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Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the generated single or double knockout strains displayed no, or only a weak, phenotype. Only the mutant defici.
The type IX secretion system (T9SS), which is involved in pathogenicity, motility, and utilization of complex biopolymers, is a novel protein secretion system confined to the phylum Bacteroidetes. Cytophaga hutchinsonii , a common cellulolytic soil bacterium belonging to the phylum Bacteroidetes , can rapidly digest crystalline cellulose using a novel strategy. In this study, the deletion mutant of chu_0174 ( gldN ) was obtained using PY6 medium supplemented with Stanier salts. GldN was verified to be a core component of C. hutchinsonii T9SS, and is indispensable for cellulose degradation, motility, and secretion of CTD proteins. Notably, gldN showed a significant growth defect in Ca 2+ and Mg 2+ deficient media. The growth defect could be
Success of microbial natural products discovery programs is dependent on quick and concise discrimination between isolates from diverse environments. However, laboratory isolation and identification of priority genera using current 16S rRNA PCR-based methods is both challenging and time-consuming. An emerging strategy for rapid isolate discrimination is protein fingerprinting via MALDI mass spectrometry. Using our in-house environmental isolate repository, we have created a main spectral (MSP) library for the Bruker Biotyper MALDI mass spectrometer that contains 95 entries including Burkholderia, Caballeronia , Paraburkholderia , and other environmentally related genera. The library creation required the acquisition of over 2,250 mass spect.
S. agnetis has been previously associated with subclinical or clinically mild cases of mastitis in dairy cattle and is one of several Staphylococcal species that have been isolated from the bone and blood of lame broilers. We reported that S. agnetis could be obtained frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers [Al-Rubaye et al. , PLoS One 10:e0143336, 2015, ]. A particular isolate, S. agnetis 908, can induce lameness in over 50% of exposed chickens, exceeding normal BCO incidences in broiler operations. We reported the assembly and annotation of the genome of isolate 908. To better understand the relationship between dairy cattle and broiler isolates, we assembled 11 additional genomes for S.
Freshwater ecosystems are exposed to multiple stressors, but their individual and combined effects remain largely unexplored. Here, we investigated the response of stream biofilm bacterial communities to warming, hydrological stress and pesticide exposure. We used 24 artificial streams onto which epilithic (growing on coarse sediments) and epipsammic (growing on fine sediments) stream biofilms were maintained. Bacterial community composition and estimated function of biofilms exposed during 30 days to individual and combined stressors were assessed using 16S rRNA gene metabarcoding. Among the individual effects by stressors, hydrological stress (i.e. a simulated low-flow situation) was the most relevant, as it significantly altered 57% of t.
Ornithobacterium rhinotracheale (ORT) is a causative agent of respiratory tract infections in avian hosts worldwide, but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of ORT, which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between ORT populations through comparative genomics of clinical isolates from different US turkey producers. ORT clinical isolates were collected from four major US turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucle.
Acidophiles play a dominant role in driving elemental cycling in natural acid mine drainage (AMD) habitats and exhibit important application value in bioleaching and bioremediation. Acidity is an inevitable environmental stress and a key factor that affects the survival of acidophiles in their acidified natural habitats; however, the regulatory strategies applied by acidophilic bacteria to withstand low pH are unclear. We identified the significance of the ferric uptake regulator (Fur) in acidophiles adapting to acidic environments and discovered that Fur is ubiquitous as well as highly conserved in acidophilic bacteria. Mutagenesis of the fur gene of Acidithiobacillus caldus ( A. caldus ), a prototypical acidophilic sulfur-oxidizing bacter.
In Candida glabrata , the transcription factor Cg Rds2 has been previously characterized as a regulator of glycerophospholipid metabolism, playing a crucial role in the response to osmotic stress. Here, we report that Cg Rds2 is also involved in the response to pH 2.0 stress. At pH 2.0, deletion of CgRDS2 led to reduced cell growth and survival by 33% and 57%, respectively, compared with those of the wild-type strain. These adverse phenotypes resulted from the down-regulation of genes related to energy metabolism in the Cgrds2 strain at pH 2.0, which led to a 34% reduction of intracellular ATP content and a 24% decrease in membrane permeability. In contrast, overexpression of CgRDS2 rescued the growth defect of the Cgrds2 strain and increas.
Anthropogenic activity impacts stream ecosystems resulting in a loss of diversity and ecosystem function; however, little is known about the response of aquatic microbial communities to changes in land use. Here, microbial communities were characterized in 82 headwater streams across a gradient of urban and agricultural land use using 16S rRNA gene amplicon sequencing and compared to a rich dataset of physicochemical variables and traditional benthic invertebrate indicators. Microbial diversity and community structure differed among watersheds with high agricultural, urban, and forested land uses, and community structure differed in streams classified in good, fair, poor, and very poor condition using benthic invertebrate indicators. Microb.
