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Plants (Basel, Switzerland) Jul 2021Heavy metals are primarily generated and deposited in the environment, causing phytotoxicity. This work evaluated fenugreek plants' morpho-physiological and biochemical...
Heavy metals are primarily generated and deposited in the environment, causing phytotoxicity. This work evaluated fenugreek plants' morpho-physiological and biochemical responses under mercury stress conditions toward Ag nanoparticles and applications. The fabrication of Ag nanoparticles by was monitored and described by UV/Vis analysis, FTIR, and SEM. The effect of mercury on vegetative growth was determined by measuring the root and shoots length, the number and area of leaves, the relative water content, and the weight of the green and dried plants; appraisal of photosynthetic pigments, proline, hydrogen peroxide, and total phenols content were also performed. In addition, the manipulation of Ag nanoparticles, and their combination were tested for mercury stress. Here, Ag nanoparticles were formed at 420 nm with a uniform cuboid form and size of 85 nm. Interestingly, the gradual suppression of vegetal growth and photosynthetic pigments by mercury, Ag nanoparticles, and were detected; however, carotenoids and anthocyanins were significantly increased. In addition, proline, hydrogen peroxide, and total phenols content were significantly increased because mercury and enhance this increase. Ag nanoparticles achieve higher levels by the combination. Thus, and Ag nanoparticles could have the plausible ability to relieve and combat mercury's dangerous effects in fenugreek.
PubMed: 34371552
DOI: 10.3390/plants10071349 -
Acta Crystallographica. Section F,... Dec 2022Serine palmitoyltransferase (SPT) catalyses the first reaction in sphingolipid biosynthesis: the decarboxylative condensation of L-serine (L-Ser) and palmitoyl-CoA to...
Serine palmitoyltransferase (SPT) catalyses the first reaction in sphingolipid biosynthesis: the decarboxylative condensation of L-serine (L-Ser) and palmitoyl-CoA to form 3-ketodihydrosphingosine. SPT from Sphingobacterium multivorum has been isolated and its crystal structure in complex with L-Ser has been determined at 2.3 Å resolution (PDB entry 3a2b). However, the quality of the crystal was not good enough to judge the conformation of the cofactor molecule and the orientations of the side chains of the amino-acid residues in the enzyme active site. The crystal quality was improved by revision of the purification procedure and by optimization of both the crystallization procedure and the post-crystallization treatment conditions. Here, the crystal structure of SPT complexed with tris(hydroxymethyl)aminomethane (Tris), a buffer component, was determined at 1.65 Å resolution. The protein crystallized at 20°C and diffraction data were collected from the crystals to a resolution of 1.65 Å. The crystal belonged to the tetragonal space group P422, with unit-cell parameters a = b = 61.32, c = 208.57 Å. Analysis of the crystal structure revealed C4-C5-C5A-O4P (77°) and C5-C5A-O4P-P (-143°) torsion angles in the phosphate-group moiety of the cofactor pyridoxal 5'-phosphate (PLP) that are more reasonable than those observed in the previously reported crystal structure (14° and 151°, respectively). Furthermore, the clear electron density showing a Schiff-base linkage between PLP and the bulky artificial ligand Tris indicated exceptional flexibility of the active-site cavity of this enzyme. These findings open up the possibility for further study of the detailed mechanisms of substrate recognition and catalysis by this enzyme.
Topics: Serine C-Palmitoyltransferase; Tromethamine; Crystallography, X-Ray; Pyridoxal Phosphate; Serine
PubMed: 36458620
DOI: 10.1107/S2053230X22010937 -
Nature Food Aug 2023China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the...
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
Topics: Animals; Humans; Anti-Bacterial Agents; Chickens; Drug Resistance, Bacterial; Farms; Metagenomics; Abattoirs; Escherichia coli; Machine Learning
PubMed: 37563495
DOI: 10.1038/s43016-023-00814-w -
International Journal of Systematic and... Aug 2021A bacterial strain, arapr2, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family...
A bacterial strain, arapr2, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family and more specifically to the genus . The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative CR11 and 98.25 % to NCCP-246. Genome relatedness indexes revealed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between arapr2 and its closest relative ( CR11) were 92.97 % and 52.00 %, respectively; for NCCP-246, the ANI and dDDH values were 82.46 and 27.6%, respectively. The genomic DNA of strain arapr2 was 6.02 Mbp long, had a DNA G+C content of 40.4 mol% and had 5504 protein-coding genes. The results obtained in this study suggests that strain arapr2 (CIP 111872=LMG 31848) represents a new species for which the name sp. nov. is proposed. Due to the fact that this strain has been isolated using wheat straw as carbon source, this novel bacterial strain represents a promising biotechnological tool for the fractionation of lignocellulosic biomass in the context of biorefinery development.
