Predominant Genera Research Articles

Comparison of Fecal Microbiota and Metabolites Between Captive and Grazing Male Reindeer

The reindeer (Rangifer tarandus) is a circumpolar member of the Cervidae family, and has adapted to a harsh environment. Summer is a critical period for reindeer, with peak digestibility facilitating body fat accumulation. The gut microbiota plays a pivotal role in nutrient metabolism, and is affected by captivity. However, differences in the composition of the gut microbiota and metabolites between captive and grazing reindeer during summer remain poorly understood. Here, we conducted a comparative study of the fecal microbiota and metabolites between captive (n = 6) and grazing (n = 6) male reindeer, using full-length 16S rRNA gene sequencing and gas chromatography–time-of-flight mass spectrometry, respectively. Our results indicated that Prevotella, Phocaeicola, Papillibacter, Muribaculum, and Bacteroides were the predominant genera in the feces of reindeer. However, microbial diversity was significantly higher in captive reindeer compared to their grazing counterparts. Principal coordinate analysis revealed significant differences in the fecal microbiota between captive and grazing reindeer. In captive reindeer, the relative abundances of the genera Clostridium, Paraprevotella, Alistipes, Paludibacter, Lentimicrobium, Paraclostridium, and Anaerovibrio were significantly higher, while those of the genera Prevotella, Phocaeicola, Pseudoflavonifractor, and Lactonifactor were significantly lower. A comparison of predicted functions indicated that pathways involved in fat digestion and absorption, histidine metabolism, lysine biosynthesis, and secondary bile acid biosynthesis were more abundant in captive reindeer, whereas the pathways of fructose and mannose metabolism and propanoate metabolism were less abundant. An untargeted metabolomic analysis revealed that 624 metabolites (e.g., amino acids, lipids, fatty acids, and bile acids) and 645 metabolites (e.g., carbohydrates and purines) were significantly increased in the feces of captive and grazing reindeer, respectively. In conclusion, we unveiled significant differences in fecal microbiota and metabolites between captive and grazing male reindeer, with the results suggesting a potentially enhanced ability to utilize plant fibers in grazing reindeer.

Molecular identification of Fusarium species in commercial vanilla and crop wild relatives in Colombia.

Vanilla is an economically important crop for low-lying humid tropical regions, but cultivated plants face serious phytosanitary problems. Fusarium wilt is a devastating disease affecting vanilla crops, caused by the fungal pathogens Fusarium oxysporum f. sp. vanillae (Fov) and F. oxysporum f. sp. radicis-vanillae (Forv), part of the F. oxysporum species complex (FOSC). We characterized 29 fungal isolates from a vanilla crop and crop wild relatives (CWR) using molecular (EF1-α and ITS-rRNA loci) and morphological traits. Fusarium was the predominant genus, followed by Colletotrichum and Clonostachys. Four Fusarium species were identified: F. oxysporum (37.9%), Fusarium solani (20.7%), Fusarium pseudocircinatum (13.8%) and Fusarium concentricum (10.3%). The latter three species were isolated only from CWR and may represent latent pathogens. Fov was isolated from both the crop and CWR, while a Forv-affiliated isolate was also found in a vanilla crop, marking the first report in the neotropical region. The EF1-α locus provided greater genotype resolution, as well as having reference sequences for Forv. However, the fungal barcode ITS locus is widely applied. We recommend the continued use of both loci for Fusarium diagnosis in vanilla to facilitate early detection and the development of effective integrated crop management strategies.

The addition of humic acid into soil contaminated with microplastics enhanced the growth of black gram (Vigna mungo L. Hepper) and modified the rhizosphere microbial community.

