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Ecotoxicology and Environmental Safety Dec 2021Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their...
Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their potentially negative environmental impacts. Recently, the degradability of neonicotinoid in soil has gained more attentions. However, what role soil microbes play in this degradation remains vastly underexplored. In this study, we compared the capacity of soil microbes sampled from different geographic regions and fields to degrade the neonicotinoid insecticide imidacloprid. Additionally, the composition of microbiota having low, middle, and high degradation activity was analyzed via high throughput sequencing. Correlations between microbiota composition and degradation activities were analyzed and reconfirmed. The results showed that the composition of soil microbiota and their degradation activity (ranged from zero to 96.25%) varied significantly between soil samples from different geographic locations. Correlation analysis showed that Paracoccus and Achromobacter bacteria were positively correlated with high degradation activity. Imidacloprid degradation experiments using these bacteria showed that Achromobacter sp. alone exhibited degradation activity reaching and sustaining 100% by day 20 while Paracoccus sp. did not. However, combining these bacteria resulted in increased degradation activity which reached 100% at day 15 relative to that achieved by Achromobacter sp. alone. This study demonstrated the capacity of soil microbes to degrade imidacloprid, and identified two promising bacterial candidates that could be potentially used in future to reduce imidacloprid accumulation in soils.
Topics: Achromobacter; Bacteria; Biodegradation, Environmental; Insecticides; Neonicotinoids; Nitro Compounds; Paracoccus; Soil; Soil Microbiology; Soil Pollutants
PubMed: 34544021
DOI: 10.1016/j.ecoenv.2021.112785 -
Microorganisms Apr 2022Cytochrome oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form... (Review)
Review
Cytochrome oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas several proteins identified to function in the biosynthesis of the common family A1 cytochrome oxidase show diversity in bacteria. Using the model organisms , , , and , the present review focuses on proteins for assembly of the heme , heme , Cu, and Cu metal centers. The known biosynthesis proteins are, in most cases, discovered through the analysis of mutants. All proteins directly involved in cytochrome oxidase assembly have likely not been identified in any organism. Limitations in the use of mutants to identify and functionally analyze biosynthesis proteins are discussed in the review. Comparative biochemistry helps to determine the role of assembly factors. This information can, for example, explain the cause of some human mitochondrion-based diseases and be used to find targets for new antimicrobial drugs. It also provides information regarding the evolution of aerobic bacteria.
PubMed: 35630371
DOI: 10.3390/microorganisms10050926 -
Microbes and Environments 2022Bacteria communicate through signaling molecules that coordinate group behavior. Hydrophobic signals that do not diffuse in aqueous environments are used as signaling...
Bacteria communicate through signaling molecules that coordinate group behavior. Hydrophobic signals that do not diffuse in aqueous environments are used as signaling molecules by several bacteria. However, limited information is currently available on the mechanisms by which these molecules are transported between cells. Membrane vesicles (MVs) with diverse functions play important roles in the release and delivery of hydrophobic signaling molecules, leading to differences in the dynamics of signal transportation from those of free diffusion. Studies on Paracoccus denitrificans, which produces a hydrophobic long-chain N-acyl homoserine lactone (AHL), showed that signals were loaded into MVs at a concentration with the potential to trigger the quorum sensing (QS) response with a "single shot" to the cell. Furthermore, stimulating the formation of MVs increased the release of signals from the cell; therefore, a basic understanding of MV formation is important. Novel findings revealed the formation of MVs through different routes, resulting in the production of different types of MVs. Methods such as high-speed atomic force microscopy (AFM) phase imaging allow the physical properties of MVs to be analyzed at a nanometer resolution, revealing their heterogeneity. In this special minireview, we introduce the role of MVs in bacterial communication and highlight recent findings on MV formation and their physical heterogeneity by referring to our research. We hope that this minireview will provide basic information for understanding the functionality of MVs in ecological systems.
Topics: Acyl-Butyrolactones; Biological Transport; Quorum Sensing; Ecosystem
PubMed: 36504177
DOI: 10.1264/jsme2.ME22083 -
Scientific Reports Sep 2023Gut microbiota is an emerging editable cardiovascular risk factor. We aim to investigate gut and coronary plaque microbiota, using fecal samples and angioplasty balloons...
