water and sediment samples. A comparison of water quality data between HF and PP revealed that HF effectively reduced the total nitrogen (TN) and total phosphorus (TP) levels in the polyculture ponds. Furthermore, Diatomea and Ciliophora were the predominant phyla in all samples. In the horizontal-flow water samples, significant alterations were observed over time in Skeletonema, Strombidium, and Gyrodinium genera. The dynamic pattern of the genus in the polyculture pond water (PPW) was similar to that in the horizontal flow water (HFW). Furthermore, Skeletonema abundance decreased over time in the horizontal flow sediment (HFS). Skeletonema and Cyclotella were dominant in polyculture pond sediment (PPS). There was a certain degree of community succession throughout the experiment in the HFW and PPW, but not in the HFS or PPS. Correlation analysis revealed that water temperature (WT), salinity(SAL)，dissolved oxygen (DO), pH, phosphate, and silicate played key roles in driving variations in the protist community. These findings contribute to our understanding of complex protist community dynamics within the HF-PP aquaculture model, shedding light on the roles of various environmental factors in shaping protist communities and water quality.

Enhancing anaerobic digestion of food waste for biogas production: Impact of graphene nanoparticles and multiwalled nanotubes on direct interspecies electron transfer mechanism

The present research investigated the effect of two carbonaceous materials, multiwalled carbon nanotubes (MWCNTs), and graphene nanoparticles (GNPs), on biogas yield from food waste (FW) in an anaerobic digestion system for 30 days. Lab scale investigations were conducted in batch mode in 250 mL glass reactor bottles and the findings were compared to the control reactor. The performance of the experimental procedure was assessed in terms of biogas output and organic matter reduction. The addition of 100 mg/L multiwalled carbon nanotubes and 100 mg/L GNPs increased the cumulative biogas production (33.55 % and 81.16 %, respectively) while decreasing the total solid content (about 25.95 % and 24.95 %, respectively). However, increasing the concentration of both carbon nanomaterials from 100 mg/L to 500 mg/L reduced the total biogas production compared to the control, which can be attributed to cytotoxic effects. A microbial diversity study was performed using 16S amplicon sequencing to understand the changes occurring in the microbial ecology. The predominant phyla found during diversity analysis were Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota. Finally, addition of carbonaceous nanomaterials to the anaerobic reactors favours organic matter degradation through the DIET mechanism. It improves the biogas production kinetics and productivity during the anaerobic digestion of FW up to a certain dose.

PSI-30 Effects of high canola meal diet with acidifiers supplementation on cecal microbiota of nursery pigs

Abstract Inclusion of canola meal (CM) in swine diets is typically limited stemming from the presence of glucosinolates (Gls), which can reduce growth performance and cause thyroid dysfunction in nursery pigs. While certain members of hindgut bacterial communities are capable of degrading dietary Gls, which would mitigate their detrimental effects, they have yet to be identified. Moreover, lowering the pH in the hindgut of the pig can break down Gls into less toxic compounds, potentially reducing harm. Thus, this study aimed to characterize major bacterial species populating the hindgut of nursery pigs fed a high CM diet supplemented with acidifier and encapsulated butyrate. A total of 315 nursery pigs weaned at 21 d old, average body weight (BW) 6.0 ± 1.2 kg, were assigned to one of five dietary treatments with 9 replicate pens (7 pigs/pen) in a randomized complete block design. The dietary treatments included PC: a corn-soybean meal-based diet with 20% CM, NC: a corn-soybean meal-based diet with 40% CM, NC+A: NC diet supplemented with an acidifier at 1,500 ppm, NC+B: NC diet supplemented with encapsulated butyrate at 500 ppm, and NC+A+B: NC diet supplemented with both an acidifier and encapsulated butyrate. All diets were formulated to meet or exceed the nutrient requirements of NRC (2012). At the end of the feeding trial (6 wk), one pig from each pen was euthanized to collect fresh cecal digesta. Samples were analyzed using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. A comparative analysis of the highly represented taxonomic groups and operational taxonomic units (OTU) using non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified candidate bacterial groups or species enriched across different diets. Bacillota was the predominant phylum across all diets, ranging from 83.2% to 86.3%. At the genus level, Lachnospiracea incertae sedis was less abundant in the NC diets with acidifier (Acidifier effect, P < 0.05), whereas Dialister was less in the NC diets with encapsulated butyrate (Butyrate effect, P < 0.05). The OTU Ssd-00001 (Lactobacillus amylovorus, 99.6%) tended to be greater in the cecal microbiota of pigs fed the NC diets with acidifier (Acidifier effect, P = 0.09). Interestingly, OTU Ssd-00188 (Agathobacter rectalis, 99.2%) tended to be higher in PC diet than in NC diet (P = 0.06), while its abundance was less in the cecal microbiota of pigs fed the NC diets with acidifier (Acidifier effect, P = 0.09). In conclusion, these results provide valuable insights into the microbiome of pigs fed high CM diets. Understanding the interplay between microbial communities and high CM diet with acidifier supplementation is crucial for optimizing swine diets and mitigating challenges associated with the antinutritional effects of dietary Gls from CM.