Microplastics have polluted agricultural soils, posing a substantial risk to crop productivity. Moreover, the presence of microplastic pollution has caused a disturbance in the composition of the microbial community in the soil surrounding plant roots, therefore impacting the growth of beneficial bacteria. A study was conducted to examine if humic acid (HA) can counteract the harmful effects of microplastics (MPs) on the growth of black gram crops and the composition of the rhizosphere soil microbial community, to reduce the negative impacts of microplastics on these microorganisms and crops. The research was carried out using mud pots and the plastic utilized for the experiment consisted of 60% high-density polyethylene (HDPE) and 40% polypropylene (PP). The soil was enriched with lignite-based potassium humate, which had a pH range of 8.0-9.5 and with 65% humic acid. The experiment consisted of six treatments: T1, which served as the control without HA and MP; T2, which involved the use of HA at a concentration of 0.15% w/w; T3, which involved the use of MP at a concentration of 0.2% w/w; T4, which involved the use of MP at a concentration of 0.4% w/w; T5, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.2% w/w; and T6, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.4% w/w. The plant growth characteristics, including germination percentage, nodule number, and chlorophyll content, were measured. In addition, the DNA obtained from the rhizosphere soil was analyzed using metagenomics techniques to investigate the organization of the microbial population. Seedlings in soil polluted with MP exhibited delayed germination compared to seedlings in uncontaminated soil. Following 60days of growth, the soil samples treated with T5 (0.2% MP and 0.15% HA w/w) had the highest population of bacteria and rhizobium, with counts 5.58 ± 0.02 and 4.90 ± 0.02CFUg-1 soil. The plants cultivated in T5 had the most elevated chlorophyll-a concentration (1.340 ± 0.06mgg-1), and chlorophyll-b concentration (0.62 ± 0.02mgg-1) while those cultivated in T3 displayed the lowest concentration of chlorophyll-a (0.59 ± 0.02mgg-1) and chlorophyll-b (0.21 ± 0.04mgg-1). Within the phylum, Proteobacteria had the highest prevalence in all treatments. However, when the soil was polluted with MPs, its relative abundance was reduced by 8.4% compared to the control treatment (T1). Conversely, treatment T5 had a 3.76% rise in relative abundance when compared to treatment T3. The predominant taxa found in soil polluted with MP were Sphingomonas and Bacillus, accounting for 19.3% of the total. Sphingomonas was the predominant genus (21.2%) in soil polluted with MP and supplemented with humic acid. Humic acid can be used as a soil amendment to mitigate the negative effects of MPs and enhance their positive advantages. Research has demonstrated that incorporating humic acid into soil is a viable method for maintaining the long-term integrity of soil's physical, chemical, and biological characteristics.

The role of genus Bacillus in biodegradation of microcystins: Implications for the removal of cyanotoxins from tropical freshwaters

AbstractThe proliferation of harmful cyanobacterial blooms poses a threat to the ecosystem and human health. Microcystins (MCs) are the most frequently detected cyanotoxin released by cyanobacteria, including Microcystis sp. Our study aimed to isolate potential MC‐degrading bacteria in Sri Lankan freshwater and determine their possible MC‐degradation pathways. Twenty‐two morphologically distinct bacterial strains from 13 freshwater bodies were isolated following the enrichment assay. MC‐biodegradation assays further confirmed the MC‐degradation potential of 21 strains, with Bacillus being the predominant genus. The strain Bacillus altitudinis BL1, isolated from Beira Lake, showed the highest efficiency in Microcystis sp. cell lysis (80%) and MC‐degradation (87%). PCR assay results confirmed the absence of mlrABCD genes in all strains, indicating the presence of uncharacterized alternative MC‐degradation mechanisms that require further exploration. The dual functions of Microcystis sp. cell lysis and MC‐degradation in 21 strains support developing efficient bacteria‐mediated strategies to remediate microcystins and eradicate Microcystis‐blooms in tropical freshwaters.

