Pseudomonas Research Articles

Detection of Aerobic Bacterial Species Causing Pneumonia in Sheep and Goats and their Susceptibility to Antibiotics in Sudan

Aims: This study was conducted in Khartoum and Gezira States slaughterhouses to investigate the bacterial spp. associated with pneumonia in condemned sheep and goat lungs. Study Design: A total of 2085 animals were examined grossly for respiratory lesions (sheep= 1601 and goats= 484). Place and Duration of Study: Khartoum and Gezira States slaughterhouses during different seasons, from 2018-2020 and conducted in Central Veterinary Research Laboratory, Sudan. Methodology: Bacterial spp. were isolated and identified using analytical profile index strips then more characterization done using Polymerase chain reaction for representative 20 selected isolates and finally antimicrobial susceptibility test was performed. Results: Out of 320 pneumonic lung samples, 116 samples showed pure colonies and 41 were mixed culture while 163 revealed no bacterial growth. The main bacteria isolated were Staphylococcus aureus, Escherichia coli, Pasteurella multocida, Mannheimia haemolytica, Streptococcus spp. Corynebacterium spp. Pseudomonas spp. Staph spp. and Bacillus spp. Twenty representative bacterial isolates examined by PCR technique 10 were Staph aureus and 10 were E. coli to confirm identification. Seven of each were found positive. The Gram-positive bacteria resulted in 41 resistant isolates, 21 intermediate and 141 sensitive to different antibiotics. Ten bacterial species were reported resistant for more than two Antibiotics from different classes mainly tetracycline, methicillin, penicillin and erythromycin. The Gram-negative bacteria resulted in 59 were resistant, 13 intermediate and 108 sensitive to antibiotics. Seventeen of them were multidrug resistance to tetracycline, gentamicin, Imipenem and ceftriaxone. Conclusion: It was concluded that bacteria could be the main cause responsible for pneumonia in sheep and goats, some of these bacterial isolates were resistance to several Antibiotic which have an impact on public health.

Development of Aptamer-Functionalized Gold Nanoparticles as Probes in Point-of-Care Diagnostic Device for Rapid Detection of Multidrug-Resistant Bacteria in Bombyx mori L. .

The sericulture industry suffers severe crop losses due to various silkworm diseases, necessitating the development of further technologies for rapid pathogen detection. Here, we report an all-in-one portable biosensor that combines conjugated gold nanoparticles (Au NPs) with an aptamer-based lateral flow assay (LFA) platform for the real-time analysis of Mammaliicoccus sp. and Pseudomonas sp. Our platform enables sample-to-answer naked eye detection within 5 min without any cross-reactivity with other representatives of the silkworm pathogenic bacterial group. This assay was based on the sandwich-type format using a bacteria-specific primary aptamer (Apt1) conjugated with 23 nm ± 1.27 nm Au NPs as a signal probe and another bacteria-specific secondary aptamer (Apt2)-coated nitrocellulose membrane as a capture probe. The hybridization between the signal probe and the capture probe in the presence of bacteria develops a red band in the test line, whose intensity is directly proportional to the bacterial concentration. Under the optimal experimental conditions, the visual limit of detection of the strip for Mammaliicoccus sp. and Pseudomonas sp. was 1.5 × 104 CFU/mL and 1.5 × 103 CFU/mL, respectively. Additionally, the performance of the LFA device was validated by using a colorimetric assay, and the results from the colorimetric assay are consistent with those obtained from the LFA. Our findings indicate that the developed point-of-care diagnostic device has significant potential for providing a cost-effective, scalable alternative for the rapid detection of silkworm pathogens.

Metabolic engineering of Pseudomonas bharatica CSV86T to degrade Carbaryl (1-naphthyl-N-methylcarbamate) via the salicylate-catechol route.

Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.

Bacterial Communities Associated with the Leaves and the Roots of Salt Marsh Plants of Bayfront Beach, Mobile, Alabama, USA.

Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress.

Biodegradation of combined pollutants of polyethylene terephthalate and phthalate esters by esterase-integrated Pseudomonas sp. JY-Q with surface-co-displayed PETase and MHETase

The waste pollution problem caused by polyethylene terephthalate (PET) plastics poses a huge threat to the environment and human health. As plasticizers, Phthalate esters (PAEs) are widely used in PET production and become combined pollutants with PET. Synthetic biology make it possible to construct engineered cells for microbial degradation of combined pollutants of PET and PAEs. PET hydroxylase (PETase) and monohydroxyethyl terephthalate hydroxylase (MHETase) isolated from Ideonella sakaiensis 201-F6 exhibit the capability to depolymerize PET. However, PET cannot enter cells, thus enzymatic degradation or cell surface displaying technology of PET hydrolase are the potential strategies. In this study, Pseudomonas sp. JY-Q was selected as a chassis strain, which exhibits robust stress tolerance. First, a truncated endogenous outer membrane protein cOmpA and its variant Signal (OprF)-cOmpA were selected as anchor motifs for exogenous protein to display on the cell surface. These anchor motifs were fused at the N-terminal of PET hydrolase and MHETase and transformed into Pseudomonas sp. JY-Q, the mutant strains successfully display the enzymes on cell surface, after verification by green fluorescent protein labeling and indirect immunofluorescence assay. The resultant strains also showed the catalytic activity of co-displaying PETase and MHETase for PET biodegradation. Then, the cell surface displaying PET degradation module was introduced to a JY-Q strain which genome was integrated with PAEs degrading enzymes and exhibited PAEs degradation ability. The resultant strain JY-Q-R1-R4-SFM-TPH have the ability of degradation PET and PAEs simultaneously. This study provided a promising strain resource for PET and PAEs pollution control.

Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants.

Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.

Biosurfactant Production by Pseudomonas: a Systematic Review.

It is of fundamental interest to research and develop innovative biotechnologies, as well as bioproducts that replace or are alternatives to those of non-renewable origin, such as biosurfactants in relation to traditional surfactants used in various sectors. Consequently, there are a large number of experimental studies addressing different subjects, especially with the use of bacteria of the genus Pseudomonas; however, there is a lack of work that demonstrates the evaluation of this science produced to date. Therefore, this article discusses the production of biosurfactants by Pseudomonas with the aim of surveying and analyzing experimental articles on this topic. To realize this, a systematic search was carried out with well-defined temporal space, databases, and inclusion and exclusion criteria, based on metric studies that guided what information would be collected and the method of evaluation. Therefore, a large number of articles were selected, which demonstrated Pseudomonas aeruginosa as the bioagent mostly used in the tests, which aimed to improve the process in the area. Furthermore, interest in this field has increased over the years, predominantly in emerging market countries, where the most prominent authors on the topic are found. Therefore, it is necessary that there is an expansion of interest in the area to make the production of biosurfactants cheaper in areas that currently have greater development deficiencies, such as means of purifying the bioprocess and reducing foam formation in the bioprocess.

Ferulic acid-arabinoxylan conjugates: Synthesis, characterization and applications in antibacterial film formation

A novel antibacterial film based on arabinoxylan (AX) was prepared by introducing ferulic acid (FA) to AX through a laccase-catalyzed procedure. The ferulic acid-arabinoxylan conjugates (FA-AX conjugates) have been characterized. Results showed that FA was successfully grafted onto the AX chains by covalent linkages, likely through nucleophilic addition between O-Ph in the phenolic hydroxyl group of FA, or through Michael addition via O-quinone intermediates. FA-AX conjugates showed improved crystallinity, thermal stability, and rheological properties, as well as a distinct surface morphology, compared with those of native AX. Moreover, FA-AX conjugates exhibited enhanced antibacterial ability against Staphylococcus aureus, Escherichia coli, Shewanella sp., and Pseudomonas sp. Mechanistic studies revealed that the enhanced antibacterial ability was due to the penetration of bacterial membrane by the phenolic molecule and the steric effect of FA-AX conjugates. The study demonstrates that the laccase-induced grafting method was effective in producing FA-AX conjugates; we have demonstrated its antibacterial ability and great potential in prolonging the shelf life of fresh seafood products.

