Symbiotic nitrogen fixation (SNF) is an energetically expensive process performed by bacteria during endosymbiotic relationships with plants. The bacteria require the plant to provide a carbon source for generation of reductant to power SNF. While C4-dicarboxylates (succinate, fumarate, malate) appear to be the primary, if not sole, carbon source provided to the bacteria, the contribution of each C4-dicarboxylate is not known. Read More
Appl Environ Microbiol 2017 Sep 15. Epub 2017 Sep 15.
Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, Surrey KT1 2EE, UK
Campylobacter jejuni is a foodborne pathogen recognized as the leading cause of human bacterial gastroenteritis. The wide use of antibiotics in medicine and in animal husbandry has led to an increased incidence of antibiotic resistance in Campylobacter In addition to a role in multidrug resistance, the Campylobacter CmeABC RND-type efflux pump, which is associated with multidrug resistance (MDR), may also be involved in virulence. As a vehicle of pathogenic microorganisms, the protozoan Acanthamoeba is a good model for the investigation of bacterial survival in the environment and molecular mechanisms of pathogenicity. Read More
The filamentous fungus Trichoderma reesei is predominantly found in the tropics, but also in more temperate regions, such as Europe and is widely known as producer of high amounts of plant cell wall degrading enzymes. We sequenced the genome of the sexually competent isolate CBS999.97, which is phenotypically different from female sterile QM6a, but can cross sexually with QM6a. Read More
Bradyrhizobium encompasses a variety of bacteria that can live in symbiotic and endophytic associations with leguminous and non-leguminous plants such as rice. Therefore, it can be expected that rice endophytic bradyrhizobia can be applied in the rice-legume crop rotation system. Some endophytic bradyrhizobial strains were isolated from rice (Oryza sativa L. Read More
The genomes of many bacteria that participate in nitrogen cycling through the process of nitrification contain putative genes associated with acyl-homoserine lactone (AHL) quorum sensing (QS). AHL QS or bacterial cell-cell signaling is a method of bacterial communication and gene regulation and may be involved in nitrogen oxide fluxes or other important phenotypes in nitrifying bacteria. Here, we carried out a broad survey of AHL production in nitrifying bacteria in three steps. Read More
The human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications, however a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. Read More
Hanseniaspora uvarum (anamorph Kloeckera apiculata) is a predominant yeast on wine grapes and other fruits and has a strong influence on wine quality, even when Saccharomyces cerevisiae starter cultures are employed. In this work we sequenced and annotated approximately 93% of the H. uvarum genome. Read More
The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in United States (US) beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) beef cattle. Samples (N = 719) were collected during harvest and distributed over a year. Read More
A dense exopolysaccharide (EPS) matrix is crucial for cyanobacterial survival in terrestrial xeric environments, in which cyanobacteria undergo frequent expansion and shrinkage processes during environmental desiccation-rehydration cycles. However, it is unclear how terrestrial cyanobacteria coordinate the structural dynamics of the EPS matrix upon the expansion and shrinkage to avoid potential mechanical stress while benefiting from the matrix. In the present study, we sought to answer this question by investigating the gene expression, protein dynamics, enzymatic characteristics and biological roles of WSPA, an abundantly secreted protein, in the representative terrestrial cyanobacterium Nostoc flagelliforme The results demonstrated that WSPA is a novel β-galactosidase that facilitates softening of the EPS matrix by breaking the polysaccharide backbone under substantial moisture or facilitates the thickening and re-linkage of the broken matrix upon drying process, and thus these regulations are well correlated with moisture availability or desiccation-rehydration cycles. Read More
The dental caries pathogen Streptococcus mutans is continually exposed to several types of stress in the oral biofilm environment. Oxidative stress generated by reactive oxygen species has a major impact on the establishment, persistence and virulence of S. mutans. Read More
Appl Environ Microbiol 2017 Sep 8. Epub 2017 Sep 8.
Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C., Denmark
The chitinolytic system of Listeria monocytogenes thus far comprises two chitinases, ChiA and ChiB, and a lytic polysaccharide monooxygenase, Lmo2467. The role of the system in the bacterium appears to be pleiotropic, as besides mediating hydrolysis of chitin, the second most ubiquitous carbohydrate in nature, the chitinases have been deemed important for colonization of unicellular moulds, as well as mammalian hosts. In order to identify additional components of the chitinolytic system, we screened a transposon mutant library for mutants exhibiting impaired chitin hydrolysis. Read More
The productivity of industrial fermentation processes is essentially limited by the biomass specific substrate consumption rate (qS) of the applied microbial production system. Since qS depends on the growth rate (μ), we highlight the potential of the fastest growing non-pathogenic bacterium, Vibrio natriegens, as novel candidate for future biotechnological processes. V. Read More
RNA stable isotope probing and high throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing roots and rhizosphere soil of oilseed rape, to identify taxa assimilating plant-derived carbon following (13)CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Read More
Human noroviruses (hNoVs) are a known public health concern associated with the consumption of leafy green vegetables. While a number of studies have investigated pathogen reduction on the surfaces of leafy greens during the postharvest washing process, there remains a paucity of data on the level of treatment needed to inactivate viruses in the wash water, which is critical for preventing cross-contamination. The objective of this study was to quantify the susceptibility of hNoV GI, hNoV GII, murine norovirus (MNV), and bacteriophage MS2 to free chlorine in whole leaf, chopped romaine, and shredded iceberg lettuce industrial leafy green wash waters, each sampled three times over a 4-month period. Read More
Appl Environ Microbiol 2017 Sep 1. Epub 2017 Sep 1.
Department of Biological Sciences, Department of Food, Nutrition, and Packaging Science, Clemson University, Clemson, SC 29634, United States
Carpet been attributed to prolonged and reoccurring outbreaks of human noroviruses (HuNoV), the leading cause of acute gastroenteritis worldwide. Viral recovery from environmental surfaces, such as carpet, remains undeveloped. Our aim was to determine survival of HuNoV surrogates on an understudied environmental surface, carpet. Read More
Glyphosate is the most widely used herbicide worldwide and a critical tool for weed control in no-till cropping systems. However, there are concerns about non-target impacts of long-term glyphosate use on soil microbial communities. We investigated the impacts of repeated glyphosate treatments on bacterial communities in the soil and rhizosphere of wheat in soils with and without long-term history of glyphosate use. Read More
Heterotrophic bacteria producing sulfide (H2S, HS(-), and S(2-)) during aerobic growth is a common phenomenon. Some with sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO) can oxidize self-produced sulfide to sulfite and thiosulfate, but others without these enzymes will release sulfide into the medium, from which H2S can volatilize into the gas phase. Here, we report Cupriavidus necator H16 with the fccAB genes, encoding flavocytochrome c-sulfide dehydrogenases (FCSDs), also oxidized self-produced H2S. Read More
The pathogenic Vibrio species (cholerae, parahaemolyticus and vulnificus) represent a constant threat to human health, causing food-borne and skin wound infections as a result of ingestion or exposure to contaminated water and seafood. Recent studies have highlighted Vibrio's ability to acquire fatty acids from environmental sources and assimilate them into cell membranes. The possession and conservation of such machinery provokes consideration of fatty acids as important factors in the pathogenic lifestyle of Vibrio species. Read More
Complete utilization of carbohydrate fractions is one of the prerequisites for obtaining an economically favourable lignocellulosic biomass conversion. This study shows that xylan in untreated rice straw was saccharified to xylose in one step without chemical pretreatment, yielding 58.2% of the theoretically maximum value by Paenibacillus curdlanolyticus B-6 PcAxy43A, a weak lignin-binding trifunctional xylanolytic enzyme, endoxylanase/β-xylosidase/arabinoxylan arabinofuranohydrolase. Read More
Appl Environ Microbiol 2017 Aug 25. Epub 2017 Aug 25.
Department of Food, Bioprocessing and Nutrition Sciences, and Center for Human health and the Environment, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA; Agricultural Research Service, United States Department of Agriculture (USDA), Peoria, Illinois, USA.
In the foodborne pathogen Listeria monocytogenes, arsenic resistance is primarily encountered in serotype 4b clones considered to have enhanced virulence, and is associated with an arsenic resistance gene cluster within a 35 kb chromosomal region, Listeria genomic island 2 (LGI2). LGI2 was first identified in strain Scott A and includes genes putatively involved in arsenic and cadmium resistance, DNA integration, conjugation and pathogenicity. However, genomic localization and sequence content of LGI2 remain poorly characterized. Read More
The mechanism of whole-genome duplication (WGD) in yeast has been intensively studied because it has a large impact on yeast evolution. WGD has shaped the genomic architecture of modern Saccharomyces cerevisiae; however, the mechanism for restoring fertility after interspecies hybridization, which would be involved in the process of WGD, has not been thoroughly elucidated. In this study, we obtained a draft genome sequence of salt-tolerant yeast Zygosaccharomyces rouxii NBRC110957 and revealed that it is a hybrid lineage of Z. Read More
Lactobacillus brevis is an obligatory heterofermentative lactic acid bacterium that produces high levels of acetate which improves the aerobic stability of silages against deterioration by yeasts and molds. However, the mechanism involved in acetate accumulation has yet to be understood. Here, experimental evidence indicated that aerobiosis resulted in the conversion of lactate to acetate after glucose exhaustion in L. Read More
Whooping cough is a highly-contagious respiratory disease caused by Bordetella pertussis. Despite vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. Read More
Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4 produces a novel bacteriocin, lactolisterin BU, with strong antimicrobial activity against many species of Gram-positive bacteria, including important food spoilage and food-borne pathogens such as Listeria monocytogenes, Staphylococcus aureus, Bacillus sp. Read More
We studied the diversity of Limnohabitans using Reverse Line Blot Hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov Reservoir (CZ). To examine the succession of distinct lineages we performed two studies: (i) an intensive spring sampling program at the lacustrine part of the Římov Reservoir (from ice melt through a phytoplankton peak to the clear water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the composition of distinct Limnohabitans lineages allowed for the identification of 'generalists' that were always present throughout the whole season as well as 'specialists' that appeared in the reservoir only for limited periods of time or irregularly. Read More
Vibrio parahaemolyticus naturally-occurs in brackish and marine waters and is one of the leading causes of seafood-borne illness. Previous work studying the ecology of V. parahaemolyticus is often limited in geographic extent and lacking a full range of environmental measures. Read More
Appl Environ Microbiol 2017 Aug 25. Epub 2017 Aug 25.
