journal
MENU ▼
Read by QxMD icon Read
search

Environmental Microbiology Reports

journal
https://www.readbyqxmd.com/read/28631340/insights-into-the-genomic-plasticity-of-pseudomonas-putida-kf715-a-strain-with-unique-biphenyl-utilizing-activity-and-genome-instability-properties
#1
Hikaru Suenaga, Hidehiko Fujihara, Nobutada Kimura, Jun Hirose, Takahito Watanabe, Taiki Futagami, Masatoshi Goto, Jun Shimodaira, Kensuke Furukawa
Pseudomonas putida KF715 exhibits unique properties in both catabolic activity and genome plasticity. Our previous studies revealed that the DNA region containing biphenyl and salycilate metabolism gene clusters (termed the bph-sal element) was frequently deleted and transferred by conjugation to closely related P. putida strains. In this study, we first determined the complete nucleotide sequence of the KF715 genome. Next, to determine the underlying cause of genome plasticity in KF715, we compared the KF715 genome with the genomes of one KF715 defective mutant, two transconjugants, and several P...
June 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28631290/a-h2-oxidizing-1-2-3-trichlorobenzene-reducing-multienzyme-complex-isolated-from-the-obligately-organohalide-respiring-bacterium-dehalococcoides-mccartyi-strain-cbdb1
#2
Stefanie Hartwig, Nadya Dragomirova, Anja Kublik, Dominique Türkowsky, Martin von Bergen, Ute Lechner, Lorenz Adrian, R Gary Sawers
Dehalococcoides mccartyi is a small, slow-growing bacterium of the phylum Chloroflexi that conserves energy using aliphatic and aromatic organohalides as electron acceptors, and hydrogen as sole electron donor. A recent study identified a protein complex in the membrane of strain CBDB1 comprising a Hup hydrogenase, a complex iron-sulphur molybdoprotein and a reductive dehalogenase (RdhA) that catalyses reduction of 1,2,3,4-tetrachlorobenzene. Using a combination of size-exclusion chromatography, in-gel hydrogenase activity-staining, immunological analysis and mass spectrometry, we identified here a large molecular mass protein complex solubilized from the cytoplasmic membrane of D...
June 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618204/bacterial-weathering-of-fossil-organic-matter-and-organic-carbon-mobilization-from-subterrestrial-kupferschiefer-black-shale-long-term-laboratory-studies
#3
Robert Stasiuk, Agnieszka Włodarczyk, Przemysław Karcz, Marcin Janas, Aleksandra Skłodowska, Renata Matlakowska
A large part of the organic carbon present in the lithosphere is trapped in fossil organic matter deposited in sedimentary rocks. Only specialized microorganisms are able to degrade it contributing to the return of the carbon to the global cycle. The role of bacteria in this process is not yet completely understood. In the present laboratory studies, subterrestrial organic-rich ∼256-million-year-old Kupferschiefer black shale was exposed to the activity of an indigenous consortium of lithobiontic bacteria for 365 days under aerobic conditions...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618201/targeted-quantification-of-functional-enzyme-dynamics-in-environmental-samples-for-microbially-mediated-biogeochemical-processes
#4
Minjing Li, Yuqian Gao, Wei-Jun Qian, Liang Shi, Yuanyuan Liu, William C Nelson, Carrie D Nicora, Charles T Resch, Christopher Thompson, Sen Yan, James K Fredrickson, John M Zachara, Chongxuan Liu
Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass, and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618195/novel-reductive-dehalogenases-from-the-marine-sponge-associated-bacterium-desulfoluna-spongiiphila
#5
Jie Liu, Nora Lopez, Young-Beom Ahn, Tatyana Goldberg, Yana Bromberg, Lee J Kerkhof, Max M Häggblom
Desulfoluna spongiiphila strain AA1 is an organohalide respiring bacterium, isolated from the marine sponge Aplysina aerophoba, that can use brominated and iodinated phenols, in addition to sulfate and thiosulfate as terminal electron acceptors. The genome of Desulfoluna spongiiphila strain AA1 is approximately 6.5 Mb. Three putative reductive dehalogenase (rdhA) genes involved in respiratory metabolism of organohalides were identified within the sequence. Conserved motifs found in respiratory reductive dehalogenases (a twin arginine translocation signal sequence and two iron-sulfur clusters) were present in all three putative AA1 rdhA genes...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618172/dominance-of-sulfuritalea-species-in-nitrate-depleted-water-of-a-stratified-freshwater-lake-and-arsenate-respiration-ability-within-the-genus
#6
Tomohiro Watanabe, Aya Miura, Tomoya Iwata, Hisaya Kojima, Manabu Fukui
Facultatively autotrophs of the genus Sulfuritalea within the class Betaproteobacteria have been predicted to be an important bacterial population in stratified freshwater lakes based on previous PCR-based studies. Here, we designed a new probe specific for the genus Sulfuritalea and performed catalyzed reporter deposition-fluorescence in situ hybridization to enumerate cells of Sulfuritalea species throughout the water column in a stratified freshwater lake. The cells stained with the Sulfuritalea-specific probe were detected in all hypoxic water samples collected in different seasons and years...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28585781/interspecies-cross-talk-between-co-cultured-pseudomonas-putida-and-escherichia-coli
#7
Carlos Molina-Santiago, Zulema Udaondo, Baldo F Cordero, Juan L Ramos
Pseudomonas putida and Escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters-environments in which they likely co-exist. Despite this, the potential interactions between these microbes have not been studied in detail. To analyze these interactions, we carried out RNA-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. Our results show that co-culture of these microbes significantly alters transcriptional profiles...
