Search

This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour's seahorse (Hippocampus barbouri) using a combination of shotgun metagenomics and bioinformatics. The analyses revealed that Pseudomonadota and Bacillota were the dominant phyla in the seahorse skin microbiome, whereas Pseudomonadota and, to a lesser extent, Bacillota and Bacteroidota were the dominant phyla in the seahorse gut microbiome. Several metabolic pathway categories were found to be enriched in the skin microbiome, including amino acid metabolism, carbohydrate metabolism, cofactor and vitamin metabolism, energy metabolism, nucleotide metabolism, as well as membrane transport, signal transduction, and cellular community-prokaryotes. In contrast, the gut microbiome exhibited enrichment in metabolic pathways associated with the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, xenobiotics biodegradation and metabolism, and quorum sensing. Additionally, although the relative abundance of bacteriocins in the skin and gut was slightly similar, notable differences were observed at the class level. Specifically, class I bacteriocins were found to be more abundant in the skin microbiome, whereas class III bacteriocins were more abundant in the gut microbiome. To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in Barbour's seahorse. These findings can greatly contribute to a deeper understanding of the seahorse-associated microbiome, which can play a pivotal role in predicting and controlling bacterial infections, thereby contributing to the success of aquaculture and health-promoting initiatives., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide ( sul1 and sul2 ) and tetracycline ( tet(C) , tet(G) , and tetR ) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier B.V. on behalf of Chinese Society for Environmental Sciences, Harbin Institute of Technology, Chinese Research Academy of Environmental Sciences.)

Organic fertilizer microbiomes play substantial roles in soil ecological functions, including improving soil structure, crop yield, and pollutant dissipation. However, limited information is available about the ecological functions of phages and phage-encoded auxiliary metabolic genes (AMGs) in orga9nic fertilizers. Here we used a combination of metagenomics and phage transplantation trials to investigate the phage profiles and their potential roles in pesticide degradation in four organic fertilizers from different sources. Phage annotation results indicate that the two vermicomposts made from swine (PV) and cattle (CV) dung had more similar phage community structures than the swine (P) and cattle (C) manures. After vermicomposting, the organic fertilizers (PV and CV) exhibited enriched phage-host pairings and phage AMG diversity in relative to the two organic fertilizers (P and C) without composting. In addition, the number of broad-host-range phages in the vermicomposts (182) was higher than that in swine (153) and cattle (103) manures. Notably, phage AMGs associated with metabolism and pesticide biodegradation were detected across the four organic fertilizers. The phage transplantation demonstrated that vermicompost phages were most effective at facilitating the degradation of pesticide precursor p-nitrochlorobenzene (p-NCB) in soil, as compared to swine and cattle manures (P < 0.05). Taken together, our findings highlight the significance of phages in vermicompost for biogeochemical cycling and biodegradation of pesticide-associated chemicals in contaminated soils., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The addition of conductive materials to the anaerobic digestion bioreactor was suggested to enhance microbial activity. In the present work, an anaerobic membrane bioreactor treating municipal wastewater was operated for 385 days. The impact of different graphene oxide concentrations on the removal target pharmaceuticals and microbial community dynamics was investigated. The addition of graphene oxide did not impact the reactor stability, whereas the removals of antibiotics (e.g., trimethoprim and metronidazole) were enhanced. A shift in the microbial community was detected after the addition of 50-900 mg L -1 of graphene oxide, with the proliferation hydrogenotrophic methanogens. The proliferation of syntrophic microorganisms may indicate interactions via direct interspecific electron transfer. The obtained results suggest that the addition of graphene oxide at low mg L -1 concentrations to an anaerobic membrane bioreactor may be considered to improve the removal of antibiotics from municipal wastewater., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The effect of graphene oxide on the anaerobic digestion of waste activated sludge was investigated at two graphene oxide concentrations (0.025 and 0.075 g graphene oxide per g volatile solids) using biochemical methane potential tests. The occurrence of 36 pharmaceuticals was monitored in the solid and liquid phases before and after the anaerobic treatment. The addition of graphene oxide improved the removal of most pharmaceuticals detected, even those that are considered persistent to biological degradation, such as azithromycin, carbamazepine, and diclofenac. No significant differences were observed in the final specific methane production without graphene oxide and with the lowest graphene oxide concentration, yet the highest graphene oxide concentration partially inhibited methane production. The relative abundance of antibiotic resistance genes was not affected by the graphene oxide addition. Finally, significant changes in the microbial community including bacteria and archaea were detected with graphene oxide addition., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg -1 ). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.

