Biodegradation of gentamicin by bacterial consortia AMQD4 in synthetic medium and raw gentamicin sewage

Glutamicibacter nicotianae AT6: A new strain for the efficient biodegradation of tilmicosin

The degradation of tilmicosin (TLM), a semi-synthetic 16-membered macrolide antibiotic, has been receiving increasing attention. Conventionally, there are three tilmicosin degradation methods, and among them microbial degradation is considered the best due to its high efficiency, eco-friendliness, and low cost. Coincidently, we found a new strain, Glutamicibacter nicotianae sp. AT6, capable of degrading high-concentration TLM at 100 mg/L with a 97% removal efficiency. The role of tryptone was as well investigated, and the results revealed that the loading of tryptone had a significant influence on TLM removals. The toxicity assessment indicated that strain AT6 could efficiently convert TLM into less-toxic substances. Based on the identified intermediates, the degradation of TLM by AT6 processing through two distinct pathways was then proposed.

Exploring the sorption and degradation dynamics of validamycin-A in agricultural soils for environmental management

Validamycin A (VA) is one of the antibiotics that have been utilized in agriculture in Asia; nevertheless, there haven't been many investigations on what happens to VA in soil. The rate at which pesticides are adsorbed into the soil must be determined, since their usage in agriculture is growing. In order to accomplish this, the current study investigated the sorption and degradation of VA in ten distinct soil samples via batch equilibrium studies while maintaining strict laboratory controls. In thermodynamic analysis with a C-type curve, the negative values of Gibbs free energy (ΔG) are thoroughly evaluated using both linear and Freundlich models. These values vary from - 16.8 to - 22.2 kJ/mol. Impact of temperature (18, 23, and 30 °C) and pH (5, 7, and 9) on the degradation of this antibiotic in soil was also scrutinized. Our findings demonstrated that, as a result of enhanced microbial activity at higher temperatures, VA deteriorated more quickly at 23 °C and 30 °C than at 18 °C. In comparison to lower pH values, the VA removal efficiencies with sample-4 was significantly greater at pH 7.4 (92.9%) and pH 9 (97.4%). Moreover, first order reaction kinetics were followed in the degradation of VA. The results demonstrated that VA bound to the selected soils, resulting in medium to low persistence as demonstrated by degradation values. In summary, this study provides important information regarding the behavior and fate of VA in different types of soil, information that might be useful in developing workable management strategies and environmental risk assessments.

Analysis of a novel strain Brevundimonas KX-1 capable of degrading 3-chlorocarbazole based on the whole genome sequence

In this study, a strain was isolated from a sewage treatment plant in Jiangsu Province, China. The strain was identified as Brevundimonas sp. KX-1. After 5 days, 50.2% 3-chlorocarbazole (3-CCZ) was degraded under the optimum condition as follows: 1 g/L starch, 30 °C, pH 6.5 and 50 mg/L 3-CCZ. The degradation of 3-CCZ by KX-1 conformed to the first-order kinetic model under different initial concentrations in this experiment. The intermediate product of 3-CCZ degradation was identified as (2E,4Z)-6-(2-amino-5-chlorophenyl)-2-hydroxy-6-oxohexa-2,4-dienoic acid. The activities of the meta-cleavage enzymes for biphenyl-2,3-diol (the analogs of intermediate product 2'-amino-5'-chloro-[1,1'-biphenyl]-2,3-diol) were measured with the crude extracts of cells grown in the presence of 3-CCZ. The complete genome of KX-1 was sequenced and compared with the Brevundimonas diminuta BZC3. BZC3 and KX-1 belonged to the same species, displaying the genetic similarity of 99%. But BZC3 could efficiently degrade gentamicin for the potential microbial function analysis. Compared with BZC3, KX-1 possessed the primary function annotations about transportation and metabolism of amino acids (6.65%) and the transportation and metabolism of carbohydrates (5.96%). In addition, KX-1 was rich in sucrose and starch metabolism pathways (ko00500) compared with the genome of BZC3, indicating the high efficiency of KX-1 for starch utilization during degradation. This article reveals the difference between strain KX-1 and bacteria of the same genus in terms of the whole genome sequence, demonstrating that KX-1 is a novel strain Brevundimonas with the ability to degrade 3-CCZ.

Volatile Metabolites from Brevundimonas diminuta and Nematicidal Esters Inhibit Meloidogyne javanica

Brevundimonas diminuta is broadly distributed in terrestrial and aquatic environments and has various biological activities. In this study, we found that B. diminuta exhibited nematicidal activity against the plant root-knot nematode, Meloidogyne javanica. A total of 42 volatile organic compounds (VOCs) from B. diminuta were identified using gas chromatography-mass spectrometry (GC-MS). The nematicidal activity of the 10 main VOCs was tested against M. javanica. Butyl butanoate (4 µL) caused the mortality of 80.13% of M. javanica after 4 h. The nematicidal activity of an additional 38 butyl-butyrate-like volatile esters was also investigated. Of these, seven had strong nematicidal activity against M. javanica, five of which showed egg-hatching inhibitory activity. This study is the first to report that butyl butanoate, ethyl 2-methylbutanoate, ethyl 4-methylpentanoate, ethyl pent-4-enoate, and methyl undecanoate have nematicidal activity against M. javanica. The results indicated that B. diminuta could serve as a candidate microorganism for the biocontrol of plant root-knot nematodes, showing that volatile esters have great potential as nematicides.