Gut microbiota is an emerging editable cardiovascular risk factor. We aim to investigate gut and coronary plaque microbiota, using fecal samples and angioplasty balloons from patients with acute coronary syndrome (ACS), chronic coronary syndrome (CCS) and control subjects. We examined bacterial communities in gut and coronary plaques by 16S rRNA sequencing and we performed droplet digital PCR analysis to investigate the gut relative abundance of the bacterial genes CutC/CntA involved in trimethylamine N-oxide synthesis. Linear discriminant analysis effect size (LEfSe) at the genus and species levels displayed gut enrichment in Streptococcus, Granulicatella and P. distasonis in ACS compared with CCS and controls; Roseburia, C. aerofaciens and F. prausnitzii were more abundant in controls than in patients. Principal component analysis (PCA) of 41 differentially abundant gut taxa showed a clustering of the three groups. In coronary plaque, LEfSe at the genus level revealed an enrichment of Staphylococcus and Streptococcus in ACS, and Paracoccus in CCS, whereas PCA of 15 differentially abundant plaque taxa exhibited clustering of ACS and CCS patients. CutC and CntA genes were more abundant in ACS and CCS than in controls while no significant difference emerged between ACS and CCS. Our results indicate that ACS and CCS exhibit a different gut and plaque microbial signature, suggesting a possible role of these microbiotas in coronary plaque instability.
Topics: Humans; Acute Coronary Syndrome; RNA, Ribosomal, 16S; Heart; Angioplasty, Balloon; Carnobacteriaceae
PubMed: 37679428
DOI: 10.1038/s41598-023-41867-y -
Applied Microbiology and Biotechnology Mar 2020Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked... (Review)
Review
Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.
Topics: Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Membrane Proteins; Paracoccus denitrificans; Quorum Sensing
PubMed: 32002601
DOI: 10.1007/s00253-020-10400-w -
Applied and Environmental Microbiology Aug 2021Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as...
Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, sp. 363 and sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of sp. 363 carries three synthase genes and transcribes genes along three PHA pathways (I to III), whereas sp. 392 carries only one gene and transcribes genes along one pathway (I). Thus, sp. 363 has a versatile repertoire of genes and pathways enabling production of both short- and medium-chain-length PHA products. Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, sp. 363 and sp. 392, are able to produce various types of PHA from inexpensive carbon sources. sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.
Topics: Bacterial Proteins; Cold Temperature; Genome, Bacterial; Halomonas; Ice Cover; Paracoccus; Phylogeny; Polyhydroxyalkanoates; Seawater; Temperature
PubMed: 34160268
DOI: 10.1128/AEM.00929-21 -
International Journal of Molecular... Mar 2016His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs). An overview is presented on various surfaces ranging from flat to... (Review)
Review
His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs). An overview is presented on various surfaces ranging from flat to spherical and modified with linker molecules with nitrile-tri-acetic acid (NTA) terminal groups to bind his-tagged proteins in a strict orientation. The bound proteins are submitted to in situ dialysis in the presence of lipid micelles to form a so-called protein-tethered bilayer lipid membrane (ptBLM). MRPs, such as the cytochrome c oxidase (CcO) from R. sphaeroides and P. denitrificans, as well as photosynthetic reactions centers (RCs) from R. sphaeroides, were thus investigated. Electrochemical and surface-sensitive optical techniques, such as surface plasmon resonance, surface plasmon-enhanced fluorescence, surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced resonance Raman spectroscopy (SERRS), were employed in the case of the ptBLM structure on flat surfaces. Spherical particles ranging from µm size agarose gel beads to nm size nanoparticles modified in a similar fashion were called proteo-lipobeads (PLBs). The particles were investigated by laser-scanning confocal fluorescence microscopy (LSM) and UV/Vis spectroscopy. Electron and proton transfer through the proteins were demonstrated to take place, which was strongly affected by the membrane potential. MRPs can thus be used for biosensing purposes under quasi-physiological conditions.