In this study, the frequency of canines infected with Leishmania spp. in an area endemic to leishmaniasis in humans was determined. A descriptive pilot study was conducted between the months of October and December 2020 on dogs from Rota, a community in the municipality of León, which included 45 specimens from the peridomestic area. Different variables from each specimen were monitored, such as age, sex, breed, body condition, and clinical characteristics, as well as information on the owners and cases of human leishmaniasis presented in less than 5 years. Blood samples were collected from the cephalic vein and peripheral blood was separated. A complete blood count (CBC) was performed using venous blood samples with ethylene diamine tetraacetic acid (EDTA), as well as a conventional PCR was applied for the detection of Leishmania spp. Amastigotes were found in 22% of venous or peripheral blood samples, whereas a high prevalence of 28.89% (95% CI: 14.53-43.24) was found by PCR. Only 1/12 of positive dogs in PCR presented dry exfoliative dermatitis, therefore, there was no significant difference ( p ≥ 0.05), the age and sex of the dogs were also not factors associated with infection ( p ≥ 0.05). This study reports for the first time the molecular detection of Leishmania in dogs in an endemic area of leishmaniasis in humans in Nicaragua. The high frequency of dogs infected with Leishmania suggests that they play an important role in the transmission cycle of human leishmaniasis., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2022 Byron Flores et al.)

This study aimed to explore the effect of a bacteriophage cocktail, pyophage, on the treatment of wastewater containing antibiotics in an anaerobic membrane bioreactor (AnMBR). During the operational period, performance of the AnMBR was monitored through the changes in chemical oxygen demand (COD), antibiotic removal, transmembrane pressure, and biogas production. Microbial community structure and composition, as well as the occurrence of antibiotic resistance genes were analyzed through shotgun metagenomics analysis. When exposed to pyophage, COD removal efficiency was enhanced up to 96%, whereas membrane fouling was delayed by 25%. Average biogas production was doubled from 224.2 mL/d in control with antibiotics to 447.3 mL/d when exposed to pyophage cocktail with considerable alterations to the archaeal and bacterial community structures. Most notably, the methanogenic community shifted from dominance of Methanothermobacter to Methanoculleus, along with syntrophic bacteria. The results provide insight into the synergistic effects of phage-bacteria and methanogenic communities and illustrate the potential of bacteriophages as bio-enhancers., Competing Interests: Declaration of competing interest The authors declare no conflicts of interest., (Copyright © 2022 Elsevier B.V. All rights reserved.)

In the present paper, the mesophilic (35 °C) and thermophilic (55 °C) biomethanization of poultry and cattle manures were investigated using biochemical methane potential (BMP) tests. Specific methane production (SMP), 24 pharmaceutical compounds (PhACs), and five antibiotic resistance genes (ARGs) (bla KPC , ermB, qnrS, sul1 and tetW) together with the microbial community were analyzed. Mesophilic BMP tests resulted in the highest SMP when poultry manure was used (285.5 mL CH 4 /g VSS with poultry vs 239.6 mL CH 4 /g VSS with cattle manure) while thermophilic temperatures led to the highest SMP with cattle manure (231.2 mL CH 4 /g VSS with poultry vs 238.0 mL CH 4 /g VSS with cattle manure). Higher removals of veterinary pharmaceuticals were detected at 55 °C with both manures indicating that thermophilic digestion is better suited for the removal of these compounds. Tylosin, tilmicosin, chlortetracycline, and sulfamethoxazole presented removals higher than 50%, being the first two completely removed under mesophilic and thermophilic conditions. When comparing the relative abundance of ARGs at the end of each treatment, the most significant removal was found for qnrS which was not detected after the anaerobic treatment. The remaining ARGs did not suffer significant changes. Finally, microbial composition analysis showed that temperature affected the final microbial population more than the microorganisms present in the substrate or inoculum., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils., (© 2022. The Author(s).)

The effect of anaerobic treatment of swine manure at 35 °C (mesophilic) and 55 °C (thermophilic) on methane production, microbial community and contaminants of emerging concern was investigated. Pasteurization pretreatment and post treatment was also investigated in combination with anaerobic treatment at 35 °C. Specific methane production (SMP), 26 pharmaceutical compounds (PhACs) and five antibiotic resistance genes (ARGs) (qnrS, tetW, ermB, sul1 and bla TEM ) were evaluated. Mesophilic treatment resulted in the highest SMP regardless of whether pasteurization was applied. Marbofloxacin was the most abundant antibiotic in swine manure. In general, all groups of PhACs showed higher removals under thermophilic temperatures as compared to mesophilic. In general, pasteurization pretreatment followed by mesophilic anaerobic digestion provided the highest removals of ARGs. Finally, the genera Streptococcus, Clostridium and Pseudomonas which contain pathogenic species, were present in the swine manure. Streptococcus, which was the most abundant, was decreased during all the treatments, while the others only decreased under certain treatments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

