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MSystems Jun 2024The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the...
UNLABELLED
The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, their CO fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing species can fix inert N released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.
IMPORTANCE
The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing species could fix N in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.
PubMed: 38940525
DOI: 10.1128/msystems.00243-24 -
MSystems Jun 2024Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community...
Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (), giant viruses (, or NCLDV), and RNA viruses (). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.IMPORTANCEAs seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.
PubMed: 38940524
DOI: 10.1128/msystems.00753-24 -
MSystems Jun 2024We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain...
Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA.
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs ( = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (, , and ), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea ( Methanoperedens) in anoxic depths and uncultured bacteria (. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. . Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the . Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured archaea in the . Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the . Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
PubMed: 38940520
DOI: 10.1128/msystems.00314-24 -
ChemistryOpen Jun 2024Metal corrosion is a challenge for the world with heavy impacts on the economy. Study on the development of effectiveness anticorrosion additives is a promising...
Metal corrosion is a challenge for the world with heavy impacts on the economy. Study on the development of effectiveness anticorrosion additives is a promising strategery for the protection industry. This research focuses on the modification of hydrotalcite Mg-Al (HT) loading tannic acid (TA) with 3-(trimethoxy silyl) propyl methacrylate organo-silane (TMSPM) for applicating as an anti-corrosion additive for epoxy coating on the steel substrate. The suitable ratio of HT and modifiers was investigated and the suitable content of modified HT in epoxy matrix was found based on mechanical properties of the epoxy-based coating. The characteristics of modified HT were assessed through infrared (IR) spectroscopy, X-ray diffraction pattern (XRD), scanning electron microscopy (SEM), thermal gravimetry analysis (TGA), water contact angle (WCA), dynamic light scattering (DLS). Detailly, HT-TA3-S3 shows good stability in distilled water when HT/TA was modified with TMSPM which makes Zeta potential decreases significantly. Besides, SEM analysis presented HT-TA-S has a cylindrical shape about of 500 nm. Moreover, the crystallite size of HT/TA after being modified by TMSPM decreases sharply. All of these prove successfully synthesize HT loading TA with modified TMSPM. Water contact angle (WCA) decreases in case of loading TA and increases in case of modifying with TMSPM (WCA changed from HT (116.3°) to HT-TA (102.4°) and HT-TA-S (120.1°) which indicates the increased hydrophobicity of the sample. The obtained results showed HT/TA was modified successfully with TMSPM. The modification affected the size distribution and surface properties of HT nanoparticles while it did not impact on the crystal structure of HT. After incorporating modified HT/TA into the epoxy coating, the adhesion of coating to steel substrate was improved significantly. Consequently, the adhesion of epoxy/3 wt. % modified HT/TA coating was increased 3 times as compared to epoxy neat (from 0.76 MPa to 2.77 MPa). In addition, the relative hardness and gloss retention of epoxy/3 wt. % modified HT/TA coating reached the maximum values as compared to the others. Owing to salt spraying results, the epoxy/3 wt. % modified HT/TA exhibited an excellent anticorrosion ability for the steel substrate. All the above results show the potential of HT nanoparticles loading TA modified with TMSPM as anticorrosive additives for protective coatings on steel substrates.
PubMed: 38940235
DOI: 10.1002/open.202400120 -
Annals of Agricultural and... Jun 2024Ultraviolet light in the UV-C band is known as germicidal radiation and was widely used for both sterilization of the equipment and creation of a sterile environment....
INTRODUCTION AND OBJECTIVE
Ultraviolet light in the UV-C band is known as germicidal radiation and was widely used for both sterilization of the equipment and creation of a sterile environment. The aim of the study is to assess the effectiveness of inactivation of microorganisms deposited on surfaces with various textures by UV-C radiation disinfection devices.
MATERIAL AND METHODS
Five microorganisms (3 bacteria, virus, and fungus) deposited on metal, plastic, and glass surfaces with smooth and rough textures were irradiated with UV-C light emitted by low-pressure mercury lamp and ultraviolet emitting diodes (LEDs), from a distance of 0.5 m, 1 m, and 1.5 m to check their survivability after 20-minute exposure.
RESULTS AND CONCLUSIONS
Both tested UV-C sources were effective in inactivation of microorganisms; however, LED emitter was more efficient in this respect than the mercury lamp. The survival rate of microorganisms depended on the UV-C dose, conditioned by the distance from UV-C source being the highest at 0.5 m and the lowest at 1.5 m. For the tested microorganisms, the highest survival rate after UV-C irradiation was usually visible on glass and plastic surfaces. This observation should be considered in all environments where the type of material (from which the elements of technical equipment are manufactured and may be contaminated by specific activities) is important for maintaining the proper level of hygiene and avoiding the unwanted and uncontrolled spread of microbiological pollution.