Topics: Bacterial Proteins; Biomimetics; Biosensing Techniques; Electrochemical Techniques; Electron Transport Complex IV; Immobilized Proteins; Lipid Bilayers; Oxidation-Reduction; Paracoccus denitrificans; Photosynthetic Reaction Center Complex Proteins; Rhodobacter sphaeroides; Spectrophotometry, Infrared; Spectrum Analysis, Raman; Surface Plasmon Resonance
PubMed: 26950120
DOI: 10.3390/ijms17030330 -
Marine Drugs Mar 2023Astaxanthin (3,3-dihydroxy-β, β-carotene-4,4-dione) is a ketocarotenoid synthesized by , , , , , , some bacteria (), yeasts, and lobsters, among others However, it is... (Review)
Review
Astaxanthin (3,3-dihydroxy-β, β-carotene-4,4-dione) is a ketocarotenoid synthesized by , , , , , , some bacteria (), yeasts, and lobsters, among others However, it is majorly synthesized by alone (about 4%). The richness of natural astaxanthin over synthetic astaxanthin has drawn the attention of industrialists to cultivate and extract it via two stage cultivation process. However, the cultivation in photobioreactors is expensive, and converting it in soluble form so that it can be easily assimilated by our digestive system requires downstream processing techniques which are not cost-effective. This has made the cost of astaxanthin expensive, prompting pharmaceutical and nutraceutical companies to switch over to synthetic astaxanthin. This review discusses the chemical character of astaxanthin, more inexpensive cultivating techniques, and its bioavailability. Additionally, the antioxidant character of this microalgal product against many diseases is discussed, which can make this natural compound an excellent drug to minimize inflammation and its consequences.
Topics: Antioxidants; Biological Availability; Xanthophylls; Carotenoids; Chlorophyceae
PubMed: 36976225
DOI: 10.3390/md21030176 -
Frontiers in Immunology 2021Microbiota acquired during labor and through the first days of life contributes to the newborn's immune maturation and development. Mother provides probiotics and... (Observational Study)
Observational Study
Microbiota acquired during labor and through the first days of life contributes to the newborn's immune maturation and development. Mother provides probiotics and prebiotics factors through colostrum and maternal milk to shape the first neonatal microbiota. Previous works have reported that immunoglobulin A (IgA) secreted in colostrum is coating a fraction of maternal microbiota. Thus, to better characterize this IgA-microbiota association, we used flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in human colostrum and neonatal feces. We identified IgA bound bacteria (IgA+) and characterized their diversity and composition shared in colostrum fractions and neonatal fecal bacteria. We found that IgA2 is mainly associated with , , and , among other genera shared in colostrum and neonatal fecal samples. We found that metabolic pathways related to epithelial adhesion and carbohydrate consumption are enriched within the IgA2+ fecal microbiota. The association of IgA2 with specific bacteria could be explained because these antibodies recognize common antigens expressed on the surface of these bacterial genera. Our data suggest a preferential targeting of commensal bacteria by IgA2, revealing a possible function of maternal IgA2 in the shaping of the fecal microbial composition in the neonate during the first days of life.
Topics: Antigens; Bacteria; Colostrum; Feces; Female; Gastrointestinal Microbiome; Humans; Immunoglobulin A; Infant, Newborn; Linear Models; Longitudinal Studies; Pregnancy; Prospective Studies; RNA, Ribosomal, 16S
PubMed: 34804008
DOI: 10.3389/fimmu.2021.712130 -
Current Issues in Molecular Biology 2019Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of... (Review)
Review
Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of methanol or methylamine. The growing availability of genome sequence data has made it possible to investigate methylotrophy in other . The examination of a large number of spp. genomes reveals great variability in C1 metabolism, which have been shaped by different evolutionary mechanisms. Surprisingly, the methylotrophy schemes of many strains appear to have quite different genetic and biochemical bases. Besides the expected 'autotrophic methylotrophs', many strains of this genus possess another C1 assimilatory pathway, the serine cycle, which seems to have at least three independent origins. Analysis of the co-occurrence of different methylotrophic pathways indicates, on the one hand, evolutionary linkage between the Calvin cycle and the serine cycle, and, on the other hand, that genes encoding some C1 substrate-oxidizing enzymes occur more frequently in association with one or the other. This suggests that some genetic module combinations form more harmonious enzymatic sets, which act with greater efficiency in the methylotrophic process and thus undergo positive selection.
Topics: Alphaproteobacteria; Biodiversity; Biological Evolution; Genome, Bacterial; Metabolic Networks and Pathways; Methanol; Methylamines; Oxidation-Reduction; Paracoccus
PubMed: 31166188
DOI: 10.21775/cimb.033.117