This study investigates the effect of psychrophilic, mesophilic and thermophilic temperatures on the anaerobic treatment of slaughterhouse wastewater, in terms of biogas production, occurrence of 30 pharmaceutical compounds of veterinary use, 4 antibiotic resistance genes (ARGs) which provide resistance to tetracyclines (tetW), fluoroquinolones (qnrS), macrolide-lincosamide-streptogramin (ermB) and sulfonamides (sul1) antibiotics, as well as class I integron-integrase gene (intI1), related to horizontal gene transfer. The highest methane yield was obtained at a mesophilic temperature (35 °C) (323 mL CH 4 /g TCOD) followed by the yield obtained at thermophilic temperature (53 °C) (242 mL CH 4 /g TCOD). Regarding pharmaceuticals, chlortetracycline, oxytetracycline, tilmicosin, and lincomycin were the most abundant in the slaughterhouse wastewater, being detected predominantly in the solid phase (with median concentrations >200 μg/kg dry weight). On the other hand, ciprofloxacin, ofloxacin, norfloxacin, lincomycin and ibuprofen were the most predominant in the anaerobic digestate regardless of the treatment temperature. Psychrophilic temperatures (21 °C) exhibited moderate to low pharmaceuticals removal, while a large fraction of them were removed at a thermophilic temperature reaching 70-90% removals for tetracycline, macrolides and one sulfonamide (sulfapyridine). The highest relative abundance of the quantified ARGs was found at 53 °C, suggesting that thermophilic temperatures normally associated with better removals of pathogens do not necessarily show better removals of antibiotic resistance genes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 10 3 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A laboratory scale anaerobic membrane bioreactor was operated for 11 months treating synthetic wastewater that mimicked the concentrate from a forward osmosis process treating municipal wastewater with 80% water recovery. The effect of temperature variation on reactor performance was assessed. The reactor operated during 4 months at 34 °C and then temperature was decreased to 23 °C, 17 °C and 15 °C mimicking the typical temperature seasonal variations of the sewage. Average COD removal efficiencies were 95, 87, 76 and 67% at 34, 23, 17 and 15 °C respectively, obtaining lower biogas production and lower COD removal at lower temperatures. Dissolved methane in the permeate averaged 8.2 mg CH 4 /L and did not significantly change with temperature. After 2 months operating at 15 °C, temperature was progressively increased, resulting in an immediate increase of methane production and COD removal efficiencies. Microbial analysis showed important changes in the archaeal community when temperature was changed from 34 to 23 °C., (Copyright © 2019 Elsevier B.V. All rights reserved.)

One hundred and twenty bacterial isolates were obtained from the intestinal mucus of Nile tilapia (Oreochromis niloticus) and screened for antagonistic activity and adherence abilities. Based on in vitro antagonism against two pathogens (Streptococcus iniae and Edwardsiella piscicida), five isolates were selected and identified by 16S rRNA gene sequence analysis. All antagonistic isolates were affiliated to the genus Bacillus, which showed inhibitory activity against S. iniae. Only the isolate B191 (closely related to Bacillus mojavensis) inhibited the growth of both pathogens. Moreover, isolate B191 adhered significantly better to fish intestinal mucus than other antagonistic isolates. According to our results, these bacterial isolates, particularly isolate B191, should be further studied to explore their probiotic effects under in vivo conditions., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Although antibiotic resistance has become a major threat to human health worldwide, this phenomenon has been largely overlooked in studies in environmental settings. Aquatic environments may provide an ideal setting for the acquisition and dissemination of antibiotic resistance, because they are frequently impacted by anthropogenic activities. This review focuses primarily on the emergence and dissemination of antibiotic resistance in the aquatic environment, with a special emphasis on the role of antibiotic resistance genes., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

In this study, vegetative cell suspensions of two Bacillus subtilis strains, L10 and G1 in equal proportions, was administered at two different doses 10(5) (BM5) and 10(8) (BM8) CFU ml(-1) in the rearing water of shrimp (Litopenaeus vannamei) for eight weeks. Both probiotic groups showed a significant reduction of ammonia, nitrite and nitrate ions under in vitro and in vivo conditions. In comparison to untreated control group, final weight, weight gain, specific growth rate (SGR), food conversion ratio (FCR) and digestive enzymatic activity were significantly greater in the BM5 and BM8 groups. Significant differences for survival were recorded in the BM8 group as compared to the control. Eight weeks after the start of experiment, shrimp were challenged with Vibrio harveyi. Statistical analysis revealed significant differences in shrimp survival between probiotic and control groups. Cumulative mortality of the control group was 80%, whereas cumulative mortality of the shrimp that had been given probiotics was 36.7% with MB8 and 50% with MB5. Subsequently, real-time RT-PCR was employed to determine the mRNA levels of prophenoloxidase (proPO), peroxinectin (PE), lipopolysaccharide- and β-1,3-glucan- binding protein (LGBP) and serine protein (SP). The expression of all immune-related genes studied was only significantly up-regulated in the BM5 group compared to the BM8 and control groups. These results suggest that administration of B. subtilis strains in the rearing water confers beneficial effects for shrimp aquaculture, considering water quality, growth performance, digestive enzymatic activity, immune response and disease resistance., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs), their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP) effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, bla TEM, bla CTX-M, bla SHV, erm(B), sul(I), sul(II), tet(O) and tet(W) were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river.