Biodegradability and formulation of triclosan-degrading and plant-growth-promoting Pseudomonas sp. MS45

Abstract. Sipahutar MK. 2024. Biodegradability and formulation of triclosan-degrading and plant-growth-promoting Pseudomonas sp. MS45. Biodiversitas 25: 2980-2992. This study presents the isolation of Pseudomonas sp. MS45, a microorganism that can consume triclosan (TCS) as its only carbon and energy source, leading to its detoxification. The rarity of a toxicity study of TCS before and after biodegradation treatment is addressed in this study. Allium cepa's genotoxicity exposed TCS's cytotoxicity, generating multiple damaged chromosomes, in contrast to the insignificant consequences of its broken-down metabolites. The study also optimized the different kinetic parameters for TCS-specific biodegradation and Pseudomonas sp. MS45-specific growth. The biodegradation pattern followed the Michaelis-Menten model with a maximum specific biodegradation rate (Vmax) of 0.01 µmole h-1 mg cell protein-1 and a half saturation constant (Ks) of 21.98 µM. The growth pattern followed the Haldane model with a maximum specific growth rate (µmax) of 0.03 h-1, half saturation constant (Ks) of 4.56 µM, and TCS inhibition constant (Ki) of 32.81 µM. In addition to its TCS-degrading ability, Pseudomonas sp. MS45 also possesses various plant growth promotion traits, and it was incorporated into two solid carrier formulations: vermiculite and rice bran. The study found that vermiculite, especially with PEG, was the most consistent formulation for Pseudomonas sp. MS45, in terms of maintaining bacterial survival and TCS-degrading ability. This study marks the initial report on the biodegradation and formulation of TCS-destroying and Plant-Growth-Promoting (PGP) Pseudomonas sp. MS45, offering promising implications for environmental and agricultural applications.

Effects of antibacterial peptides from Brevibacillus texasporus on growth performance, meat quality and gut health of cultured largemouth bass (Micropterus salmoides)

The aim of this study was to investigate the effects of antibacterial peptides from Brevibacillus texasporus (BT) on the growth performance, meat quality and gut health of cultured largemouth bass (Micropterus salmoides). Largemouth bass (36.17 ± 1.52 g) were divided into 2 groups and each group was fed with diets supplemented with or without 200 ppm of BT peptides for 130 days. The results showed that BT peptides had no significant influences on growth performance and body indexes, but significantly enhanced total antioxidant capacity and lysozyme content in the serum. Moreover, digestive enzymes activities and intestinal villous height were also prominently increased. From meat quality aspect, no significant differences were found in nutritional components, amino acid composition, fatty acid composition and texture property, except the values of hardness, gumminess and γ-linolenic acid (C18:3n6) were remarkably increased after BT peptides intervention. Finally, the results of gut microbiota and short chain fatty acids revealed that BT peptides significantly decreased the relative abundances of harmful bacteria such as genus Acinetobacter and Pseudomonas, and increased the production of short chain fatty acids. In conclusion, this study confirmed that BT peptides could be used to improve the health of largemouth bass, which provided novel insights into the application of antimicrobial peptides in aquacultures.

Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea

Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m3 water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.

