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Polymers Oct 2022Microplastics (MP) are a global environmental problem because they persist in the environment for long periods of time and negatively impact aquatic organisms. Possible...
Microplastics (MP) are a global environmental problem because they persist in the environment for long periods of time and negatively impact aquatic organisms. Possible solutions for removing MP from the environment include biological processes such as bioremediation, which uses microorganisms to remove contaminants. This study investigated the biodegradation of polystyrene (PS) by two bacteria, and , isolated from environmental samples in which MPs particles were present. First, determining significant factors affecting the biodegradation of MP-PS was conducted using the Taguchi design. Then, according to preliminary experiments, the optimal conditions for biodegradation were determined by a full factorial design (main experiments). The RSM methodology was applied, and statistical analysis of the obtained models was performed to analyze the influence of the studied factors. The most important factors for MP-PS biodegradation by were agitation speed, concentration, and size of PS, while agitation speed, size of PS, and optical density influenced the process by . However, the optimal conditions for biodegradation of MP-PS by were achieved at = 66.20, MP size = 413.29, and agitation speed = 100.45. The best conditions for MP-PS biodegradation by were 161.08, 334.73, and 0.35, as agitation speed, MP size, and OD, respectively. In order to get a better insight into the process, the following analyzes were carried out. Changes in CFU, TOC, and TIC concentrations were observed during the biodegradation process. The increase in TOC values was explained by the detection of released additives from PS particles by LC-MS analysis. At the end of the process, the toxicity of the filtrate was determined, and the surface area of the particles was characterized by FTIR-ATR spectroscopy. Ecotoxicity results showed that the filtrate was toxic, indicating the presence of decomposition by-products. In both FTIR spectra, a characteristic weak peak at 1715 cm was detected, indicating the formation of carbonyl groups (-C=O), confirming that a biodegradation process had taken place.
PubMed: 36297877
DOI: 10.3390/polym14204299 -
Molecules (Basel, Switzerland) Apr 2021The present study was aimed to evaluate the suitability of agro-wastes and crude vegetable oils for the cost-effective production of poly-β-hydroxybutyrate (PHB), to...
The present study was aimed to evaluate the suitability of agro-wastes and crude vegetable oils for the cost-effective production of poly-β-hydroxybutyrate (PHB), to evaluate growth kinetics and PHB production in RZS4 and sp. RZS1 with these carbon substrates and to study the biodegradation of PHB accumulated by these cultures. RZS4 and sp. RZS1 accumulates higher amounts of PHB corn (79.90% of dry cell mass) and rice straw (66.22% of dry cell mass) medium respectively. The kinetic model suggests that the sp. RZS1 follows the Monod model more closely than RZS4. Both the cultures degrade their PHB extract under the influence of PHB depolymerase. Corn waste and rice straw appear as the best and cost-effective substrates for the sustainable production of PHB from RZS4 and sp. RZS1. The biopolymer accumulated by these organisms is biodegradable in nature. The agro-wastes and crude vegetable oils are good and low-cost sources of nutrients for the growth and production of PHB and other metabolites. Their use would lower the production cost of PHB and the low-cost production will reduce the sailing price of PHB-based products. This would promote the large-scale commercialization and popularization of PHB as an ecofriendly bioplastic/biopolymer.
Topics: Agriculture; Alcaligenes; Biodegradation, Environmental; Biomass; Biopolymers; Fermentation; Kinetics; Plastics; Pseudomonas; Spectrum Analysis; Waste Products
PubMed: 33922162
DOI: 10.3390/molecules26092443 -
Clinical Microbiology and Infection :... Jun 2022To characterize Alcaligenes faecalis metallo-β-lactamase (MBL) AFM-2 and AFM-3 from clinical Pseudomonas aeruginosa isolates NDTH10366, NDTH9845 and WTJH17.
OBJECTIVES
To characterize Alcaligenes faecalis metallo-β-lactamase (MBL) AFM-2 and AFM-3 from clinical Pseudomonas aeruginosa isolates NDTH10366, NDTH9845 and WTJH17.