Evaluation of corn fermented protein (CFP) on the fecal microbiome of cats.

Co-products from the ethanol industry, such as distillers dried grains with solubles (DDGS), can provide alternative protein sources for pet food. Corn fermented protein (CFP) is produced using post-fermentation technology to split the protein and yeast from fiber prior to drying. This results in a higher protein ingredient compared to DDGS, increasing its appeal for pet food. In addition, the substantial yeast component, at approximately 20-25%, may promote gut health through modulation of the microbiome and the production of short chain fatty acids. Therefore, the objective of this study was to determine the effect of CFP on the fecal microbiome of cats. The four experimental diets included a control with no yeast (T1) and diets containing either 3.5% brewer's dried yeast (T2), 2.5% brewer's dried yeast plus 17.5% DDGS (T3), or 17.5% CFP (T4). All diets except T1 were formulated to contain 3.5% yeast. Diets were fed to adult cats (n = 11) in an incomplete 4 x 4 replicated Latin square design. Cats were adapted to diet for 9 days followed by a 5-d total fecal collection. During each collection period, fresh fecal samples from each cat were collected and stored at -80°C until analysis. Fresh fecal samples (n = 44) were analyzed by 16S rRNA gene sequencing. Raw sequences were processed through Mothur (v.1.44.1). Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance was analyzed within the 50 most abundant operational taxonomic units (OTU) using a mixed model of SAS (v9.4, SAS Institute, Inc., Cary, NC). Diet was the fixed effect and cat and period were random effects. Results were considered significant at P < 0.05. Alpha-diversity indices (Observed, Chao1, Shannon, Simpson) and beta-diversity metric (principal coordinate analysis) were similar for all treatments. Predominant phyla were Firmicutes (66%), Bacteroidetes (25%), Actinobacteria (8%), Proteobacteria (0.64%), and Desulfobacteria (0.54%). The relative abundance of Firmicutes and Actinobacteria was lower (P < 0.05) for T3 compared to T4 and T2, respectively. On a more specific phylogenic level, 17 genera resulted in differences (P < 0.05) among dietary treatments. Overall, this data indicates that compared to traditional yeast and distillers dried grains, CFP did not alter the overall diversity of the fecal microbiome of healthy adult cats over a 14-d period.

PSIX-2 Skin microbial compositions differ among dog body sites and are affected by dietary probiotics