Fermentation Profile, Bacterial Community Structure, Co-Occurrence Networks, and Their Predicted Functionality and Pathogenic Risk in High-Moisture Italian Ryegrass Silage

This study aimed to assess the fermentation characteristics, bacterial community structure, co-occurrence networks, and their predicted functionality and pathogenic risk in high-moisture Italian ryegrass (IR; Lolium multiflorum Lam.) silage. The IR harvested at heading stage (208 g dry matter (DM)/kg fresh weight) was spontaneously ensiled in plastic silos (10 L scale). Triplicated silos were opened after 1, 3, 7, 15, 30, and 60 days of fermentation, respectively. The bacterial community structure on days 3 and 60 were investigated using high-throughput sequencing technology, and 16S rRNA-gene predicted functionality and phenotypes were determined by PICRUSt2 and BugBase tools, respectively. After 60 days, the IR silage exhibited good ensiling characteristics indicated by large amounts of acetic acid (~58.7 g/kg DM) and lactic acid (~91.5 g/kg DM), relatively low pH (~4.20), acceptable levels of ammonia nitrogen (~87.0 g/kg total nitrogen), and trace amounts of butyric acid (~1.59 g/kg DM). Psychrobacter was prevalent in fresh IR, and Lactobacillus became the most predominant genus after 3 and 60 days. The ensilage process reduced the complexity of the bacterial community networks in IR silage. The bacterial functional pathways in fresh and ensilaged IR are primarily characterized by the metabolism of carbohydrate and amino acid. The pyruvate kinase and 1-phosphofructokinase were critical in promoting lactic acid fermentation. A greater (p < 0.01) abundance of the “potentially pathogenic” label was noticed in the bacterial communities of ensiled IR than fresh IR. Altogether, the findings indicated that the high-moisture IR silage exhibited good ensiling characteristics, but the potential for microbial contamination and pathogens still remained after ensiling.

Effects of simulated low-temperature thermal remediation on the microbial community of a tropical creosote contaminated soil.

In the search for more sustainable remediation strategies for PAH-contaminated soils, an integrated application of thermal remediation and bioremediation (TEB) may allow the use of less impacting temperatures by associating heating to biological degradation. However, the influence of heating on soil microbiota remains poorly understood, especially in soils from tropical regions. This work investigated the effects of low-temperature heating on creosote-contaminated soil bacteria. We used culture-dependent and 16S rRNA sequencing methods to compare the microbial community of soil samples heated to 60 and 100 oC for 1h in microcosms. Heating to 60°C reduced the density of cultivable heterotrophic bacteria compared to control soil (p < 0.05), and exposure to 100°C inactivated the viable heterotrophic community. Burkholderia-Caballeronia-Paraburkholderia (BCP) group and Sphingobium were the predominant genera. Temperature and incubation time affected the Bray-Curtis dissimilarity index (p < 0.05). At 60°C and 30 days incubation, the relative abundance of Sphingobium decreased and BCP increased dominance. The network of heated soil after 30 days of incubation showed fewer nodes and edges but maintained its density and complexity. Both main genera are associated with PAH degradation, suggesting functional redundancy and a likely potential of soil microbiota to maintain biodegradation ability after exposure to higher temperatures. We concluded that TEB can be considered as a potential strategy to bioremediate creosote-contaminated soils, allowing biodegradation in temperature ranges where thermal remediation does not completely remove contaminants. However, we recommend further research to determine degradation rates with this technology.

Analysis of fungal diversity in the feces of Arborophila rufipectus.