METHODS
Clinical isolates were whole-genome sequenced using the Illumina and Oxford Nanopore platforms. MICs of clinical isolates and transformants containing MBL genes were determined using broth microdilution methods. Kinetic parameters of purified AFM and NDM-1 were measured using a spectrophotometer. The AFM structure was modelled with SWISS-MODEL.
RESULTS
NDTH10366 and NDTH9845 were extensively drug-resistant (XDR) isolates carrying bla and multiple copies of bla, whereas WTJH17 was an XDR isolate carrying bla. The plasmid-borne bla and bla genes are associated with a novel ISCR element, ISCR29. AFM-2 and AFM-3, differing from AFM-1 by one amino acid substitution each, shared 86.2% and 86.6% amino acid sequence identity with NDM-1, respectively. Phylogenetic analysis confirmed the close relationship between AFM and NDM. Expression of AFM and NDM-1 under their native promoters in DH5α and PAO1 led to elevated MICs for all tested β-lactams except aztreonam. Comparable catalytic abilities were observed for AFM and NDM-1 when hydrolysing nitrocefin, cefepime, imipenem and biapenem, whereas for other tested β-lactams AFM displayed weaker enzymatic activities. Modelling AFM structure revealed a characteristic αβ/βα fold with two zinc-binding active sites.
CONCLUSIONS
AFM from clinical P. aeruginosa isolates demonstrated β-lactamase activity comparable to NDM-1. Co-carriage of bla and bla renders clinical P. aeruginosa isolates non-susceptible to all antipseudomonal β-lactams. The association of bla genes with translocatable genetic elements and plasmids highlights their concerning potential for dissemination.
Topics: Alcaligenes faecalis; Anti-Bacterial Agents; Humans; Microbial Sensitivity Tests; Phylogeny; Pseudomonas Infections; Pseudomonas aeruginosa; beta-Lactamases; beta-Lactams
PubMed: 34826621
DOI: 10.1016/j.cmi.2021.11.012 -
Applied Bionics and Biomechanics 2021The pollution of toxic heavy metals is considered one of the most important environmental issues which has accelerated dramatically due to changing industrial... (Review)
Review
The pollution of toxic heavy metals is considered one of the most important environmental issues which has accelerated dramatically due to changing industrial activities. This review focuses on the most common methods, strategies, and biological approaches of heavy metal bioremediation. Also, it provides a general overview of the role of microorganisms in the bioremediation of heavy metals in polluted environments. Advanced methods of heavy metal remediation include physicochemical and biological methods; the latter can be further classified into in situ and ex situ bioremediation. The in situ process includes bioventing, biosparging, biostimulation, bioaugmentation, and phytoremediation. Ex situ bioremediation includes land farming, composting, biopiles, and bioreactors. Bioremediation uses naturally occurring microorganisms such as , , , , and . Generally, bioremediation is of very less effort, less labor intensive, cheap, ecofriendly, sustainable, and relatively easy to implement. Most of the disadvantages of bioremediation relate to the slowness and time-consumption; furthermore, the products of biodegradation sometimes become more toxic than the original compound. The performance evaluation of bioremediation might be difficult as it has no acceptable endpoint. There is a need for further studies to develop bioremediation technologies in order to find more biological solutions for bioremediation of heavy metal contamination from different environmental systems.
PubMed: 34804199
DOI: 10.1155/2021/1609149 -
Microorganisms Jun 2021The rhizobacterium AVO110 exhibits antagonism toward the phytopathogenic fungus . This strain efficiently colonizes hyphae and is able to feed on their exudates. Here,...
The rhizobacterium AVO110 exhibits antagonism toward the phytopathogenic fungus . This strain efficiently colonizes hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of AVO110. The phylogeny of all available genomes separates environmental isolates, including AVO110, from those obtained from infected human blood and oyster tissues, which cluster together with . Core and pan-genome analyses showed that strains encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of genes related to biofilm formation, several of which are transcriptionally modulated by exudates. One of these genes () encodes a GGDEF/EAL domain protein specific to spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water samples. We also show that CmpA has a role in biofilm formation and that the integrity of its EAL domain is involved in this function. This study contributes to a better understanding of the niche-specific adaptations and lifestyles of , including the mycophagous behavior of strain AVO110.
