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Journal of Thermal Biology Feb 2024Heat stress is a common environmental factor in livestock breeding that has been shown to impact the development of antibiotic resistance within the gut microbiota of...
Heat stress is a common environmental factor in livestock breeding that has been shown to impact the development of antibiotic resistance within the gut microbiota of both human and animals. However, studies investigating the effect of temperature on antibiotic resistance in Enterococcus isolates remain limited. In this study, specific pathogen free (SPF) mice were divided into a control group maintained at normal temperature and an experimental group subjected to daily 1-h heat stress at 38 °C, respectively. Gene expression analysis was conducted to evaluate the activation of heat shock responsive genes in the liver of mice. Additionally, the antibiotic-resistant profile and antibiotic resistant genes (ARGs) in fecal samples from mice were analyzed. The results showed an upregulation of heat-inducible proteins HSP27, HSP70 and HSP90 following heat stress exposure, indicating successful induction of cellular stress within the mice. Furthermore, heat stress resulted in an increase in the proportion of erythromycin-resistant Enterococcus isolates, escalating from 0 % to 0.23 % over a 30-day duration of heat stress. The resistance of Enterococcus isolates to erythromycin also had a 128-fold increase in minimum inhibitory concentration (MIC) within the heated-stressed group compared to the control group. Additionally, a 2∼8-fold rise in chloramphenicol MIC was observed among these erythromycin-resistant Enterococcus isolates. The acquisition of ermB genes was predominantly responsible for mediating the erythromycin resistance in these Enterococcus isolates. Moreover, the abundance of macrolide, lincosamide and streptogramin (MLS) resistant-related genes in the fecal samples from the heat-stressed group exhibited a significant elevation compared to the control group, primarily driven by changes in bacterial community composition, especially Enterococcaceae and Planococcaceae, and the transfer of mobile genetic elements (MGEs), particularly insertion elements. Collectively, these results highlight the role of environmental heat stress in promoting antibiotic resistance in Enterococcus isolates and partly explain the increasing prevalence of erythromycin-resistant Enterococcus isolates observed among animals in recent years.
Topics: Humans; Animals; Mice; Erythromycin; Enterococcus; Anti-Bacterial Agents; Feces; Heat-Shock Response
PubMed: 38428103
DOI: 10.1016/j.jtherbio.2024.103786 -
Nucleic Acids Research Apr 2024RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in...
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
Topics: RNA Ligase (ATP); Substrate Specificity; Archaeal Proteins; Planococcaceae; Protein Engineering; Mutation; Models, Molecular; Adenosine Triphosphate; Oligonucleotides
PubMed: 38421610
DOI: 10.1093/nar/gkae149 -
The Science of the Total Environment Apr 2024Bioremediation based on microbial-induced carbonate precipitation (MICP) was conducted in cadmium and lead contaminated soil to investigate the effects of MICP on Cd and...
Bioremediation based on microbial-induced carbonate precipitation (MICP) was conducted in cadmium and lead contaminated soil to investigate the effects of MICP on Cd and Pb in soil. In this study, soil indigenous nitrogen was shown to induce MICP to stabilize heavy metals without inputting exogenous urea. The results showed that applying Bacillus pasteurii coupled with CaCl reduced Cd and Pb bioavailability, which could be clarified through the proportion of exchangeable Cd and Pb in soil decreasing by 23.65 % and 12.76 %, respectively. Moreover, B. pasteurii was combined separately with hydroxyapatite (HAP), eggshells (ES), and oyster shells (OS) to investigate their effects on soil heavy metals' chemical fractions, toxicity characteristic leaching procedure (TCLP)-extractable Cd and Pb as well as enzymatic activity. Results showed that applying B. pasteurii in soil significantly decreased the heavy metals in the exchangeable fraction and increased them in the carbonate phase fraction. When B. pasteurii was combined with ES and OS, the content of carbonate-bound Cd increased by 114.72 % and 118.81 %, respectively, significantly higher than when B. pasteurii was combined with HAP, wherein the fraction of carbonate-bound Cd increased by 86 %. The combination of B. pasteurii and biogenic calcium effectively reduced the leached contents of Cd and Pb in soil, and the TCLP-extractable Cd and Pb fractions decreased by 43.88 % and 30.66 %, respectively, in the BP + ES group and by 52.60 % and 41.77 %, respectively, in the BP + OS group. This proved that MICP reduced heavy metal bioavailability in the soil. Meanwhile, applying B. pasteurii and calcium materials significantly increased the soil urease enzyme activity. The microstructure and chemical composition of the soil samples were studied, and the results from scanning electron microscope, Fourier transform infra-red spectroscopy, and X-ray diffraction demonstrated the MICP process and identified the formation of CaCO, CaCdCO, and PbCO in heavy metal-contaminated soil.