Intestinal fungal composition plays a crucial role in modulating host health, and thus is of great significance in the conservation of endangered bird species. However, research on gut fungal composition in birds is limited. Therefore, in this study, we aimed to examine gut fungal community and potential fecal pathogen composition in wild Arborophila rufipectus. Fecal samples were collected from the habitats of wild A. rufipectus and Lophura nycthemera (a widely distributed species belonging to the same family as A. rufipectus) in summer and autumn. Thereafter, RNA was collected and the internal transcribed spacer rRNA gene was sequenced via high-throughput sequencing to investigate seasonal variations in intestinal core fungi, microbial fungi, and potential pathogenic fungi. The gut microbiota of A. rufipectus and L. nycthemera were highly similar and mainly consisted of three phyla, Ascomycota (58.46%), Basidiomycota (28.80%), and Zygomycota (3.56%), which accounted for 90.82% of the fungal community in all the samples. Further, the predominant genera were Ascomycota_unclassified (12.24%), Fungi_unclassified (8.37%), Davidiella (5.18%), Helotiales_unclassified (2.76%), Wickerhamomyces (1.84%), and Pleosporales_unclassified (1.14%), and the potential fecal pathogens identified included Candida, Cryptococcus, Trichosporon, and Malassezia. Our results provide evidence that the diversity of intestinal fungi in the endangered species, A. rufipectus, is similar to that in the common species, L. nycthemera, and may serve as a basis for monitoring the status of A. rufipectus and for developing conservation measures.

Assessment of Fungal and Contamination of Ochratoxin A and Patulin in Foods Susceptible to Contamination in the Yangzhou Market, China

The conducive conditions of warm and humid climates can facilitate mold proliferation and subsequent mycotoxin production during food processing and distribution, thereby posing a potential risk to consumer health. However, there exists a significant lack of research regarding the diversity of molds and the presence of ochratoxin A (OTA) and patulin (PAT) in food products available in the Yangzhou market. This study was conducted to assess OTA contamination levels and fungal presence in 57 cereal-based food samples, as well as PAT contamination levels and fungal presence in 50 types of foods, including apples, hawthorn berries, pears, and their derivatives. Ochratoxin A (OTA) was detected in 17 out of 57 cereal-based food samples, with concentrations ranging from 0.93 to 32.69 μg/kg. The contamination rate was determined to be 31.48%, and no samples exceeded the established regulatory limits. Furthermore, seven apple products were identified as contaminated with patulin (PAT), exhibiting concentrations between 26.85 and 192.78 μg/kg. Additionally, three food samples derived from hawthorn showed PAT contamination levels ranging from 29.83 to 88.56 μg/kg. Through purification on potato dextrose agar (PDA) medium, observation of colony morphology, and analysis of internal transcribed spacer (ITS) sequences, a total of 35 fungal strains belonging to 13 genera were identified in cereal-based foods. The predominant genera in cereals included Talaromyces, Fusarium, Aspergillus, and Penicillium. Additionally, twelve fungal strains from five genera (Penicillium, Cladosporium, Aureobasidium, Curvularia, and Alternaria) were isolated and identified in fruits and their derivatives. The findings indicate that OTA and PAT toxins are one of the important risk factors that threaten consumer health. Furthermore, the contamination of some other toxigenic strains is also a matter of substantial concern, with potential implications for consumer health.

Fungal communities in three root herbs: Insights and implications

The roots of Astragali Radix (AM), Dioscoreae Rhizome (DR), and Codonopsis Radix (CR) are frequently used in classical tonic formulations and dietary supplements. Given the extended exposure of rhizomes to complex biological environments, it is necessary to investigate the fungal composition of their surface. In this study, the fungal communities in the three root herbs were analyzed by DNA metabarcoding, and an extensive comparison of the fungal diversity at each taxonomic level was carried out. Furthermore, we examined the effects of species, collection site, and processing method on the fungal community. In Astragali Radix and Codonopsis Radix samples, Cladosporium was the predominant genus, with relative abundances of 1.98 %-76.81 % and 1.69 %-85.59 %, respectively. Aspergillus (0.08 %–99.92 %) was the prevailing genus in Dioscoreae Rhizome samples. Meanwhile, a total of 12 potential toxigenic fungi were identified, including Aspergillus restrictus, Fusarium oxysporum, and Penicillium citrinum. Moreover, the variations in fungal diversity and community composition from different collection sites and processing approaches were observed. Linear discriminant analysis effect size indicated significant differences in the relative abundance of genera among the three root herbs. Gibberella and Mucor genera were significantly enriched in Astragali Radix samples, while Yarrowia and Cladosporium genera exhibited significant enrichment in Dioscoreae Rhizome and Codonopsis Radix samples, respectively (p≤0.001). This study presents novel insights into the fungal profiles of three root herbs, thereby providing references for their safe utilization and quality improvement.