Topics: Agriculture; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; France; Lignin; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium
PubMed: 34406922
DOI: 10.1099/ijsem.0.004963 -
Scientific Reports Feb 2021Phoma stem canker (caused by the ascomycetes Leptosphaeria maculans and Leptosphaeria biglobosa) is an important disease of oilseed rape. Its effect on endophyte...
Phoma stem canker (caused by the ascomycetes Leptosphaeria maculans and Leptosphaeria biglobosa) is an important disease of oilseed rape. Its effect on endophyte communities in roots and shoots and the potential of endophytes to promote growth and control diseases of oilseed rape (OSR) was investigated. Phoma stem canker had a large effect especially on fungal but also on bacterial endophyte communities. Dominant bacterial genera were Pseudomonas, followed by Enterobacter, Serratia, Stenotrophomonas, Bacillus and Staphylococcus. Achromobacter, Pectobacter and Sphingobacterium were isolated only from diseased plants, though in very small numbers. The fungal genera Cladosporium, Botrytis and Torula were dominant in healthy plants whereas Alternaria, Fusarium and Basidiomycetes (Vishniacozyma, Holtermaniella, Bjerkandera/Thanatephorus) occurred exclusively in diseased plants. Remarkably, Leptosphaeria biglobosa could be isolated in large numbers from shoots of both healthy and diseased plants. Plant growth promoting properties (antioxidative activity, P-solubilisation, production of phytohormones and siderophores) were widespread in OSR endophytes. Although none of the tested bacterial endophytes (Achromobacter, Enterobacter, Pseudomonas, Serratia and Stenotrophomonas) promoted growth of oilseed rape under P-limiting conditions or controlled Phoma disease on oilseed rape cotyledons, they significantly reduced incidence of Sclerotinia disease. In the field, a combined inoculum consisting of Achromobacter piechaudii, two pseudomonads and Stenotrophomonas rhizophila tendencially increased OSR yield and reduced Phoma stem canker.
Topics: Achromobacter; Ascomycota; Brassica napus; Disease Resistance; Endophytes; Mycobiome; Phoma; Plant Diseases; Plant Roots; Stenotrophomonas
PubMed: 33589671
DOI: 10.1038/s41598-021-81937-7 -
International Journal of Molecular... Jul 2021and sp. are well known for their ability to decontaminate many environmental pollutants while sp. have been exploited for their thermostable enzymes. This study...
and sp. are well known for their ability to decontaminate many environmental pollutants while sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of , and EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.
Topics: Bacterial Proteins; Biodegradation, Environmental; Biofilms; DNA, Bacterial; Genome, Bacterial; Geobacillus; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Phylogeny; Polyesters; Pseudomonas aeruginosa; Sphingobacterium
PubMed: 34299026
DOI: 10.3390/ijms22147385 -
BMC Microbiology Dec 2021House fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising...
BACKGROUND
House fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae.
RESULTS
Bacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities.
CONCLUSIONS
House fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.
Topics: Animals; Archaea; Bacteria; Carbon; Cattle; Eukaryota; Houseflies; Larva; Manure; Microbiota; Nitrogen; RNA, Ribosomal
PubMed: 34911456
DOI: 10.1186/s12866-021-02418-5 -
The Science of the Total Environment Feb 2021Previous studies have provided evidence that bioremediation deals a novel approach to graffiti removal, thereby overcoming well-known limitations of current cleaning...
Previous studies have provided evidence that bioremediation deals a novel approach to graffiti removal, thereby overcoming well-known limitations of current cleaning methods. In the present study eight bacteria aerobic, mesophilic and culturable from the American ATCC and the German DSMZ collections of microorganisms, some isolated from car paint waste, colored deposits in a pulp dryer and wastewater from dye works, were tested in the removal of silver and black graffiti spray paints using immersion strategies with glass slides. Absorbance at 600 nm and live/dead assays were performed to estimate bacterial density and activity in all samples. Also, pH and dissolved organic carbon (DOC) and inorganic carbon (DIC) measurements in the liquid media were made, as well as, thickness, colorimetric and infrared (FTIR) spectroscopy measurements in graffiti paint layers were used to evaluate the presence of the selected bacteria in the samples and the graffiti bioremoval capacity of bacteria. Data demonstrated that of the eight bacteria studied, Enterobacter aerogenes, Comamonas sp. and a mixture of Bacillus sp., Delftia lacustris, Sphingobacterium caeni, and Ochrobactrum anthropi were the most promising for bioremoval of graffiti. According to significant changes in FTIR spectra, indicating an alteration of the paint polymeric structure, coupled with the presence of a consistent quantity of live bacteria in the medium as well as a significant increase of DIC (a measure of metabolic activity) and a change in paint color.