Topics: Cadmium; Calcium; Lead; Soil; Metals, Heavy; Bacteria; Calcium Carbonate; Biodegradation, Environmental; Carbonates; Soil Pollutants; Sporosarcina
PubMed: 38378057
DOI: 10.1016/j.scitotenv.2024.171060 -
International Journal of Systematic and... Feb 2024A Gram-staining-positive, motile, aerobic and rod-shaped bacterium, designated strain MA9 was isolated from wetland soil of ecology park, in Seoul, Republic of Korea....
A Gram-staining-positive, motile, aerobic and rod-shaped bacterium, designated strain MA9 was isolated from wetland soil of ecology park, in Seoul, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. Strain MA9 grew at 10-37 °C and at pH 6.0-9.5 on TSB. Menaquinone MK-7 was the predominant respiratory quinone and iso-C, iso-C and C c alcohol were the major fatty acids. The main polar lipids were phosphatidylethanolamine (PE), phosphatidylserine (PS), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The peptidoglycan type of the cell wall was A4α l-Lys-d-Glu. Based on 16S rRNA gene sequencing, strain MA9 clustered with species of the genus and appeared closely related to DSM 12223 (97.8 % sequence similarity), DSM 21993 (97.6 %), DSM 21046 (97.6 %) and DSM 101595 (96.6 %). The G+C content of the genomic DNA was 37.0 mol%. Digital DNA-DNA hybridization between strain MA9 and type strains of , , and resulted in values below 70 %. Strain MA9 could be differentiated genotypically and phenotypically from the recognized species of the genus . The isolate therefore represents a novel species, for which the name sp. nov. is proposed, with the type strain MA9 (=KACC 22212 = LMG 32188).
Topics: Fatty Acids; Soil; RNA, Ribosomal, 16S; Wetlands; Soil Microbiology; DNA, Bacterial; Base Composition; Phylogeny; Sequence Analysis, DNA; Bacterial Typing Techniques; Planococcaceae
PubMed: 38323635
DOI: 10.1099/ijsem.0.006065 -
Microorganisms Dec 2023In an attempt to isolate new probiotic bacteria, two Gram-variable, spore-forming, rod-shaped aerobic bacteria designated as strain A4 and A15 were isolated from the...
In an attempt to isolate new probiotic bacteria, two Gram-variable, spore-forming, rod-shaped aerobic bacteria designated as strain A4 and A15 were isolated from the feces of Canada geese (). Strain A4 was able to grow in high salt levels and exhibited lipase activity, while A15 did not propagate under these conditions. Both were positive for starch hydrolysis, and they inhibited the growth of . The strains of the 16S rRNA sequence shared only 94% similarity to previously identified spp. The ANI (78.08%) and AAI (82.35%) between the two strains were less than the species threshold. Searches for the most similar genomes using the Mash/Minhash algorithm showed the nearest genome to strain A4 and A15 as sp. P13 (distance of 21%) and (distance of 17%), respectively. spp. strains A4 and A15 contain urease genes, and a fibronectin-binding protein gene indicates that these bacteria may bind to eukaryotic cells in host gastrointestinal tracts. Phenotypic and phylogenetic data, along with low dDDH, ANI, and AAI values for strains A4 and A15, indicate these bacteria are two novel isolates of the genus: sp. A4 sp. nov., type strain as and sp. A15 sp. nov., type strain .
PubMed: 38257897
DOI: 10.3390/microorganisms12010070 -
ACS Applied Materials & Interfaces Jan 2024Microbially induced calcium carbonate precipitation (MICP) has emerged as a novel technology with the potential to produce building materials through lower-temperature...
Microbially induced calcium carbonate precipitation (MICP) has emerged as a novel technology with the potential to produce building materials through lower-temperature processes. The formation of calcium carbonate bridges in MICP allows the biocementation of aggregate particles to produce biobricks. Current approaches require several pulses of microbes and mineralization media to increase the quantity of calcium carbonate minerals and improve the strength of the material, thus leading to a reduction in sustainability. One potential technique to improve the efficiency of strength development involves trapping the bacteria on the aggregate surfaces using silane coupling agents such as positively charged 3-aminopropyl-methyl-diethoxysilane (APMDES). This treatment traps bacteria on sand through electrostatic interactions that attract negatively charged walls of bacteria to positively charged amine groups. The APMDES treatment promoted an abundant and immediate association of bacteria with sand, increasing the spatial density of ureolytic microbes on sand and promoting efficient initial calcium carbonate precipitation. Though microbial viability was compromised by treatment, urea hydrolysis was minimally affected. Strength was gained much more rapidly for the APMDES-treated sand than for the untreated sand. Three injections of bacteria and biomineralization media using APMDES-treated sand led to the same strength gain as seven injections using untreated sand. The higher strength with APMDES treatment was not explained by increased calcium carbonate accrual in the structure and may be influenced by additional factors such as differences in the microstructure of calcium carbonate bridges between sand particles. Overall, incorporating pretreatment methods, such as amine silane coupling agents, opens a new avenue in biomineralization research by producing materials with an improved efficiency and sustainability.