Topics: Ultraviolet Rays; Disinfection; Fungi; Bacteria; Viruses; Surface Properties; Microbial Viability; Plastics; Glass
PubMed: 38940114
DOI: 10.26444/aaem/189695 -
Frontiers in Bioscience (Landmark... Jun 2024Mesenchymal stem/stromal cells (MSCs) have emerged as a promising therapeutic approach for a variety of diseases due to their immunomodulatory and tissue regeneration... (Review)
Review
Mesenchymal stem/stromal cells (MSCs) have emerged as a promising therapeutic approach for a variety of diseases due to their immunomodulatory and tissue regeneration capabilities. Despite their potential, the clinical application of MSC therapies is hindered by limited cell retention and engraftment at the target sites. Electrospun scaffolds, with their high surface area-to-volume ratio and tunable physicochemical properties, can be used as platforms for MSC delivery. However, synthetic polymers often lack the bioactive cues necessary for optimal cell-scaffold interactions. Integrating electrospun scaffolds and biological polymers, such as polysaccharides, proteins, and composites, combines the mechanical integrity of synthetic materials with the bioactivity of natural polymers and represents a strategic approach to enhance cell-scaffold interactions. The molecular interactions between MSCs and blended or functionalized scaffolds have been examined in recent studies, and it has been shown that integration can enhance MSC adhesion, proliferation, and paracrine secretion through the activation of multiple signaling pathways, such as FAK/Src, MAPK, PI3K/Akt, Wnt/β-catenin, and YAP/TAZ. Preclinical studies on small animals also reveal that the integration of electrospun scaffolds and natural polymers represents a promising approach to enhancing the delivery and efficacy of MSCs in the context of regenerating bone, cartilage, muscle, cardiac, vascular, and nervous tissues. Future research should concentrate on identifying the distinct characteristics of the MSC niche, investigating the processes involved in MSC-scaffold interactions, and applying new technologies in stem cell treatment and biofabrication to enhance scaffold design. Research on large animal models and collaboration among materials scientists, engineers, and physicians are crucial to translating these advancements into clinical use.
Topics: Humans; Mesenchymal Stem Cells; Tissue Scaffolds; Mesenchymal Stem Cell Transplantation; Animals; Polymers; Tissue Engineering
PubMed: 38940050
DOI: 10.31083/j.fbl2906228 -
Euro Surveillance : Bulletin Europeen... Jun 2024In 2022, an outbreak with severe bloodstream infections caused by occurred in an adult intensive care unit (ICU) in Hungary. Eight cases, five of whom died, were...
In 2022, an outbreak with severe bloodstream infections caused by occurred in an adult intensive care unit (ICU) in Hungary. Eight cases, five of whom died, were detected. Initial control measures could not stop the outbreak. We conducted a matched case-control study. In univariable analysis, the cases were more likely to be located around one sink in the ICU and had more medical procedures and medications than the controls, however, the multivariable analysis was not conclusive. Isolates from blood cultures of the cases and the ICU environment were closely related by whole genome sequencing and resistant or tolerant against the quaternary ammonium compound surface disinfectant used in the ICU. Thus, was able to survive in the environment despite regular cleaning and disinfection. The hospital replaced the disinfectant with another one, tightened the cleaning protocol and strengthened hand hygiene compliance among the healthcare workers. Together, these control measures have proved effective to prevent new cases. Our results highlight the importance of multidisciplinary outbreak investigations, including environmental sampling, molecular typing and testing for disinfectant resistance.