Department of Food Science and Center for Molecular Immunology and Infectious Disease, Pennsylvania State University, University Park, PA, USA
In this study, the effect of individual lecithin phospholipids on the antimicrobial properties of eugenol against E. coli C600 was investigated. We tested five major phospholipids common in soy or egg lecithin (DPPC, DSPC, DPPE, DPPA and DPPS) and one synthetic cationic phospholipid (EPC 18:0). Read More
This study aimed at improving the functional attributes and shelf-life of burrata cheese by using protective lactobacilli (Lactobacillus plantarum LPAL and Lactobacillus rhamnosus LRB), fructoligosaccharides and inulin. Six burrata cheeses were made by using: i) the traditional protocol (control); ii) addition of 0.5% fructoligosaccharides and inulin (DF cheese); iii) protective lactobacilli in milk alone (PL cheese); iv) protective lactobacilli in milk and governing liquid (2PL cheese); v) protective lactobacilli in milk and dietary fibers (DF_PL cheese); and vi) protective lactobacilli in milk, governing liquid and dietary fibers (DF_2PL cheeses). Read More
Soil is a complex niche, where survival of microorganisms is at risk due to the presence of antimicrobial agents. Many microbes chemically modify cytotoxic compounds to block their deleterious effects. Streptothricin is a broad-spectrum antibiotic produced by streptomycetes that affects Gram-positive and Gram-negative bacteria alike. Read More
Biofilms are microbial communities that inhabit various surfaces and are surrounded by extracellular matrices (ECMs). Clinical microbiologists have shown that the majority of chronic infections are caused by biofilms, after introduction of the first biofilm infection model by J.W. Read More
The model white-rot basidiomycete Ceriporiopsis (Gelatoporia) subvermispora B encodes putative natural product biosynthesis genes. Among them is the gene for the seven-domain nonribosomal peptide synthetase CsNPS2. It is a member of the as-yet uncharacterized fungal type VI siderophore synthetase family which is highly conserved and widely distributed among the basidiomycetes. Read More
This study presents the biodiversity and ecology of microbial mats developed in thermal gradients (20-65 °C) in the surroundings of three drillings (CH, CI, MB) tapping a hyperthermal aquifer from Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physico-chemical factors were explored. Read More
The glucose/mannose-PTS permease EII(Man) encoded by manLMN in the dental caries pathogen Streptococcus mutans has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in manL affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance and competence. Using promoter:reporter fusions, expression of the manLMN and the fruRKI operons, encoding a transcriptional regulator, a fructose-1-P kinase and a fructose-PTS permease EII(Fru), respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR, and components of EII(Man) Expression of genes for EII(Man) and EII(Fru) was directly regulated by CcpA and CR, as evinced by in vivo and in vitro methods. Read More
n-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of n-alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. The alkane oxidation operon, alkW1-alkX, in an alkane-degrading strain Dietzia sp. Read More
Previously, we reported that when agar is autoclaved with phosphate buffer, H2O2 is formed in the resulting medium (PT) and the colony count on the medium inoculated with environmental samples becomes much lower than that on a medium in which agar and phosphate are autoclaved separately (PS) (Appl Environ Microbiol 80:7659-7666). However, the physicochemical mechanisms underlying this observation remain largely unknown. Here, we determined the factors affecting H2O2 formation in agar. Read More
Certain strains of biocontrol Pseudomonas fluorescens produce the secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) to antagonize the soil-borne phytopathogens in the rhizosphere. The gene cluster responsible for the biosynthesis of 2,4-DAPG is named phlACBDEFGH and it is still unclear how the pathway-specific regulator phlH within this gene cluster regulates the metabolism of 2,4-DAPG. Here, we found that PhlH in Pseudomonas fluorescens strain 2P24 represses the expression of the phlG gene encoding the 2,4-DAPG hydrolase by binding to a sequence motif overlapping with the -35 site recognized by σ(70) factors. Read More
Past results have suggested that bacterial antibiotic susceptibility is altered during space flight. To test this notion, Bacillus subtilis cells were cultivated in matched hardware, medium, and environmental conditions either in spaceflight microgravity on the International Space Station, termed Flight (FL) samples, or at Earth-normal gravity, termed Ground Control (GC) samples. Susceptibility of FL and GC samples was compared to 72 antibiotics and growth-inhibitory compounds using the Omnilog Phenotype Microarray (PM) system. Read More