Novel nonylphenol-degrading bacterial strains isolated from sewage sludge: Application in bioremediation of sludge

Nonylphenol (NP) is an anthropogenic pollutant frequently found in sewage sludge due to the insufficient degrading effectiveness of conventional WWTPs and has attracted attention as an endocrine disruptor. The aim of this study was to isolate specific NP-degrading bacteria from sewage sludge to be used in the degradation of this contaminant through bioaugmentation processes in aqueous solution and sewage sludge. Up to eight different bacterial strains were isolated, six of them not previously described as NP degraders. Bacillus safensis CN12 presented the best NP degradation in solution, and glucose used as an external carbon source increased its effect, reaching DT₅₀ degradation values (time to decline to half the initial concentration of the pollutant) of only 0.9 days and a complete degradation in <7 days. Four NP metabolites were identified throughout the biodegradation process, showing higher toxicity than the parent contaminant. In sewage sludge suspensions, the endogenous microbiota was capable of partially degrading NP, but a part remained adsorbed as bound residue. Bioaugmentation was used for the first time to remove NP from sewage sludge to obtain more environmentally friendly biosolids. However, B. safensis CN12 was not able to degrade NP due to its high adsorption on sludge, but the use of a cyclodextrin (HPBCD) as availability enhancer allowed us to extract NP and degrade it in solution. The addition of glucose as an external carbon source gave the best results since the metabolism of the sludge microbiota was activated, and HPBCD was able to remove NP from sewage sludge to the solution to be degraded by B. safensis CN12. These results indicate that B. safensis CN12 can be used to degrade NP in water and sewage sludge, but the method must be improved using consortia of B. safensis CN12 with other bacterial strains able to degrade the toxic metabolites produced.

The Effect of Operating Strategies on the Anaerobic Digestion of Gentamicin Mycelial Residues: Insights into the Enhancement of Methane Production and Attenuation of Gentamicin Resistance

Anaerobic digestion (AD) has been widely employed for converting various biowastes into renewable energy. However, AD of gentamicin mycelial residues (GMRs, a byproduct of gentamicin production) is limited by ammonia inhibition and antimicrobial resistance risk. Compared to mesophilic AD (MMAD) of GMRs, this study looked into three semicontinuous AD processes, i.e., codigestion with wheat straw, thermophilic digestion (TAcoD), and AD at shortened retention time (RT). Results showed that a stable and safe AD could be achieved under suitable operating conditions. Co-digestion could effectively mitigate the adverse effect of ammonia inhibition. The methane production increased by 35.86% in TAcoD compared to that in MMAD and 43.99% of hazardous waste was reduced in TAcoD. Concerning the antimicrobial resistance of AD system, gentamicin was degraded efficiently and the degradation process was not involved in the expression of antibiotic resistance genes (ARGs) related to modifying enzyme. Effective removal of ARGs under three operating strategies was associated with a higher reduction in bacterial abundance of potential hosts. In addition, the changes in the relevant proteins for transformation and conjugation as predicted by PICRUSt suggested that thermophilic condition and shorter RT were conducive to the reduction of the dissemination risks of ARGs.

Isolation, characterization and degradation performance of oxytetracycline degrading bacterium Planococcus sp. strain pw2

Oxytetracycline (OTC), is a widely used veterinary antibiotic for treatment and prophylaxis in aquaculture. As an emerging pollutant, OTC in the environment exerts selective pressure on aquatic organisms causing proliferation of antibiotic resistant genes. In the present study, an OTC tolerant isolate labelled as pw2 was selected among the 11 OTC tolerant isolates, isolated from the aquaculture effluent, for investigating its OTC degrading potential. The cell morphology, biochemical characteristics, and 16S ribosomal RNA (rRNA) gene sequence of the isolated strain indicated that it belonged to the genus Planococcus. The OTC removal percentage was estimated through measuring its residual concentration in the culture medium with high performance liquid chromatography. The strain exhibited maximum removal efficiency of 90.62%, with initial OTC concentration of 10 µg/ml. The optimum degrading conditions were 35 °C and pH 7. The degradation rate of OTC with (biotic) and without strain pw2 (abiotic) was 3.253 and 1.149 mg/l/d, respectively. The half-life was recorded to be 2.13 d in the presence of strain pw2, in contrast to 6.03 days recorded without strain pw2. The total (biotic + abiotic) OTC degradation efficiency was 75.74, 83.93, 90.62, and 86.47% for the initial OTC concentrations of 1 to 25 µg/ml, respectively. Addition of carbon and nitrogen did not influence the OTC removal which indicates Planococcus sp. pw2 use OTC as sole energy source. Thus, Planococcus sp. pw2 plays a vital role in reducing the OTC concentration in the environment, offering a promising method for treatment of aquaculture effluent containing OTC.