Topics: Humans; Serratia marcescens; Disease Outbreaks; Cross Infection; Hungary; Intensive Care Units; Serratia Infections; Disinfectants; Case-Control Studies; Male; Female; Adult; Middle Aged; Whole Genome Sequencing; Disinfection; Aged; Infection Control; Drug Resistance, Bacterial
PubMed: 38940004
DOI: 10.2807/1560-7917.ES.2024.29.26.2300492 -
Frontiers in Bioscience (Elite Edition) Jun 2024(), also called biotech yeast, is a yeast species with many applications in the biotechnology and pharmaceutical industries. This methylotrophic yeast has garnered... (Review)
Review
(), also called biotech yeast, is a yeast species with many applications in the biotechnology and pharmaceutical industries. This methylotrophic yeast has garnered significant interest as a platform for the production of recombinant proteins. Numerous benefits include effective secretory expression that facilitates the easy purification of heterologous proteins, high cell density with rapid growth, post-translational changes, and stable gene expression with integration into the genome. In the last thirty years, has also been refined as an adaptable cell factory that can produce hundreds of biomolecules in a laboratory setting and on an industrial scale. Indeed, over 5000 recombinant proteins have been generated so far using the expression method, which makes up 30% of the total cell protein or 80% of the total released protein. has been used to manufacture more than 70 commercial products in addition to over 300 industrial processes that have been granted licenses. Among these are useful enzymes for industrial biotechnology, including xylanase, mannanase, lipase, and phytase. The others are biopharmaceuticals, which include human serum albumin, insulin, hepatitis B surface antigen, and epidermal growth factor. Compared to other expression systems, this yeast is also considered a special host for synthesizing subunit vaccines, which have recently been supplanted by alternative vaccination types, such as inactivated/killed and live attenuated vaccines. Moreover, efficient production of recombinant proteins is achieved through multi-level optimization methods, such as codon bias, gene dosage, promoters, signal peptides, and environmental factors. Therefore, although expression systems are efficient and simple with clearly established process procedures, it is still necessary to determine the ideal conditions since these vary depending on the target protein to ensure the highest recombinant protein generation. This review addresses the expression system, its importance in industrial and biopharmaceutical protein production, and some bioprocessing and genetic modification strategies for efficient protein production. will eventually continue contributing as a potent expression system in research areas and industrial applications.
Topics: Saccharomycetales; Recombinant Proteins; Biological Products; Biotechnology; Pichia
PubMed: 38939917
DOI: 10.31083/j.fbe1602019 -
Journal of Extracellular Biology Feb 2024Colon cancer is one of the most commonly occurring tumours among both women and men, and over the past decades the incidence has been on the rise. As such, the need for...
Colon cancer is one of the most commonly occurring tumours among both women and men, and over the past decades the incidence has been on the rise. As such, the need for biomarker identification as well as an understanding of the underlying disease mechanism has never been greater. Extracellular vesicles are integral mediators of cell-to-cell communication and offer a unique opportunity to study the machinery that drives disease progression, and they also function as vectors for potential biomarkers. Tumour tissue and healthy mucosal tissue from the colons of ten patients were used to isolate tissue-resident EVs that were subsequently subjected to global quantitative proteomic analysis through LC-MS/MS. In total, more than 2000 proteins were identified, with most of the common EV markers being among them. Bioinformatics revealed a clear underrepresentation of proteins involved in energy production and cellular adhesion in tumour EVs, while proteins involved in protein biosynthesis were overrepresented. Additionally, 53 membrane proteins were found to be significantly upregulated in tumour EVs. Among them were several proteins with enzymatic functions that degrade the extracellular matrix, and three of these, Fibroblast activating factor (FAP), Cell surface hyaluronidase (CEMIP2), as well as Ephrin receptor B3 (EPHB3), were validated and found to be consistent with the global quantitative results. These stark differences in the proteomes between healthy and cancerous tissue emphasise the importance of the interstitial vesicle secretome as a major player of disease development.
PubMed: 38939898
DOI: 10.1002/jex2.127 -
Chemical & Biomedical Imaging Jun 2024There is significant and increasing interest in using the photothermal effect to record infrared (IR) absorption spectra localized to volumes that are considerably...
There is significant and increasing interest in using the photothermal effect to record infrared (IR) absorption spectra localized to volumes that are considerably smaller than the wavelength of excitation, i.e., subdiffraction imaging. As opposed to conventional IR microscopy, in which absorption and scattering of the illuminating light is measured, subdiffraction imaging can be achieved through detection of the sample's thermal response to IR absorption-induced heating. While this relationship has been examined by a variety of coarse-grained models, a generalized analysis of the dependence of temperature and surface deformation arising from an absorber below the surface has not been reported. Here, we present an analytical model to understand a sample's thermoelastic response in photothermal measurements. The model shows important dependence of the ability to record subdiffraction data on modulation frequency of exciting light, limitations imposed by optical sensing, and the potential to discern location of objects ultimately limited by noise and sharpness of the detecting mechanism. This foundational analysis should allow for better modeling, understanding, and harnessing of the relationship between absorption and sample response that underlies IR photothermal measurements.
PubMed: 38939874
DOI: 10.1021/cbmi.4c00018