Topics: Bacteria; Biodegradation, Environmental; Delftia; Sphingobacterium
PubMed: 33280882
DOI: 10.1016/j.scitotenv.2020.144075 -
PeerJ 2021is a fungus that parasitizes insects. Compounds from are valuable in medicine and functional food. There are many kinds of bacteria in the natural sclerotia of ....
BACKGROUND
is a fungus that parasitizes insects. Compounds from are valuable in medicine and functional food. There are many kinds of bacteria in the natural sclerotia of . However, the community structure of microorganisms in samples from different places may be different, and their corresponding ecological functions require experimental verification.
METHODS
We used high-throughput sequencing technology to analyze bacterial 16S rRNA gene sequences in sclerotia of three samples of from Liaoning Province, China. We isolated, identified and verified the function of culturable bacterial strains from the sclerotia.
RESULTS
, , , and were the dominant bacterial genera in the sclerotia. And function prediction showed that and could be heterotrophic, could decompose urea, and could reduce nitrate. Two strains of bacteria isolated from the sclerotia of , N-2 and N-26, were identified as and , respectively, based on culture and biochemical characteristics. When these isolated strains were co-cultured with , the mycelium biomass and mycelium pellet diameter decreased, and the content of extracellular polysaccharide increased. Strain N-26 decreased the cordycepin content in .
CONCLUSIONS
Bacteria in sclerotia have an important effect on the growth of and the production of its metabolites.
PubMed: 34900429
DOI: 10.7717/peerj.12511 -
Scientific Reports Mar 2020Returning crop residues is a possible practice for balancing soil carbon (C) loss. The turnover rate of organic C from crop residues to soil C is dependent on soil...
Returning crop residues is a possible practice for balancing soil carbon (C) loss. The turnover rate of organic C from crop residues to soil C is dependent on soil microbial community dynamics. However, the relationship between any temporal changes in the soil microbial community after crop straw inputs and the dynamics of straw-C distribution in the soil organic carbon (SOC) pool remains unclear. The present study investigated the allocation of straw-C into soil dissolved organic carbon (DOC), microbial biomass carbon (MBC), particulate organic carbon (POC) and mineral-associated organic carbon (MaOC) using stable isotope probing, as well as the temporal changes in the soil bacterial and fungal communities using high-throughput sequencing. After the first 180 days of straw decomposition, approximately 3.93% and 19.82% of straw-C was transformed into soil MaOC and POC, respectively, while 0.02% and 2.25% of straw-C was transformed into soil DOC and MBC, respectively. The temporal change of the soil microbial community was positively correlated with the dynamics of straw-C distribution to SOC (R > 0.5, P < 0.05). The copiotrophic bacteria (e.g., Streptomyces, Massilia and Sphingobacterium), cellulolytic bacteria and fungi (e.g., Dyella and Fusarium, Talaromyces), acidophilic bacteria (e.g., Edaphobacter and unclassified Acidobacteriaceae), denitrifying and N-fixing microbes (e.g., Burkholderia-Paraburkholderia, Paraphaeosphaeria and Bradyrhizobium), and fungi unclassified Sordariomycetes were significantly correlated with straw-C distribution to specific SOC fractions (P < 0.05), which explained more than 90% of the variation of straw-C allocation into soils. Copiotrophic, certain cellulolytic and denitrifying microbes had positively correlated with DOC- and MaOC-derived from straw, and other cellulolytic fungi (e.g., Talaromyces) and specific bacteria (e.g. Bradyrhizobium) were positively correlated with POC-derived from straw. Our results highlight that the temporal change of soil microbial community structure well reflects the conversion and distribution process of straw-C to SOC fractions.
Topics: Bacteria; Carbon; Carbon Sequestration; DNA, Bacterial; DNA, Fungal; Fungi; High-Throughput Nucleotide Sequencing; Isotope Labeling; Microbiota; Phylogeny; Sequence Analysis, DNA; Soil; Soil Microbiology
PubMed: 32218459
DOI: 10.1038/s41598-020-62198-2