June 6, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28585771/thermal-sensitivity-of-bacteriocytes-constrains-the-persistence-of-intracellular-bacteria-in-whitefly-symbiosis-under-heat-stress
#8
Hong-Wei Shan, Wen-Hao Deng, Jun-Bo Luan, Min-Jing Zhang, Zhen Zhang, Shu-Sheng Liu, Yin-Quan Liu
Temperature affects the persistence of diverse symbionts of insects. Our previous study indicates that the whitefly symbionts confined within bacteriocytes or scattered throughout the body cavity outside bacteriocytes may have differential thermal sensitivity. However, the underlying mechanisms remain largely unknown. Here, we report that following continuous heat stress, Portiera and Hamiltonella were almost completely depleted in two species of Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) of the Bemisia tabaci whitefly cryptic species complex...
June 6, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28585763/a-combinatorial-strategy-of-alternative-promoter-use-during-differentiation-in-a-heterocystous-cyanobacterium
#9
Alicia M Muro-Pastor, Manuel Brenes-Álvarez, Agustín Vioque
Heterocystous cyanobacteria such as Nostoc sp. are filamentous photosynthetic organisms that, in response to nitrogen deficiency, undergo a differentiation process transforming certain, semi-regularly spaced cells into heterocysts, devoted to nitrogen fixation. During transition to a nitrogen-fixing regime, growth of most vegetative cells in the filament is temporarily arrested due to nutritional deprivation, but developing heterocysts require intense transcriptional activity. Therefore, the coexistence of arrested vegetative cells and actively developing prospective heterocysts relies on the simultaneous operation of somewhat opposite transcriptional programs...
June 6, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28574206/genome-wide-analyses-of-listeria-monocytogenes-from-food-processing-plants-reveals-clonal-diversity-and-dates-the-emergence-of-persisting-sequence-types
#10
Gitte M Knudsen, Jesper Boye Nielsen, Rasmus L Marvig, Yin Ng, Peder Worning, Henrik Westh, Lone Gram
Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food-borne diseases. This requires in-depth understanding of pathogen emergence, persistence, and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time-period of 20 years, and analyzed the sequences together with 10 public available reference genomes to advance our understanding of inter- and intra-plant genomic diversity of L...
June 2, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28557335/identification-evolution-and-functional-characterization-of-two-zn-cdf-family-transporters-of-the-ectomycorrhizal-fungus-suillus-luteus
#11
Joske Ruytinx, Laura Coninx, Hoai Nguyen, Nick Smisdom, Emmanuelle Morin, Annegret Kohler, Ann Cuypers, Jan V Colpaert
Two genes, SlZnT1 and SlZnT2, encoding Cation Diffusion Facilitator (CDF) family transporters were isolated from Suillus luteus mycelium by genome walking. Both gene models are very similar and phylogenetic analysis indicates that they are most likely the result of a recent gene duplication event. Comparative sequence analysis of the deduced proteins predicts them to be Zn transporters. This function was confirmed by functional analysis in yeast for SlZnT1. SlZnT1 was able to restore growth of the highly Zn sensitive yeast mutant Δzrc1 and localized to the vacuolar membrane...
May 30, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28557300/diversity-and-ecology-of-and-biomineralization-by-magnetotactic-bacteria
#12
REVIEW
Wei Lin, Yongxin Pan, Dennis A Bazylinski
Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-bounded crystals of magnetite (Fe3 O4 ) and/or greigite (Fe3 S4 ) called magnetosomes. MTB play important roles in the geochemical cycling of iron, sulfur, nitrogen and carbon. Significantly, they also represent an intriguing model system not just for the study of microbial biomineralization but also for magnetoreception, prokaryotic organelle formation and microbial biogeography. Here we review current knowledge on the ecology of and biomineralization by MTB, with an emphasis on more recent reports of unexpected ecological and phylogenetic findings regarding MTB...