Enhanced biodegradation of polychlorinated biphenyls by co-cultivation of resuscitated strains with unique advantages

The investigation into viable but non-culturable (VBNC) bacteria through the implementation of resuscitation promoting factors (Rpfs) has broadened the potential sources for isolating strains capable of degrading polychlorinated biphenyls (PCBs). Nonetheless, there has been limited research on the efficacy of resuscitated strains and the potential improvement of their performance through co-cultivation. In this work, the PCB degradation potential of resuscitated strains, specifically Pseudomonas sp. HR1 and Achromobacter sp. HR2, as well as their co-cultures, was investigated. Of particular importance was the comparative analysis between the optimal co-culture and individual strains regarding their ability to degrade PCB homologs and mineralize intermediate metabolites. The results suggested that the resuscitated strains HR1 and HR2 demonstrated robust growth and effective degradation of Aroclor 1242. The co-culture CO13, with an optimal HR1 to HR2 ratio of 1:3, exhibited a remarkable improvement in PCB degradation and intermediate metabolite mineralization compared to individual strains. Analysis of functional genes and degradation metabolites revealed that both the individual strains and co-culture CO13 degraded PCBs via the HOPDA-benzoate pathway, then mineralized through protocatechuate meta- and ortho-cleavage pathways, as well as the catechol ortho-cleavage pathway. This study represents the first documentation of the improved PCB degradation through the co-cultivation of resuscitated strains, which highlights the great promise of these resuscitated strains and their co-cultures as effective bio-inoculants for enhanced bioremediation.

Bioremediation mechanisms of chlorophenol-Cr(Ⅵ): The role of amines, immobilization, and DEGs in Pseudomonas sp. PC

The combined pollution of p-Chlorophenol (4-CP) and hexavalent chromium [Cr(VI)] is widespread in the environment. However, little information is available on the relationship between the fate of Cr(VI) and its amines during dechlorination, which are dominant in pH value changes. Here, Pseudomonas sp. PC can degrade 4-CP and convert Cr(VI). The removal efficiency of Cr(VI) accords with the first-order reaction kinetics. Notably, the pH value (7.95) of the chlorophenol-Cr(VI) systems increased compared to the 4-CP treatment due to the significant accumulation of amines, especially ethambutol, which was 1.06 folds higher than 4-CP treatment. The pH value of the 4-CP treatment decreased to 5.89. Thus, Cr(III) was more likely to immobilize on the surface of the cell in the form of Cr(OH)3. Interestingly, Catechol 1,2-dioxygenase (catA) was 0.98 folds higher than Catechol 2,3-dioxygenase (dmpB) in chlorophenol-Cr(Ⅵ) systems, indicating that the presence of Cr(Ⅵ) changed the metabolic pathway of Pseudomonas sp. PC for 4-CP from the dmpB meta-cleavage pathway to the catA ortho-cleavage pathway. These conclusions deepen the cognizance of the relationship between the degradation pathway of chlorophenols, the fixation of Cr(VI) and the amines, providing a better basis for the bioremediation application of chlorophenol-Cr(VI) sites.

Drug-degrading bacteria isolated from the effluent water of a sewage plant.

Endocrine disruptors are potential environmental contaminants that can cause toxicity in aquatic ecosystems, so the Water Framework Directive has established limits for these compounds. During our research, 41 bacterial strains were isolated and identified from sewage effluent and tested for their degradation capacities for bisphenol A, 17β-estradiol, and nonylphenol. All the isolated bacteria belonged to the Gammaproteobacteria class of Pseudomonadota phylum (members of Citrobacter, Enterobacter, Escherichia, Klebsiella, Kluyvera, Leclercia, Raoultella, Shigella. Acinetobacter, Aeromonas, and Pseudomonas genera). During the experiments, only strains HF17, HF18 (Pseudomonas aeruginosa), and HF31 (Citrobacter freundii) were unable to grow on these compounds, all other bacterial strains could grow in the presence of the investigated endocrine disruptors. Based on the genomic analysis of the type strains, a set of genes involving aromatic compound degradation was detected, among the peripheral metabolic pathways, the quinate and benzoate degradation pathways proved to be widespread, among the central aromatic intermediates metabolism, the catechol branch of the beta-ketoadipate pathway was the most dominant. Pseudomonas fulva HF16 strain could utilize the investigated endocrine disruptors: bisphenol A by 34%, 17β-estradiol by 52%, and nonylphenol by 54%.