PubMed: 34202389
DOI: 10.3390/microorganisms9071388 -
Molecular Microbiology Jun 1998Alternative sigma factors provide a means of regulating gene expression in response to various extracellular changes. One such class of sigma factors appears to control... (Review)
Review
Alternative sigma factors provide a means of regulating gene expression in response to various extracellular changes. One such class of sigma factors appears to control a variety of functions, including expression of heat-shock genes in Escherichia coli, biosynthesis of alginates and carotenoids in Pseudomonas aeruginosa and Myxococcus xanthus, respectively, iron uptake in E. coli and Pseudomonas spp., nickel and cobalt efflux in Alcaligenes europhus, plant pathogenicity in Pseudomonas syringae and synthesis of outer membrane proteins in Photobacterium sp. strain SS9. Most of these activities deal with extracytoplasmic functions, and such sigmas have been designated as ECF sigma factors. They have also been characterized in Mycobacteria as well as gram-positive bacteria such as Streptomyces coelicolor and Bacillus subtilus and the archaea Sulpholobus acidocaldarius. ECF factors belong to a subfamily of the sigma 70 class, based on their sequence conservation and function across bacterial species. The promoter consensus sequences recognized by the ECF factors are also highly conserved. In most of the cases, the activity of these factors is modulated by a cognate inner membrane protein that has been shown, both in E. coli and in P. aeruginosa, to act as an anti-sigma activity. This inner membrane protein is presumed to serve as a sensor and signalling molecule, allowing an adaptive response to specific environmental change. Presumably, an on-and-off switch of the anti-sigma activity leads to the release of the sigma factor and thereby to the co-ordinate transcription of the specific regulon it governs.
Topics: Gene Expression Regulation, Bacterial; Genes, Bacterial; Regulon; Sigma Factor; Signal Transduction; Transcription, Genetic
PubMed: 9680198
DOI: 10.1046/j.1365-2958.1998.00865.x -
Molecules (Basel, Switzerland) Feb 2020Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in... (Review)
Review
Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in agricultural practices has led to environmental toxicity and human health issues. Oxidation, incineration, adsorption, and microbial degradation methods have been developed to remove insecticidal residues from soil/water environments. Compared with physicochemical methods, biodegradation is considered to be a cost-effective and ecofriendly approach to the removal of pesticide residues. Therefore, micro-organisms have become a key component of the degradation and detoxification of methomyl through catabolic pathways and genetic determinants. Several species of methomyl-degrading bacteria have been isolated and characterized, including , , , , , , , , and . The degradation pathways of methomyl and the fate of several metabolites have been investigated. Further in-depth studies based on molecular biology and genetics are needed to elaborate their role in the evolution of novel catabolic pathways and the microbial degradation of methomyl. In this review, we highlight the mechanism of microbial degradation of methomyl along with metabolic pathways and genes/enzymes of different genera.
Topics: Adsorption; Alcaligenes; Bacillus; Biodegradation, Environmental; Cholinesterase Inhibitors; Flavobacterium; Humans; Incineration; Insecticides; Metabolic Networks and Pathways; Methomyl; Oxidation-Reduction; Paracoccus; Pseudomonas; Serratia; Soil Pollutants; Trametes; Water Pollutants, Chemical
PubMed: 32046287
DOI: 10.3390/molecules25030738 -
International Journal of Food Science 2021Yellow cured codfish has a typical yellow colour, distinctive taste, and low salt content due to its special curing process of the raw salted codfish involving several...