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. Read More
The photosynthetic complexes of the thermophile Thermochromatium tepidum are of considerable interest in biohybrid solar cell applications because of the capability of thermophilic proteins to tolerate elevated temperatures. Synthetic operons encoding reaction centre (RC) and light harvesting 1 (LH1) pigment-protein complexes of T. tepidum were expressed in the mesophile Rhodobacter sphaeroides The T. Read More
Soil microorganisms have to rapidly respond to salt-induced osmotic stress. Type II methanotrophs of the genus Methylocystis are widely distributed in upland soils, but are known to have a low salt tolerance. Here, we tested the ability of Methylocystis sp. Read More
The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farms environment after manure application on land. Manure and soil samples were collected on day0 before and after manure application on six farms in North Carolina and sequential soil samples were recollected on day7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella and their plasmid contents were further characterized. Read More
Appl Environ Microbiol 2017 Aug 11. Epub 2017 Aug 11.
Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
The first report of members of the spirochete genus Borrelia in the seabird tick, Ixodes uriae, and seabird colonies occurred during the early 1990s. Since then, Borrelia spp. have been detected in these ticks and seabird colonies around the world. Read More
Biological nitrogen fixation is accomplished by a diverse group of organisms known as diazotrophs, and requires the function of the complex metalloenzyme nitrogenase. Nitrogenase and many of the accessory proteins required for proper cofactor biosynthesis and incorporation into the enzyme have been characterized, but a complete picture of the reaction mechanism and key cellular changes that accompany biological nitrogen fixation remain to be fully elucidated. Studies have revealed that specific disruptions to the anti-activator encoding gene nifL result in the deregulation of the nif transcriptional activator NifA in the nitrogen-fixing bacterium Azotobacter vinelandii, triggering the production of extracellular ammonium levels approaching 30 mM during the stationary phase of growth. Read More
Bacterial biofilm formation is linked to several infections and foodborne disease outbreaks. To address this challenge, there is an unmet need to develop rechargeable antimicrobial materials that can provide continuous sanitation of contact surfaces especially in the food industry. This study was aimed at evaluating a novel rechargeable antimicrobial polymer formed using PVA-co-PE with halamine functionality to prevent biofilm formation with repeated exposure to high loads of bacteria and organic content and also aid in inactivation of pre-formed biofilms upon contact with this novel material. Read More
Bacillus thuringiensis three domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Read More
Radioactive strontium ((90)Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant after a nuclear accident. Since the removal of (90)Sr using general adsorbents (e.g. Read More
Appl Environ Microbiol 2017 Aug 11. Epub 2017 Aug 11.
Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
Putrescine is an important polyamine that participates in a variety of stress responses. Ornithine decarboxylase (ODC) is a key enzyme that catalyzes the biosynthesis of putrescine. A homolog of the gene encoding ODC was cloned from Ganoderma lucidum In the ODC-silenced strains, the transcript levels of the ODC gene and the putrescine content were significantly decreased. Read More
This study explored transient inactivation of the gene encoding the DNA mismatch repair enzyme MutS as a tool for adaptive evolution of Lactobacillus casei MutS deletion derivatives of L. casei 12A and ATCC 334 were constructed and subject to a 100-day adaptive evolution process to increase lactic acid resistance at low pH. Wild-type parental strains were also subject to this treatment. Read More
The locus of heat resistance (LHR) is a 15 - 19 kb genomic island conferring exceptional heat resistance to organisms in the family Enterobacteriaceae including pathogenic strains of Salmonella enterica and Escherichia coli The complement of LHR-encoded genes that is necessary for heat resistance and the stress- or growth-phase induced expression of LHR-encoded genes are unknown. This study determined the contribution of the 7 LHR-encoded genes yfdX1GI, yfdX2, hdeDGI, orf11, trxGI, kefB, and psiEGI by comparison of the heat resistance of E. coli strains harboring plasmid-encoded derivatives of the LHR differing in these genes. Read More