The environmental microbial retrieving assessment of cell-processing facilities for cell therapy in a hospital laboratory.

Cell therapy represents a promising treatment modality. A critical component in the production of cell therapy products is maintaining the sterility of cell therapy clean rooms (CTCRs). This study aimed to evaluate the environmental microbial load within CTCRs. We systematically monitored microbial load in CTCRs, following established guidelines. Cultured microbial samples underwent metagenomic sequencing, and alpha and beta diversity analyses, functional annotation, and resistance gene profiling were performed using various bioinformatics tools to assess microbial diversity and function. From November 2023 to January 2024, we collected 42 environmental microbial colony samples from various sources within the CTCR and performed metagenomic sequencing on 39 samples. Alpha diversity analysis revealed no significant differences among surface, settle_plate, and airborne categories, but significant disparities within surface subgroups were revealed. Beta diversity analysis showed notable differences between surface and airborne categories and among surface subgroups. Species distribution analysis identified Bacillus as the predominant genus on surfaces. Functional annotation and resistance gene analysis indicated distinct resistance patterns, with significant variations between subgroups, such as microscopes and transfer windows, and hands and other Grade_B environments. Resistance to hydrogen peroxide was notably higher in the transfer window group. These findings highlight the importance of stringent disinfection protocols and enhanced hand hygiene to maintain sterility in CTCRs. These findings provide valuable insights for implementing effective measures to maintain cleanliness throughout CTCRs. The annotation and study of resistance genes can help rapidly identify methods to control cellular contamination under circumstances of environmental microbial pollution.IMPORTANCEMaintaining the sterility of cell therapy clean rooms (CTCRs) is crucial for the production of safe and effective cell therapy products. Our study systematically evaluated the environmental microbial load within CTCRs, revealing significant microbial diversity and distinct resistance patterns to disinfection methods. These findings underscore the need for stringent disinfection protocols and enhanced hand hygiene practices to ensure CTCR sterility. By identifying key microbial species and their resistance genes, our research provides essential insights into controlling contamination and safeguarding the production environment, ultimately contributing to the reliability and success of cell therapy treatments.

Exploring the effect of lipid loading on acidogenic fermentation of food waste: Insights from microbiome, quorum sensing and carbon metabolic pathway

The high lipid loading in food waste (FW) is widely regarded as one of the main bottlenecks in the traditional anaerobic digestion, but the effect of lipid on FW acidogenic fermentation has been historically ignored. This study attempted to reveal the influence of lipid loading on volatile fatty acids (VFAs) production and the corresponding synthesis mechanisms during FW acidogenic fermentation. The VFAs production reached 27.10 ± 1.00 g COD/L when the lipid loading comprised 25 % of the FW dry weight, increasing by 36.88 % compared to the CK group. Lactobacillus, with a relative abundance of 59.43 %, was the predominant genus under lipid loading. In quorum sensing (QS) system, the relative abundance of luxS that is involved in the biosynthetic pathway of the Autoinducer-2 (AI-2) signal molecule increased from 0.066 % to 0.10 % in the presence of lipid. The relative abundance of Genetic Information Processing increased from 16.36 % to 24.25 % under lipid loading, with up-regulation of Translation and Replication and repair. Lipid loading not only promoted the conversion of acetyl-CoA to acetic acid, as evidenced by a 1.36-fold increase in pta gene abundance, but also concurrently suppressed the consumption of acetic acid, reflected in the 96.83 % and 77.16 % decreases in ALDH and aldB abundance, thus accumulating acetic acid. Carbon emission was also constrained under lipid loading, in which the conversion from formate to CO2 and passing Tricarboxylic acid (TCA) cycle were restricted over 60 %. Together, lipid loading in FW represents a potential strategy for enhancing VFAs production in FW acidogenic fermentation.