Abstract The study aimed to characterize the skin microbiota across four distinct body sites and investigate the impact of dietary probiotics on the skin microbiota of healthy adult dogs. Healthy adult dogs [n = 60; mean age = 6.2 ± 2.8 yr; mean body weight (BW) = 13.1 ± 4.0 kg] were randomly assigned into three treatment groups and fed for 60 d: a control kibble diet (CON; n = 20; 29.0% crude protein, 10.1% crude fat, 9.9% crude fiber, 7.1% ash, as-fed), CON supplemented with Bifidobacterium longum 548 (CON-B; n = 20), or CON supplemented with Bifidobacterium longum 548 and Lactobacillus rhamnosus 451 (CON-B-L; n = 20). All dogs were individually housed in a temperature- and humidity-controlled research facility. Protocols were approved by the facility’s Institutional Animal Care and Use Committee before the study. On d 60, skin swab samples were collected from the dorsal lumbar area, right axilla, right groin, and right ear concave pinnae of each dog using sterile swabs. These samples were placed into bead tubes and stored at -20°C until analysis. DNA extraction from skin swab samples was followed by sequencing the V4 region of 16S rRNA using Illumina sequencing on a MiSiq. Sequence data were processed through QIIME 2.0, and statistical analysis was performed using R 4.3.1. to test differences between body sites and diets, with a significance threshold set at P &amp;lt; 0.05. The predominant bacterial phyla observed across all body sites were Actinobacteria (40 ± 21.7%), Firmicutes (31.2 ± 17.9 %), Proteobacteria (17.9 ± 13.3%), and Bacteroidetes (6.6 ± 6.1%). Additionally, Acidobacteria, Gemmatimonadetes, and Verrucomicrobia were exclusive to the groin region. Considering data from all body sites, diets affected relative abundances of phyla and genera in dogs. At phylum level, dogs fed the CON-B diet displayed greater (P &amp;lt; 0.05) relative abundance of Actinobacteria compared with those on the CON diet. The CON-B diet also resulted in a greater (P &amp;lt; 0.05) relative abundance of Firmicutes than dogs on either the CON or CON-B-L diets. At genus level, dogs on the CON-B diet showed significantly greater (P &amp;lt; 0.05) relative abundance of Clostridium, Clostridiaceae unclassified, and Lachnospiraceae unclassified compared with the other diet groups. Dogs on the CON diet displayed a greater (P &amp;lt; 0.05) relative abundance of Dietzia compared with those on probiotic-supplemented diets. These findings underscore the variation in skin microbial composition across distinct body sites, contributing valuable data to limited information available on the skin microbiota of dogs. Moreover, consumption of probiotic influenced the skin microbial compositions in dogs, which warrant further studies to elucidate the relationship between probiotics, skin microbiota, and skin health in dogs.

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii.

Amphibians face the threat of decline and extinction, and their health is crucially affected by the microbiota. Their health and ecological adaptability essentially depend on the diverse microbial communities that are shaped by unique host traits and environmental factors. However, there is still limited research on this topic. In this study, cutaneous (C) and gut (G) microbiota in Rana amurensis (A) and R. dybowskii (D) was analyzed through 16S amplicon sequencing. Groups AC and DC significantly differed in alpha diversity, while the gut groups (AG and DG) showed no such differences. Analyses of Bray-Curtis dissimilarity matrix and unweighted UniFrac distances showed significant differences in cutaneous microbiota between groups AC and DC, but not between groups AG and DG. Stochastic processes significantly influenced the assembly of cutaneous and gut microbiota in amphibians, with a notably higher species dispersal rate in the gut. The predominant phyla in the skin of R. amurensis and R. dybowskii were Bacteroidetes and Proteobacteria, respectively, with significant variations in Bacteroidota. Contrarily, the gut microbiota of both species was dominated by Firmicutes, Proteobacteria, and Bacteroidetes, without significant phylum-level differences. Linear discriminant analysis effect size (LEfSe) analysis identified distinct microbial enrichment in each group. Predictive analysis using phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) revealed the significant functional pathways associated with the microbiota, which indicates their potential roles in immune system function, development, regeneration, and response to infectious diseases. This research underscores the critical impact of both host and environmental factors in shaping amphibian microbial ecosystems and emphasizes the need for further studies to explore these complex interactions for conservation efforts.

Bacterial Communities within the Freshwater Lymnaeid Snail Kamtschaticana kamtschatica (Middendorff, 1850) in Northeastern Siberia

This is the first report on microbial communities associated with the freshwater snail Kamtschaticana kamtschatica inhabiting diverse types of water basins in Eastern Siberia and the Russian Far East. Using metabarcoding data based on the 16S rRNA gene fragments, taxonomic profiling of bacterial communities associated with snails from three basins of the Magadan Oblast was carried out. Predominant phyla in the studied bacterial communities were Pseudomonadota, Bacillota, Cyanobacteriota, Actinomycetota, Verrucomicrobiota, Planctomycetota, and Bacteroidota. The highest alpha-diversity, according to the Chao1 index, was revealed in the mollusks from the Orotukan reservoir. The relative abundance of bacteria of the genera Snowella, Leptolyngbya, Nodosilinea, Arenimonas, and Polaromonas significantly distinguished the mollusks of this habitat from those of the other two. The greatest similarities in the composition of the microbiota in K. kamtschatica were found for the genus Pseudomonas, which was present in the majority of samples in the amount of more than 1% and was not found in the sediment samples. Obtained data on the diversity and composition of bacterial communities associated with lymnaeid snails are of fundamental importance for the ecology of freshwater mollusks.