Yellow cured codfish has a typical yellow colour, distinctive taste, and low salt content due to its special curing process of the raw salted codfish involving several soaks in water of the raw salted codfish, alternated with drying steps. The purpose of this study was to assess the main functional groups of bacteria involved in this process and relate them with physicochemical properties of the product. A total of 28 codfish from Iceland were supplied by two local companies. Seven stages of the curing process were analyzed. From each of these seven stages, four fish samples were collected to carry out the microbial and physicochemical analyses (moisture, salt content, pH, total volatile basic nitrogen (TVB-N), and trimethylamine nitrogen (TMA-N)). Bacteria counts were performed using the MPN method and adequate culture media for aerobic, proteolytic, sulphite-reducing, biogenic amine, and trimethylamine-producing and ammonifying bacteria. Strains isolated from the highest dilutions with microbial growth were used to characterize the predominant bacteria. The results showed that total aerobic counts increased from 3.9 log MPN/g in raw salted codfish to 5.9 log MPN/g in the final. Proteolytic, ammonifying, and trimethylamine bacteria producers also increased to 8, 7.5, and 6.5 log MPN/g, respectively. The salt content decreases (from 17% until 8%) and moisture increases (53% until 67%) during the salted-raw-codfish soaking, favoring sulphite-reducing and biogenic amine-producing species, confirming that desalting enhances potential spoilers. The subsequent drying step benefits proteolytic, ammonifying, and trimethylamine-producing bacteria, with a corresponding non-protein-nitrogen content (TVB-N and TMA-N) increase. The dominant bacteria during yellow curing belong to the genera , , , and with a clear positive correlation between the content of and and TVB-N and TMA-N concentration. spp. are the dominant bacteria in the steps where the product has a higher salt concentration; thus, it could be particularly useful as an indicator to control the industrially yellow curing process and could have an important role in the development of the final characteristics of this product.
PubMed: 34778447
DOI: 10.1155/2021/6072731 -
PloS One 2021Microbes have been identified as fundamental for the good health of bees, acting as pathogens, protective agent against infection/inorganic toxic compounds, degradation...
Microbes have been identified as fundamental for the good health of bees, acting as pathogens, protective agent against infection/inorganic toxic compounds, degradation of recalcitrant secondary plant metabolites, definition of social group membership, carbohydrate metabolism, honey and bee pollen production. However, study of microbiota associated with bees have been largely confined to the honeybees and solitary bees. Here, I characterized the microbiota of indoor surface nest of four brazilian stingless bee species (Apidae: Meliponini) with different construction behaviors and populations. Bees that use predominantly plant material to build the nest (Frieseomelitta varia and Tetragonisca angustula) have a microbiome dominated by bacteria found in the phylloplane and flowers such as Pseudomonas sp. and Sphingomonas sp. Species that use mud and feces (Trigona spinipes) possess a microbiome dominated by coliforms such as Escherichia coli and Alcaligenes faecalis. Melipona quadrifasciata, which uses both mud / feces and plant resin, showed a hybrid microbiome with microbes found in soil, feces and plant material. These findings indicate that indoor surface microbiome varies widely among bees and reflects the materials used in the construction of the nests.
Topics: Animals; Bacteria; Bees; Honey; Microbiota
PubMed: 34242231
DOI: 10.1371/journal.pone.0252933 -
Microbiological Research Jan 2022The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254...
The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254 species. Although type strains have been employed to estimate Pseudomonas diversity, they represent a small fraction of the genomic diversity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified taxonomic inconsistencies with several type strains and found that 25.65 % of the Pseudomonas genomes deposited on Genbank are misclassified. The phylogenetic tree using single-copy genes from representative genomes in each species cluster in the distance network revealed at least 14 Pseudomonas groups, including the P. alcaligenes group proposed here. We show that Pseudomonas is likely an admixture of different genera and should be further divided. This study provides an overview of Pseudomonas diversity from a network and phylogenomic perspective that may help reduce the propagation of mislabeled Pseudomonas genomes.
Topics: Genetic Variation; Genome, Bacterial; Genomics; Phylogeny; Pseudomonas
PubMed: 34808515
DOI: 10.1016/j.micres.2021.126919