Biodeterioration Risk Assessment in Libraries by Airborne Fungal Spores.

Fungal growth on cellulose-based materials in libraries can have detrimental effects on books and documents. This biodeterioration affects their physical, chemical, and esthetical characteristics. Thus, this work aimed to assess fungal aerosols' concentrations and biodeterioration risk in two public libraries with artificial ventilation: the Banco de la República and CAJAMAG libraries. Air sampling was performed using a two-stage viable Andersen cascade impactor with Sabouraud dextrose agar at 4% on Petri dishes. Also, the temperature and relative humidity were measured with a digital thermo-hygrometer HOBO U12 Data Logger. The concentrations were low, with values of around 35 CFU/m3. Aspergillus, Cladosporium, and Penicillium were the predominant genera in the two libraries, with A. niger being the most abundant species. The thermo-hygrometric conditions inside the libraries were stable, with a mean temperature of 25.2 °C and a mean relative humidity of 52.1%. The calculated potential risk associated with fungal aerosols was seen to be medium in both libraries, where Aspergillus genera reported the highest cellulosic activity and hence had a higher risk of biodeterioration.

Exploring the impacts of steroid estrogens load and aeration intensity on the performance, membrane fouling characteristics, and bacterial community structure of the anoxic-oxic membrane bioreactor

Steroid estrogens (SEs) are typical endocrine-disrupting compounds, and they are inadequately eliminated in most wastewater treatment plants (WWTPs), contributing significantly to their environmental prevalence. In an effort to optimize the performance of membrane bioreactor (MBR) in mitigating SEs alike micropollutants, this study investigated the influences of influent loads of three typical SEs (estrone (E1), 17β-estradiol (E2), and 17α-ethynyestradiol (EE2)) and the aeration intensity on the pollutants removal performance, membrane fouling characteristics, and bacterial community structure in a lab-scale anoxic/oxic-MBR (A/O-MBR) process. The presence of SEs shed minimal impacts on the performance of A/O-MBR process as indicated by conventional water quality parameters due to gradual microbial acclimation. However, the presence and the rising input of SEs accelerated membrane fouling as a result of the enhanced EPS excretion and PN/PS ratio and the reduced floc size. The moderate aeration intensity was preferred from the perspectives of conventional pollutants removal, SEs biodegradation, biomass accumulation, and membrane fouling mitigation. Evolution of bacterial community structure and predominant genera were identified at different SEs loads and aeration intensities, with Candidatus Competibacter and Ferruginibacter detected as the predominant genera at different SEs input loads and Thiothrix, Azospira, and Saprospiraceae_norank at different aeration intensities with identical SEs input. The results demonstrated the potential of A/O-MBR as a promising barrier against SEs alike micropollutants through the regulation and control of aeration intensity.

Effect of temperature on the quality and microbial community during Daocai fermentation

Daocai is a traditional salted pickle in the southeastern region of Guizhou with a unique aroma, color, and taste. The quality of Daocai is greatly influenced by the fermentation temperature. In this study, high-throughput sequencing and headspace-gas chromatography-ion mobility spectrometry were used to investigate the changes in microbial community succession and volatile flavor compounds during Daocai fermentation under temperature-controlled (D group) and non-temperature-controlled (C group).We found that the predominant genera in the C group samples were Latilactobacillus(40.57 %), Leuconostoc(21.25 %), Cystofilobasidium(22.12 %), Vishniacozyma(23.89 %), and Leucosporidium(24.95 %), whereas Weissella(29.39 %), Lactiplantibacillus(45.61 %), Mucor(68.26 %), and Saccharomyces(23.94 %) were the predominant genera in the D group. A total of 92 VFCs were detected in Daocai samples, including 5 isothiocyanates, 16 esters, 14 alcohols, 24 aldehydes, 17 ketones, 3 acids, 2 pyrazines, 1 pyridines, 1 thiazoles, 3 furans, 4 alkenes, and 2 nitriles. Further analysis revealed Latilactobacillus, Leuconostoc, Lactococcus, Cystofilobasidium, Leucosporidium, Holtermanniella, and Dioszegia as key bacteria involved in flavor formation. They are closely related to the formation of flavors such as aldehydes, furans, pyridines, and alkenes. This study contributes to our understanding of the relationship between bacterial communities and the flavor formation during Daocai fermentation.