A New Bacteriophage Pseudomonas Phage Ka1 from a Tributary Stream of Lake Baikal

A New Bacteriophage Pseudomonas Phage Ka1 from a Tributary Stream of Lake Baikal

Effect of Bacterial Endophytes Isolated from Tropical Fruits against Listeria monocytogenes and Cronobacter sakazakii in Model Food Products

Listeria monocytogenes and Cronobacter sakazakii are two important foodborne bacterial pathogens. Bacterial endophytes, which reside in plant cells, can produce antimicrobial compounds to protect the host organism or inhibit pathogens. This study investigated the bacterial community of tropical fruits for their potential to inactivate L. monocytogenes or C. sakazakii in cantaloupe and liquid infant formula, respectively. Tropical fruits including papayas, dragon fruits, and sugar apples, were sourced from several countries. Candidate bacterial endophytes were recovered from these tropical fruits using blood agar and Reasoner’s 2A (R2A) agar and tested for potential inhibition against L. monocytogenes and C. sakazakii. A total of 196 bacterial endophytes were recovered from papayas, dragon fruits, and sugar apples. Among these bacterial endophytes, 33 (16.8%) and 13 (6.6%) of them demonstrated an inhibition zone against L. monocytogenes and C. sakazakii, respectively. The inhibitory strains were identified using 16S rRNA sequencing as Bacillus spp., Enterobacter spp., Klebsiella spp., Microbacterium spp., Pantoea spp., and Pseudomonas spp. A cocktail of Pantoea spp. and Enterobacter spp. was used in challenge studies with cantaloupe and significantly reduced the number of L. monocytogenes by approximately 2.5 log10 CFU/g. In addition, P. stewartii demonstrated antagonistic activity against C. sakazakii in liquid infant formula, i.e., it significantly decreased the number of C. sakazakii by at least 1 log10 CFU/mL. Thus, the use of bacterial endophytes recovered from fruits and vegetables could be a promising area of research. Their use as potential biocontrol agents to control bacterial pathogens in ready-to-eat foods warrants further investigation.

Insights into the biodegradation of fipronil through soil microcosm-omics analyses of Pseudomonas sp. FIP_ A4

Fipronil, a phenylpyrazole insecticide, is used to kill insects resistant to conventional insecticides. Though its regular and widespread use has substantially reduced agricultural losses, it has also caused its accumulation in various environmental niches. The biodegradation is an effective natural process that helps in reducing the amount of residual insecticides. This study deals with an in-depth investigation of fipronil degradation kinetics and pathways in Pseudomonas sp. FIP_A4 using multi-omics approaches. Soil-microcosm results revealed ∼87% degradation within 40 days. The whole genome of strain FIP_A4 comprises 4.09 Mbp with 64.6% GC content. Cytochrome P450 monooxygenase and enoyl-CoA hydratase-related protein, having 30% identity with dehalogenase detected in the genome, can mediate the initial degradation process. Proteome analysis revealed differential enzyme expression of dioxygenases, decarboxylase, and hydratase responsible for subsequent degradation. Metabolome analysis displayed fipronil metabolites in the presence of the bacterium, supporting the proposed degradation pathway. Molecular docking and dynamic simulation of each identified enzyme in complex with the specific metabolite disclosed adequate binding and high stability in the enzyme-metabolite complex. This study provides in-depth insight into genes and their encoded enzymes involved in the fipronil degradation and formation of different metabolites during pollutant degradation. The outcome of this study can contribute immensely to developing efficient technologies for the bioremediation of fipronil-contaminated soils.