RAD23 can repair yeast DNA lesions through nucleotide excision repair (NER), a mechanism dependent on proteasome activity and ubiquitin chains but different from photolyase-depending photorepair of ultraviolet-induced DNA damages. However, this accessory NER protein remains functionally unknown in filamentous fungi. In this study, orthologous RAD23 in Beauveria bassiana , an insect-pathogenic fungus as a main source of fungal insecticides, was found to interact with the photolyase PHR2 enabling to repair DNA lesions by degradation of UVB-induced cytotoxic (6-4)-pyrimidine-pyrimidine photoproducts under visible light, and hence play an essential role in photoreactivation of UVB-inactivated conidia but no role in reactivation of such conidia
The pathogen Listeria monocytogenes causes listeriosis, a severe foodborne disease associated with high mortality. Rapid and sensitive methods are required for specific detection of this pathogen during food production. Bioluminescence-based reporter bacteriophages are genetically engineered viruses that infect their host cells with high specificity and transduce a heterologous luciferase gene, whose activity can be detected with high sensitivity to indicate the presence of viable target cells. Here, we use synthetic biology for de novo genome assembly and activation as well as CRISPR-Cas-assisted phage engineering to construct a set of reporter phages for the detection and differentiation of viable Listeria cells. Based on a single phage b.
A nationwide study on the occurrence of extended-spectrum β-lactamase (ESBL)/AmpC in nonhospitalized horses in the Netherlands was performed. Molecular characterization was done, and questionnaires were analyzed to identify factors associated with carriage. In total, 796 horse owners were approached; 281 of these submitted a fecal sample from their horse(s), resulting in 362 samples. All samples were cultured qualitatively in Luria-Bertani (LB) broth and subsequently on MacConkey agar, both supplemented with 1 mg/liter cefotaxime (LB+ and MC+). Positive samples were subsequently cultured quantitatively on MC+. Initial extended-spectrum-β-lactamase (ESBL)/AmpC screening was performed by PCR, followed by whole-genome sequencing on selected st.
This study examined the microbicidal activity of 222-nm UV radiation (UV 222 ), which is potentially a safer alternative to the 254-nm UV radiation (UV 254 ) that is often used for surface decontamination. Spores and/or growing and stationary-phase cells of Bacillus cereus , Bacillus subtilis , Bacillus thuringiensis , Staphylococcus aureus , and Clostridioides difficile and a herpesvirus were all killed or inactivated by UV 222 and at lower fluences than with UV 254 . B. subtilis spores and cells lacking the major DNA repair protein RecA were more sensitive to UV 222 , as were spores lacking their DNA-protective proteins, the α/β-type small, acid-soluble spore proteins. The spore cores’ large amount of Ca 2+ -dipicolinic acid (~25% of the
The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus , representing a potential novel species for which the name " Candidatus Desulfobulbus rimicarensis" is proposed. Genomic and transcriptomic analyses reveal that this ba.
APSES-type transcription factors (TFs) have analogous and diverse functions in the regulation of fungal morphogenesis processes. However, little is known about these functions in microsclerotium formation. In this study, we characterized two orthologous APSES genes ( MrStuA and MrXbp ) in the entomopathogenic fungus Metarhizium rileyi . Deletion of either MrStuA or MrXbp impaired dimorphic transition, conidiation, fungal virulence, and microsclerotium formation. Compared with the wild-type strain, MrStuA and MrXbp mutants were hypersensitive to thermal and oxidative stress. Furthermore, transcriptome sequencing analysis revealed that MrStuA and MrXbp independently regulate their own distinctive subsets of signaling pathways during dimorphic.
The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales , but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chi.
To enhance the growth performance of Saccharomyces cerevisiae under osmotic stress, mutant XCG001, which tolerates up to 1.5 M NaCl, was isolated through adaptive laboratory evolution (ALE). Comparisons of the transcriptome data of mutant XCG001 and the wild-type strain identified ELO2 as being associated with osmotic tolerance. In the ELO2 overexpression strain (XCG010), the contents of inositol phosphorylceramide (IPC; t18:0/26:0), mannosylinositol phosphorylceramide [MIPC; t18:0/22:0(2OH)], MIPC (d18:0/22:0), MIPC (d20:0/24:0), mannosyldiinositol phosphorylceramide [M(IP) 2 C; d20:0/26:0], M(IP) 2 C [t18:0/26:0(2OH)], and M(IP) 2 C [d20:0/26:0(2OH)] increased by 88.3 times, 167 times, 63.3 times, 23.9 times, 27.9 times, 114 times, and 20.
The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new "species." We have previously shown that in a simple, constant envir.
Cultivated fecal indicator bacteria such as Escherichia coli and enterococci are typically used to assess the sanitary quality of recreational waters. However, these indicators suffer from several limitations, such as the length of time needed to obtain results and the fact that they are commensal inhabitants of the gastrointestinal tract of many animals and have fate and transport characteristics dissimilar to pathogenic viruses. Numerous emerging technologies that offer same-day water quality results or pollution source information or that more closely mimic persistence patterns of disease-causing pathogens that may improve water quality management are now available, but data detailing geospatial trends in wastewater across the United Sta.
The abandoned Kam Kotia Mine (Canada) is undergoing remediation. A geosynthetic-clay-liner (GCL) cover system was installed in the Northern Impounded Tailings (NIT) area in 2008 to isolate acid-generating tailings from water and oxygen and to mitigate sulfide oxidation. The cover system includes a vegetated uppermost soil layer underlain by a granular protective layer (sand), a clay moisture-retaining layer, a GCL, a granular capillary-break material (cushion sand), and a crushed waste rock-capillary break layer installed above the tailings. The goal of this study was to characterize the microbiology of the covered tailings to assess the performance of the cover system for mitigating sulfide bio-oxidation. Tailings beneath the GCL were char.

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