Vertical transfer of gut microbiota from dam to neonate calf in the early of life

The aim of this study was to investigate the vertical transfer of microbiota from dams to the offspring. We studied a pair of 20 dams and its offspring. Maternal sources (colostrum, feces and vaginal secretion) and newborn fecal samples were analyzed using 16S rDNA amplicon sequencing on days 1, 3, 7, 14 and 28. Overall, newborns were maintained healthy and did not receive antimicrobial therapy. The Source Tracker analysis indicated that the newborn fecal microbiota was similar to colostrum and vaginal secretion from day 1 up to 7. However, an unknown source (probably from the environment) showed a gradual increase in its similarity with fecal samples from calves measured from day 3 to 28. The most abundant bacteria groups on meconium (day 1) and calf fecal samples on day 3 were Escherichia-Shigella and Clostridium, respectively. On day 7, the predominant genus were Bifidobacterium and Lactobacillus, while Fusobacterium was the most abundant genus on day 14, coinciding with the diarrhea peak. Faecalibacterium showed a gradual increase throughout the neonatal period. Maternal sources contribute to the neonatal microbiota, however other unknown sources (probably environment) had a strong influence on development of the gut microbiota later in the neonate period.

Application of Biofloc-Down flow hanging sponge system to remove nitrogen components in recirculating zero water exchange aquaculture system

This study presents a novel approach to sustainable aquaculture by integrating biofloc technology (BFT) with a compact down-flow hanging sponge (DHS) reactor. The integrated BFT-DHS system effectively removed nitrogen compounds while maintaining ammonia–nitrogen (NH4+-N) concentrations below 1 mg-N L-1 without water exchange. Application of this system in a tank bred with juvenile Oreochromis niloticus showed a high NH4+-N removal rate of up to 97 % and nitrite (NO2– −N) concentrations were maintained at 0.1 ± 0.1 mg-N L-1. Microbial analysis revealed Gordonia as the predominant genus in the biofloc contributing to heterotrophic nitrification, while the Peptostreptococcaceae family dominated the DHS reactor. Heterotrophic nitrification seemed to be the primary process for enhanced nitrogen removal. Pathogenic bacteria, Vibrio sp. was absent throughout the study. This study highlights the potential integration of BFT and DHS system for sustainable aquaculture practice with effective nitrogen removal.

Microbial consortia in commercial salmon products: A comparative study using cultivation-dependent and high-throughput sequencing approaches

Despite the widespread consumption of salmon products, an all-round microbiological survey on fresh salmon and smoked salmon products sold on the market directly to consumers remains to be undertaken. The present study conducted a comprehensive microbial investigation employing both conventional cultivation-based techniques and 16S rRNA amplicon sequencing. A total of 120 fresh salmon and 95 smoked salmon products were systematically collected across all four seasons (spring, summer, fall, and winter), accompanied by temperature assessments of each product’s interior. The average aerobic plate counts for fresh salmon and smoked salmon were 3.63 log and 1.36 log CFU/g, respectively, and the highest seasonal concentrations occurred in summer. The average coliform count was higher in fresh salmon (1.50 log CFU/g) than in smoked salmon products (1.12 log CFU/g). Although smoked salmon exhibited CFU counts similar to those of fresh salmon according to culture-based methods, 16S sequencing unveiled a distinct microbial composition. Photobacterium and Pseudomonas, recognized as major spoilage-related microorganisms, were the predominant genera in all products, but especially in fresh salmon. Smoked salmon exhibited diverse variations in bacterial composition compared to fresh salmon. Three types of lactic acid bacteria—Leuconostoc, Lactobacillus, and Lactococcus—were found to be significantly more abundant in smoked salmon than in fresh salmon. The outcomes of this study contribute to an enhanced understanding of retail salmon products, shedding light on crucial areas for investigation and suggesting potential interventions regarding both sales and production of salmon products.