Isolation and comparative analysis of culturable bacterial communities associated with life stages, breeding and rearing substrates of Culicoides oxystoma Kieffer (Diptera: Ceratopogonidae) vector of bluetongue virus.

Culicoides oxystoma Kieffer (Diptera: Ceratopogonidae) has been vectoring several arboviruses, protozoa and nematodes, leading to mortality and morbidity of livestock and wild ruminants in the tropics and subtropics. Insight into the bacterial communities associated with the vector species must be worked out. This work tries to inventorize the bacterial communities associated with this important vector species. Acquisition of gut microbiota may be the parental origin, while some are obtained through feeding during larval stages. Culicoides oxystoma possesses semi-aquatic life cycle strategies for egg-laying and larval survival. The bacteria associated with C. oxystoma were compared throughout (i) life stages: egg, larval instars, pupa, adult: male and female obtained from laboratory colony; (ii) field-collected adult: male and age-graded females; and (iii) natural breeding substrate and artificial rearing substrate. The culture-dependent bacteria were identified by Sanger sequencing of 16S rRNA, and haemolytic bacteria were screened on blood agar. Results show that Firmicutes and Proteobacteria are the predominant Phyla, of which Bacillus spp. was the most abundant across the life stages. Across the life history, Bacillus cereus, Bacillus pumilus, Bacillus tropicus, Lysinibacillus sp. and Paenibacillus sp. were retrieved routinely. Bacillus cereus and Alcaligenes faecalis were detected in the lab-reared specimens and shared between the natural breeding site and rearing medium. From the adults trapped across two locations, B. cereus, Bacillus flexus, A. faecalis, Enterococcus faecium and Pseudomonas sp. were isolated. The bacterial species associated with this vector may influence various physiological traits, such as vectorial capacity, digestion and larval development, which need further investigation.

Soil Solarization Efficiently Reduces Fungal Soilborne Pathogen Populations, Promotes Lettuce Plant Growth, and Affects the Soil Bacterial Community.

Lettuce is the most cultivated leafy vegetable in Greece; however, due to the adopted intensive cropping system, its cultivation is susceptible to many soilborne pathogens that cause significant yield and quality losses. In the current study, the impact of various soil disinfestation methods such as solarization, chemical disinfestation, and application of a biofungicide were evaluated in a commercial field that has been repeatedly used for lettuce cultivation. The populations of soilborne pathogens Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Fusarium equiseti were measured via qPCR before and after the implementation of the specific disinfestation methods. Although all the tested methods significantly reduced the population of the four soilborne pathogens, soil solarization was the most effective one. In addition, solarization reduced the number of lettuce plants affected by the pathogens R. solani and F. equiseti, and at the same time, significantly influenced the growth of lettuce plants. Amplicon sequence analysis of 16S rRNA-encoding genes used to study the soil bacterial community structure showed that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla in soil samples. In general, solarization had positive effects on Firmicutes and negative effects on Proteobacteria and Actinobacteria; soil fumigation with dazomet increased the relative abundance of Firmicutes and Proteobacteria and reduced the corresponding values of Actinobacteria; and biofungicide had no significant effects on the three predominant bacterial phyla. The bacterial community composition and structure varied after the application of the soil disinfestation treatments since they imposed changes in the α- and β-diversity levels. The results of this study are expected to contribute towards implementing the most effective control method against the most common soilborne pathogens in intensively cultivated fields, such as those cultivated with leafy vegetables.

Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests.

Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems.

Microbiome and mycobiome analyses in continuous positive airway pressure devices.

