Dominance of Fructose-Associated Fructobacillus in the Gut Microbiome of Bumblebees (Bombus terrestris) Inhabiting Natural Forest Meadows

Bumblebees are key pollinators in agricultural landscapes. However, little is known about how gut microbial communities respond to anthropogenic changes. We used commercially produced colonies of buff-tailed bumblebees (Bombus terrestris) placed in three habitats. Whole guts (midgut, hindgut, and rectum) of B. terrestris specimens were dissected from the body and analyzed using 16S phylogenetic community analysis. We observed significantly different bacterial community composition between the agricultural landscapes (apple orchards and oilseed rape (Brassica napus) fields) and forest meadows, whereas differences in gut communities between the orchards and oilseed rape fields were nonsignificant. Bee-specific bacterial genera such as Lactobacillus, Snodgrassella, and Gilliamella dominated gut communities of B. terrestris specimens. In contrast, the guts of B. terrestris from forest meadows were dominated by fructose-associated Fructobacillus spp. Bacterial communities of workers were the most diverse. At the same time, those of males and young queens were less diverse, possibly reflecting greater exposure to the colony’s inner environment compared to the environment outside the colony, as well as bumblebee age. Our results suggest that habitat quality, exposure to environmental microbes, nectar quality and accessibility, and land use significantly affect gut bacterial composition in B. terrestris.

High peatland methane emissions following permafrost thaw: enhanced acetoclastic methanogenesis during early successional stages

Permafrost thaw in northern peatlands often leads to increased methane (CH4) emissions, but gaps remain in our understanding of the underlying controls responsible for increased emissions and the duration for which they persist. We assessed how shifting ecological conditions affect microbial communities, and the magnitude and stable isotopic signature (δ13C) of CH4 emissions along a thermokarst bog transect in boreal western Canada. Thermokarst bogs develop following permafrost thaw when dry, elevated peat plateaus collapse and become saturated and dominated by Sphagnum mosses. We differentiated between a young and a mature thermokarst bog stage (~30 and years ~200 since thaw, respectively). The young bog located along the thermokarst edge, was wetter, warmer and dominated by hydrophilic vegetation compared to the mature bog. Using 16S rRNA gene high throughput sequencing, we show that microbial communities were distinct near the surface and converged with depth, but lesser differences remained down to the lowest depth (160 cm). Microbial community analysis and δ13C data from CH4 surface emissions and dissolved gas depth profiles show that hydrogenotrophic methanogenesis was the dominant pathway at both sites. However, the young bog was found to have isotopically heavier δ13C-CH4 in both dissolved gases profiles and surface CH4 emissions, suggesting that acetoclastic methanogenesis was relatively more enhanced throughout the young bog peat profile. Furthermore, young bog CH4 emissions were three times greater than the mature bog. Our study suggests that interactions between ecological conditions and methanogenic communities enhance CH4 emissions in young thermokarst bogs, but these favorable conditions only persist for the initial decades after permafrost thaw.

The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection

Background In ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for microbiome analysis, yet variation in their bacterial density—and the clinical and methodologic significance of this variation—remains undetermined. We used an ultra-sensitive quantification approach—droplet digital PCR (ddPCR)—to quantify bacterial density in rectal swabs from 118 hospitalized patients. We compared bacterial density with bacterial community composition (via 16S rRNA amplicon sequencing) and clinical data to determine if variation in bacterial density has methodological, clinical, and prognostic significance. Results Bacterial density in rectal swab specimens was highly variable, spanning five orders of magnitude (1.2 × 104–3.2 × 109 16S rRNA gene copies/sample). Low bacterial density was strongly correlated with the detection of sequencing contamination (Spearman ρ = − 0.95, p < 10−16). Low-density rectal swab communities were dominated by peri-rectal skin bacteria and sequencing contaminants (p < 0.01), suggesting that some variation in bacterial density is explained by sampling variation. Yet bacterial density was also associated with important clinical exposures, conditions, and outcomes. Bacterial density was lower among patients who had received piperacillin-tazobactam (p = 0.017) and increased among patients with multiple medical comorbidities (Charlson score, p = 0.0040) and advanced age (p = 0.043). Bacterial density at the time of hospital admission was independently associated with subsequent extraintestinal infection (p = 0.0028), even when controlled for severity of illness and comorbidities. Conclusions The bacterial density of rectal swabs is highly variable, and this variability is of methodological, clinical, and prognostic significance. Microbiome studies using rectal swabs are vulnerable to sequencing contamination and should include appropriate negative sequencing controls. Among hospitalized patients, gut bacterial density is associated with clinical exposures (antibiotics, comorbidities) and independently predicts infection risk. Bacterial density is an important and under-studied feature of gut microbiome community analysis.

Taqman qPCR Quantification and Fusarium Community Analysis to Evaluate Toxigenic Fungi in Cereals

Fusarium head blight (FHB) is an economically important plant disease. Some Fusarium species produce mycotoxins that cause food safety concerns for both humans and animals. One especially important mycotoxin-producing fungus causing FHB is Fusarium graminearum. However, Fusarium species form a disease complex where different Fusarium species co-occur in the infected cereals. Effective management strategies for FHB are needed. Development of the management tools requires information about the diversity and abundance of the whole Fusarium community. Molecular quantification assays for detecting individual Fusarium species and subgroups exist, but a method for the detection and quantification of the whole Fusarium group is still lacking. In this study, a new TaqMan-based qPCR method (FusE) targeting the Fusarium-specific elongation factor region (EF1α) was developed for the detection and quantification of Fusarium spp. The FusE method was proven as a sensitive method with a detection limit of 1 pg of Fusarium DNA. Fusarium abundance results from oat samples correlated significantly with deoxynivalenol (DON) toxin content. In addition, the whole Fusarium community in Finnish oat samples was characterized with a new metabarcoding method. A shift from F. culmorum to F. graminearum in FHB-infected oats has been detected in Europe, and the results of this study confirm that. These new molecular methods can be applied in the assessment of the Fusarium community and mycotoxin risk in cereals. Knowledge gained from the Fusarium community analyses can be applied in developing and selecting effective management strategies for FHB.

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.

ENVIRONMENTAL PERFORMANCE OF MICROBIAL FUEL CELL BASED LIVE SLUDGE FOR VOLTAGE PRODUCTION AND CONGO RED DYE REMOVAL

: In this work, Single chamber Microbial fuel cells (SCMFCs) are a versatile technology is depends on the interaction mechanisms of bacteria, to produce bioelectricity simultaneously and treat Congo red (CR) dye from aqueous solution at different pH (6.5-8). Electricity generation from the biodegradable organic substrate (sucrose) accompanied by decolorization of azo dye was investigated in the batch test results showed that more than 99% decolorization demonstrated at UV-Visible Spectrophotometer (500 nm) was achieved within 20 days and maximum output voltage (889 mv) had been obtained in an open circuit at a pH value of 7.5. Microbial community analysis showed that species in live sludge and the impact of bacteria grown on removal and voltage.