Topics: Sand; Silanes; Sporosarcina; Bacteria; Carbonates; Calcium Carbonate; Amines; Chemical Precipitation
PubMed: 38176018
DOI: 10.1021/acsami.3c13971 -
Scientific Reports Dec 2023This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing...
This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing 3N-BBM medium was inoculated with Microglena sp., Tetradesmus obliquus, and Desmodesmus subspicatus mixture with a density of 1.0 × 10 cells/mL and the consortium was cultivated for 30 days. Then, the bioreactor was semi-continuously fed with liquid digestate with hydraulic retention time (HRT) of 30 days, and the treatment process was continued for the next 15 weeks. The change in the microalgal and cyanobacterial species domination was measured in regular intervals using cell counting with droplet method on a microscope slide. At the end of the experiment, Desmonostoc sp. cyanobacteria (identified with 16S ribosomal RNA genetical analysis) as well as Tetradesmus obliquus green algae along with Rhodanobacteraceae and Planococcaceae bacteria (determined with V3-V4 16sRNA metagenomic studies) dominated the microbial community in the photobioreactor. The experiment demonstrated high treatment efficiency, since nitrogen and soluble COD were removed by 89.3 ± 0.5% and 91.2 ± 1.6%, respectively, whereas for phosphates, 72.8 ± 2.1% removal rate was achieved.
Topics: Photobioreactors; Waste Disposal, Fluid; Microalgae; Vegetables; Anaerobiosis; Cyanobacteria; Nitrogen; Chlorophyceae; Biomass
PubMed: 38114556
DOI: 10.1038/s41598-023-50173-6 -
Journal of Applied Microbiology Jan 2024This study aimed to understand the morphological effects of (in)organic additives on microbially induced calcium carbonate precipitation (MICP).
AIM
This study aimed to understand the morphological effects of (in)organic additives on microbially induced calcium carbonate precipitation (MICP).
METHODS AND RESULTS
MICP was monitored in real time in the presence of (in)organic additives: bovine serum albumin (BSA), biofilm surface layer protein A (BslA), magnesium chloride (MgCl2), and poly-l-lysine. This monitoring was carried out using confocal microscopy to observe the formation of CaCO3 from the point of nucleation, in comparison to conditions without additives. Complementary methodologies, namely scanning electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction, were employed to assess the visual morphology, elemental composition, and crystalline structures of CaCO3, respectively, following the crystals' formation. The results demonstrated that in the presence of additives, more CaCO3 crystals were produced at 100 min compared to the reaction without additives. The inclusion of BslA resulted in larger crystals than reactions containing other additives, including MgCl2. BSA induced a significant number of crystals from the early stages of the reaction (20 min) but did not have a substantial impact on crystal size compared to conditions without additives. All additives led to a higher content of calcite compared to vaterite after a 24-h reaction, with the exception of MgCl2, which produced a substantial quantity of magnesium calcite.
CONCLUSIONS
The work demonstrates the effect of several (in)organic additives on MICP and sets the stage for further research to understand additive effects on MICP to achieve controlled CaCO3 precipitation.
Topics: Calcium Carbonate; Magnesium Chloride; Sporosarcina; Chemical Precipitation; Microscopy, Electron, Scanning
PubMed: 38111211
DOI: 10.1093/jambio/lxad309 -
Microbiology Spectrum Dec 2023Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific...
Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain SK 55 and broaden the knowledge of the species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.
Topics: United States; DNA, Bacterial; Bacillaceae; Planococcaceae
PubMed: 37975675
DOI: 10.1128/spectrum.00686-23 -
Biology Oct 2023The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied...
The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the , and genera were dominant in samples from both types of communities. The first type of community was also dominated by members of , , and an unclassified representative of the family. The second type of community also had a significant proportion of , SAR92, SAR11 Clade I, NS9, and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
PubMed: 37887020
DOI: 10.3390/biology12101310