May 30, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28556625/suppression-of-a-methionine-synthase-by-calmodulin-under-environmental-stress-in-the-entomopathogenic-fungus-beauveria-bassiana
#13
Jiyoung Kim, Junsang Oh, Deok-Hyo Yoon, Gi-Ho Sung
Methionine synthase (MetE, EC 2.1.1.14) catalyzes the final step in the methionine biosynthetic pathway. Methionine biosynthesis plays a major role in protein biogenesis and is the source of S-adenosyl methionine (SAM), the universal donor of methyl groups. In this study, we demonstrated that BbMetE acts as a typical MetE enzyme in the entomopathogenic fungus Beauveria bassiana. In addition, we found that BbMetE binds to calmodulin (CaM) in vitro and in vivo. The functional role of CaM binding to BbMetE was to negatively regulate BbMetE activity in B...
May 29, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28556617/discovery-of-ectosymbiotic-endomicrobium-lineages-associated-with-protists-in-the-gut-of-stolotermitid-termites
#14
Kazuki Izawa, Hirokazu Kuwahara, Kaito Sugaya, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh
The genus Endomicrobium is a dominant bacterial group in the gut of lower termites, and most phylotypes are intracellular symbionts of gut protists. Here we report the discovery of Endomicrobium ectosymbionts of termite gut protists. We found that bristle-like Endomicrobium cells attached to the surface of spirotrichosomid protist cells inhabiting the termite Stolotermes victoriensis. Transmission electron microscopy revealed that a putative Endomicrobium cell likely attached to the protist surface via a protrusion from the tip of the bacterium...
May 29, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28517238/flen-and-fleq-play-a-synergistic-role-in-regulating-lapa-and-bcs-operons-in-pseudomonas-putida-kt2440
#15
Hailing Nie, Yujie Xiao, Huizhong Liu, Jinzhi He, Wenli Chen, Qiaoyun Huang
FleN generally functions as an antagonist of FleQ in regulating flagellar genes and biofilm matrix related genes in Pseudomonas aeruginosa. Here we found that in Pseudomonas putida KT2440, FleN and FleQ play a synergistic role in regulating two biofilm matrix coding operons, lapA and bcs. FleN deletion decreased transcription of lapA and increased transcription of bcs operon, the same trend was observed in fleQ deletion mutant before. In vitro experiments showed that FleN promoted binding of FleQ to the lapA/bcs promoter DNA especially in the presence of ATP...
May 18, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28493460/single-cell-genomics-reveals-pyrrolysine-encoding-potential-in-members-of-uncultivated-archaeal-candidate-division-msbl1
#16
Yue Guan, Mohamed F Haroon, Intikhab Alam, James G Ferry, Ulrich Stingl
Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea...
May 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28489316/streptomyces-an-annotated-selection-of-world-wide-web-sites-relevant-to-the-topics-in-environmental-microbiology
#17
Lawrence P Wackett
No abstract text is available yet for this article.
May 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28488795/the-novel-bacterial-phylum-calditrichaeota-is-diverse-widespread-and-abundant-in-marine-sediments-and-has-the-capacity-to-degrade-detrital-proteins
#18
Ian P G Marshall, Piotr Starnawski, Carina Cupit, Eva Fernández Cáceres, Thijs J G Ettema, Andreas Schramm, Kasper U Kjeldsen
Calditrichaeota is a recently recognised bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognised as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time...
May 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28474433/regulation-of-nitrous-oxide-reductase-genes-by-nast-mediated-transcription-antitermination-in-bradyrhizobium-diazoefficiens
#19
Cristina Sánchez, Hisayuki Mitsui, Kiwamu Minamisawa
In Bradyrhizobium diazoefficiens, maximal expression of the nitrous oxide reductase gene (nosZ) requires oxygen limitation and the presence of a nitrogen oxide. The putative transcription antiterminator NasT is a positive regulator of nosZ; but in the absence of nitrate, NasT is counteracted by the nitrate sensor NasS. Here we examined the NasT-mediated mechanism of nosRZDFYLX gene cluster expression. We mapped two transcription start sites of nosR and identified two potential hairpins, H1 and H2, within the 5'-leader of nosR transcripts...
May 4, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28464539/vancomycin-resistant-enterococci-with-vana-and-vanb-genes-in-australian-gulls
#20
Veronika Oravcova, Pavel Svec, Ivan Literak
This study is revealing the possible dissemination of vancomycin-resistant enterococci (VRE) from humans into the wildlife. We studied silver gulls (Chroicocephalus novaehollandiae) in Australia as potential carriers and reservoirs of VRE with acquired vancomycin resistance. In New South Wales (Australia), we have found two multi-resistant isolates belonging to Enterococcus faecium (sequence type 341, vanB genotype) and Enterococcus dispar (vanA genotype). Based on our knowledge, this is the first report of VRE in Australian wildlife...
May 2, 2017: Environmental Microbiology Reports
journal
journal
42283
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"