Antibiotic residues in environment: antimicrobial resistance development, ecological risks, and bioremediation

The overuse of antibiotics and their disposal without processing are leading the environment and its inhabitants towards a serious health emergency. There is abundance of diverse antibiotic resistance genes and bacteria in environment, which demands immediate attention for the effective removal of antibiotics. There are physical and chemical methods for removal, but the generation of toxic byproducts has directed the efforts towards bioremediation for eco-friendly and sustainable elimination of antibiotics from the environment. Various effective and reliable bioremediation approaches have been used, but still antibiotic residues pose a major global threat. Recent developments in molecular and synthetic biology might offer better solution for engineering of microbe-metabolite biodevices and development of novel strains endowed with desirable properties. This review summarizes the impact of antibiotics on environment, mechanisms of resistance development, and different bioremediation approaches.

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Background

Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results.

Results

The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene.

Conclusions

The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08027-w.

Biotransformation of doxycycline by Brevundimonas naejangsanensis and Sphingobacterium mizutaii strains

The fate of doxycycline (DC), a second generation tetracycline antibiotic, in the environment has drawn increasing attention in recent years due to its wide usage. Little is known about the biodegradability of DC in the environment. The objective of this study was to characterize the biotransformation of DC by pure bacterial strains with respect to reaction kinetics under different environmental conditions and biotransformation products. Two bacterial strains, Brevundimonas naejangsanensis DD1 and Sphingobacterium mizutaii DD2, were isolated from chicken litter and characterized for their biotransformation capability of DC. Results show both strains rely on cometabolism to biotransform DC with tryptone as primary growth substrate. DD2 had higher biotransformation kinetics than DD1. The two strains prefer similar pHs (7 and 8) and temperature (30 °C), however, they exhibited opposite responses to increasing background tryptone concentration. While hydrolysis converted DC to its isomer or epimer, the two bacterial strains converted DC to various biotransformation products through a series of demethylation, dehydration, decarbonylation and deamination. Findings from the study can be used to better predict the fate of DC in the environment.

Ali S, Salerno M, Eldin MSM. Effective Elimination of Contaminant Antibiotics Using High-Surface-Area Magnetic-Functionalized Graphene Nanocomposites Developed from Plastic Waste

The presence of pharmaceutical residues in aquatic environments represents a risk for the equilibrium of the ecosystem and may seriously affect human safety itself in the long term. To address this issue, we have synthesized functional materials based on highly-reduced graphene oxide (HRGO), sulfonated graphene (SG), and magnetic sulfonated graphene (MSG). The method of synthesis adopted is simple and inexpensive and makes use of plastic bottle waste as the raw material. We have tested the fabricated materials for their adsorption efficiency against two model antibiotics in aqueous solutions, namely Garamycin and Ampicillin. Our tests involved the optimization of different experimental parameters of the adsorption process, such as starting antibiotic concentration, amount of adsorbent, and time. Finally, we characterized the effect of the antibiotic adsorption process on common living organisms, namely Escherichia coli DH5α (E. coli DH5α) bacteria. The results obtained demonstrate the efficiency of the method in addressing the issue of the emergence of antibiotic-resistant bacteria, which will help in preventing changes in the ecosystem.

Bringing Community Ecology to Bear on the Issue of Antimicrobial Resistance

Antimicrobial resistance (AMR) is a global concern, pertaining not only to human health but also to the health of industry and the environment. AMR research has traditionally focused on genetic exchange mechanisms and abiotic environmental constraints, leaving important aspects of microbial ecology unresolved. The genetic and ecological aspects of AMR, however, not only contribute separately to the problem but also are interrelated. For example, mutualistic associations among microbes such as biofilms can both serve as a barrier to antibiotic penetration and a breeding ground for horizontal exchange of antimicrobial resistance genes (ARGs). In this review, we elucidate how species interactions promote and impede the establishment, maintenance, and spread of ARGs and indicate how management initiatives might benefit from leveraging the principles and tools of community ecology to better understand and manipulate the processes underlying AMR.

Microbial consortia including methanotrophs: some benefits of living together

With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph-heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with co-cultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.

Dynamics of bacterial composition and the fate of antibiotic resistance genes and mobile genetic elements during the co-composting with gentamicin fermentation residue and lovastatin fermentation residue

Dynamics in bacterial community composition, along with 13 antibiotic resistance genes (ARGs) and eight mobile genetic elements (MGEs), were assessed during co-composting with gentamicin and lovastatin fermentation residue (GFR and LFR, respectively). Using next generation sequencing, the key bacterial taxa associated with the different stages of composting were identified. Most importantly, Bacillus, belonging to Phylum Firmicutes, was associated with enhanced degradation of gentamicin, decomposition of organic matter (OM) and dissolved organic carbon (DOC), and also extension of the thermophilic phase of the composting cycle. During the course of composting, the patterns of different ARGs/MGEs varied. However, the total and the normalized (to bacterial numbers) copies both remained high. The abundance of various ARGs was related to bacterial abundance and community composition, and the changing pattern of individual ARGs was influenced by the selectivity of MGEs and bacteria.