Stable-isotope probing combined with amplicon sequencing and metagenomics identifies key bacterial benzene degraders under microaerobic conditions

The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and 13C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of “heavy” and “light” DNA fractions. Results shed light on the fact that the availability of oxygen strongly determined the structure of the degrading bacterial communities. While members of the genus Pseudomonas were overwhelmingly dominant under clear aerobic conditions, they were almost completely replaced by members of genera Malikia and Azovibrio in the microaerobic microcosms. Investigation of the density resolved DNA fractions further confirmed the key role of these two latter genera in the microaerobic degradation of benzene. Moreover, analysis of a previously acquired metagenome-assembled Azovibrio genome suggested that benzene was degraded through the meta-cleavage pathway by this bacterium, with the help of a subfamily I.2.I-type catechol 2,3-dioxygenase. Overall, results of the present study implicate that under limited oxygen availability, some potentially microaerophilic bacteria play crucial role in the aerobic degradation of aromatic hydrocarbons.

Effect of copper on fermentative hydrogen production from sewage sludge: Insights into working mechanisms

The effect of Copper (Cu) on fermentative hydrogen production from sewage sludge (SSL) was firstly explored, and glucose was chosen as typical substrate to make a comparison. Results showed that the stimulative dosages of Cu on hydrogen production from glucose and SSL were 20–60 mg/L and 20–100 mg/L, respectively. The stimulation was more significant to SSL (6.3–43.8 %) than glucose (4.8–16.1 %). 500–1000 mg/L Cu posed obvious inhibition to hydrogen production, and the inhibition was more significant to glucose (80.6–91.9 %) than SSL (25.0–37.5 %), which was due to the protective effect of SSL to hydrogen producers from adsorbing Cu. The exposure enriched the Cu-resistant microorganisms like genus Aeromonas, Comamonas, Pseudomonas and Dechloromonas. Metabolic analysis shows that low dosages of Cu stimulated hydrogen production by strengthening the formate decomposition process, and weakening the lactate formation and homoacetogenesis processes, while high dosages of Cu inhibited hydrogen production by weakening all hydrogen-producing processes including formate decomposition, ferredoxin hydrogenation and glucose decomposition processes.

Evidence of Cooperative Interactions between Rhizobacteria and Wood-Decaying Fungi and Their Effects on Maize Germination and Growth

Advances in soil microbial communities are driving agricultural practices towards ecological sustainability and productivity, with engineering microbial communities significantly contributing to sustainable agriculture. This study explored the combined effects of two white-rot fungi (Trametes sp. and Pleurotus sp.) and six rhizobacterial strains belonging to four genera (Acinetobacter sp., Enterobacter sp., Flavobacterium sp., and Pseudomonas sp.) on maize growth and soil enzymatic activity over a 14-day period. At the plant level, germination, fresh and dry mass of the aerial and root parts, length, and stage of development of the stem, as well as the chlorophyll content, were evaluated. Furthermore, soil dehydrogenase, acid and alkaline phosphatases, pH, and electrical conductivity were evaluated. Rot fungi induced distinct effects on maize germination, with Pleurotus sp. strongly suppressing maize germination by 40% relative to that of the control. The isolated bacterial strains, except Enterobacter sp. O8, and 8 of the 12 fungus + bacterial strain combinations induced germination rates higher than those of the control (≥40%). Combinations of Flavobacterium sp. I57 and Pseudomonas sp. O81 with the rot fungus Pleurotus sp. significantly improved plant shoot length (from 28.0 to 37.0 cm) and developmental stage (fourth leaf length increase from 10.0 to 16.8 cm), respectively, compared with the same bacteria alone or in combination with the rot fungus Trametes sp. In the soil, the presence of both fungi appeared to stabilize phosphatase activity compared to their activity when only bacteria were present, while also promoting overall dehydrogenase enzymatic activity in the soil. Integrating all parameters, Trametes sp. rot fungus + Enterobacter sp. O8 may be a potential combination to be explored in the context of agricultural production, and future studies should focus on the consistency of this combination’s performance over time and its effectiveness in the field.