Microorganisms are likely present in continuous positive airway pressure (CPAP) devices used daily. Considering the potential risk of infections among CPAP device users, here we aimed to compare the microbiomes in CPAP devices with those in nasal mucosal samples obtained from corresponding individuals using these devices. We conducted a prospective cohort study at tertiary medical institutes. Samples were collected from the tubes and filters of CPAP devices and the nasal mucosa of corresponding individuals using these devices. Microbiomes and mycobiomes were analyzed using 16S ribosomal RNA and internal transcribed spacer region sequencing. Results were compared according to the sampling site and usage duration for each patient. Overall, 27 paired human nasal mucosa and CPAP samples were analyzed. Bacteria were present in 7 of 27 tubes (29.6%) and 22 of 27 filters (81.5%). Fungi were present in 2 of the 27 tubes (7.4%) and 16 of the 27 filters (59.3%). Actinobacteria and Firmicutes were the predominant phyla among all samples. Fungi were not detected in any of the nasal mucosal samples. However, Basidiomycota and Ascomycota were predominant in the CPAP filters and tube samples. No significant associations were identified among the results according to sampling site and usage duration. Bacteria or fungi can be detected to some extent in CPAP samples even if the CPAP usage period is short. The association between respiratory infections and these microbiomes or mycobiomes was not investigated. Further research might be required to determine the risk posed by CPAP devices as a microbial contamination source.

Variation on gut microbiota diversity of endangered red pandas (Ailurus fulgens) living in captivity acrosss geographical latitudes.

The gut microbiome plays important roles in metabolic and immune system related to the health of host. This study applied non-invasive sampling and 16S rDNA high-throughput sequencing to study the gut microbiota structure of red pandas (Ailurus fulgens) for the first time under different geographical latitudes in captivity. The results showed that the two predominant phyla Firmicutes (59.30%) and Proteobacteria (38.58%) constituted 97.88% of the total microbiota in all the fecal samples from north group (red pandas from Tianjin Zoo and Jinan Zoo) and south group (red pandas from Nanjing Hongshan Forest Zoo). The relative abundance of Cyanobacteria in north group was significantly higher than that in south group. At the genus level, Escherichia-Shigella (24.82%) and Clostridium_sensu_stricto_1 (23.00%) were common dominant genera. The relative abundance of norank_f__norank_o__Chloroplast, Terrisporobacter and Anaeroplasma from south group was significantly higher than that of north group. Alpha and Beta analysis consistently showed significant differences between north group and south group, however, the main functions of intestinal microbiota were basically the same, which play an important role in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in different environments, and amino acid biosynthesis. The variations in gut microbiota between the northern and southern populations of the same species, both kept in captivity, which are primarily driven by significant differences in climate and diet. These findings provide a deeper understanding of the gut microbiota in red pandas and have important implications for their conservation, particularly in optimizing diet and environmental conditions in captivity.

Impacts of Solidago canadensis and Erigeron canadensis co‐invasion on soil microbial communities

AbstractInvasive plants disrupt the structure and function of ecosystems, causing a decline in their diversity. The coexistence of Solidago canadensis and Erigeron canadensis within shared habitats is a common phenomenon, and the frequent occurrence of co‐invasion has substantial implications for ecosystems. However, the effects of the co‐invasion of two plants on the soil ecosystem across varying degrees of invasion remain uninvestigated. Therefore, we investigated how the co‐invasion of S. canadensis and E. canadensis affects soil physiochemical properties and microorganisms across various degrees of invasion. The invaded regions exhibited significantly lower soil moisture content and pH values than those in the uninvaded areas (p &lt; .05). Additionally, co‐invasion resulted in higher soil organic matter (OM), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) contents compared to single invasion by E. canadensis. Furthermore, the invaded regions exhibited a greater diversity of soil bacterial and fungal communities than the uninvaded regions. Under diverse invasion conditions, Actinobacteria and Ascomycota emerged as the predominant phyla of soil bacteria and fungi, respectively, leading to a shift in the soil microbial community structure. Moreover, homogenizing dispersal significantly influenced bacterial community succession, while ecological drift influenced the progression of fungal communities. Using structural equation modeling, this study established significant correlations between soil properties (pH, TN, and nitrate nitrogen) and bacterial interactions (diversity and community assembly) relative to microbial composition. This study revealed the influence of S. canadensis and E. canadensis co‐invasion on soil microbial communities, thereby contributing a theoretical framework delineating the impact of these two invasive plant species.