Characterization and long-read sequencing of biofilms formed by the microbiota present on inert surfaces in poultry slaughterhouses

Cross-contamination from inert slaughterhouse surfaces is among the main sources of contamination of poultry. The objective of the research reported here was to characterize the biofilms formed by the microbiota present on various surfaces in two poultry slaughterhouses in north-western Spain. Forty-four samples (22 from each slaughterhouse) were taken by swab rubbing at different points along the processing line (from stunning to cutting). The microbiota on all surfaces was able to form biofilms, which were studied by scanning confocal laser microscopy. The total biovolume in the observation field of 16,078.24 μm2 ranged from 22,106.8 ± 5544.3 μm3 to 414,229.6 ± 1621.0 μm3. Average values were higher in abattoir A than in abattoir B, with significant differences (P < 0.05) between surfaces. The percentage of biovolume of Gram-positive bacteria ranged between 0.02 % and 5.38 %. The highest percentages of Gram-positive bacteria were detected towards the beginning of the processing line. The microbiota of the biofilms was identified using long-read sequencing techniques (Oxford Nanopore). The predominant genera (found in >50.0 % of the biofilms) were Pseudomonas, Citrobacter, Klebsiella, Serratia, Escherichia, Enterobacter, Stenotrophomonas, Salmonella, Shewanella, Acinetobacter and Aeromonas. In addition, some pathogenic bacteria were detected, including Salmonella (31 surfaces), Yersinia enterocolitica (12), Escherichia coli O157:H7 (6), Campylobacter spp. (4) and Listeria monocytogenes (3). This research work has permitted identification of the most contaminated surfaces in poultry abattoirs and can serve as a starting point for the design of more effective cleaning and disinfection protocols.

Phosphomolybdic acid functionalized nano silica for enhanced anti-biofouling effect in polymer electrolyte membranes for microbial fuel cell application

Microbial fuel cells (MFCs) represent a promising technology for simultaneous electricity generation and wastewater treatment. In this study, a single-chambered MFC was fabricated utilizing a novel polymer electrolyte membrane synthesized from sulfonated polyether ether ketone grafted with styrene sulfonic acid (SPEEK/SSA) as the base polymer, and silica decorated with phosphomolybdic acid (SPMA) as a functionalized nanofiller. Various concentrations of SPMA (2.5 %, 5 %, 7.5 %, and 10 %) were incorporated into the SPEEK/SSA membranes and characterized physicochemically. The SPEEK/SSA membrane with 5 wt% SPMA demonstrated the highest proton conductivity (3.75×10−2 S cm−1) and ion exchange capacity (1.68 meq g−1). This PEM also exhibited superior tensile strength (20 MPa) and excellent chemical durability, as evidenced by Fenton's reagent test. Performance evaluation revealed that this membrane achieved a maximum power density of 196.6 mW m−2 at a maximum of 180 mA m−2 current density. Additionally, antibiofouling tests indicated that the 5 % SPMA-incorporated membrane possessed significant antibacterial properties against both gram-positive and gram-negative bacteria and exhibited high biofilm inhibition. The wastewater treatment efficacy of the MFC with the 5 % SPMA membrane was confirmed by a chemical oxygen demand (COD) removal efficiency of 81.49 %, indicating its potential for effective wastewater treatment. Phylogenetic analysis through 16S rRNA sequencing identified major bacterial phyla including Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with predominant genera such as Pseudomonas and Acidovorax. This study emphasises the potential of nanocomposite membranes to enhance the performance and durability of MFCs while mitigating biofouling, thereby paving the way for future research and development in this field.

Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage

Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.