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Environmental Microbiology Reports

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https://www.readbyqxmd.com/read/28799726/external-hyphae-of-rhizophagus-irregularis-daom-197198-are-less-sensitive-to-low-ph-than-roots-in-arbuscular-mycorrhizae-evidence-from-axenic-culture-system
#1
Ning Wang, Zengwei Feng, Yang Zhou, Honghui Zhu, Qing Yao
The growth of plant roots and arbuscular mycorrhizal fungi (AMF) can be inhibited by low pH; however, it is largely unknown which is more sensitive to low pH. This study aimed to compare the physiological and molecular responses of external hyphae (EH) and roots to low pH in terms of growth, development and functioning. We established AM symbiosis in a two-compartmented system (root compartment, RC; hyphal compartment, HC) using AMF and transformed hairy roots and exposed them to pH 6.5 and/or pH 4.5. The results showed that pH 4...
August 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28799720/its-fungal-barcoding-primers-vs-18s-amf-specific-primers-reveal-similar-amf-based-diversity-patterns-in-roots-and-soils-of-three-mountain-vineyards
#2
A Berruti, A Desirò, S Visentin, O Zecca, P Bonfante
ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs...
August 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28799718/identification-and-elucidation-of-in-vivo-function-of-two-alanine-racemases-from-pseudomonas-putida-kt2440
#3
Estrella Duque, Abdelali Daddaoua, Baldo F Cordero, Jesús De la Torre, M Antonia Molina-Henares, Juan-Luis Ramos
The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate (PLP) binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine...
August 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28799713/yeasts-dominate-soil-fungal-communities-in-three-lowland-neotropical-rainforests
#4
Micah Dunthorn, Håvard Kauserud, David Bass, Jordan Mayor, Frédéric Mahé
Forest soils typically harbour a vast diversity of fungi, but are usually dominated by filamentous (hyphae-forming) taxa. Compared to temperate and boreal forests, though, we have limited knowledge about the fungal diversity in tropical rainforest soils. Here we show, by environmental metabarcoding of soil samples collected in three Neotropical rainforests, that Yeasts dominate the fungal communities in terms of the number of sequencing reads and OTUs. These unicellular forms are commonly found in aquatic environments, and their hyperdiversity may be the result of frequent inundation combined with numerous aquatic microenvironments in these rainforests...
August 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28772060/methanotroph-derived-bacteriohopanepolyol-bhp-signatures-as-a-function-of-temperature-related-growth-survival-cell-death-and-preservation-in-the-geological-record
#5
Kate A Osborne, Neil D Gray, Angela Sherry, Peter Leary, Obioma Mejeha, Juliane Bischoff, Darci Rush, Frances R Sidgwick, Daniel Birgel, Marina G Kalyuzhnaya, Helen M Talbot
Interpretation of bacteriohopanepolyol (BHP) biomarkers tracing microbiological processes in modern and ancient sediments relies on understanding environmental controls of production and preservation. BHPs from methanotrophs (35-aminoBHPs) were studied in methane-amended aerobic river-sediment incubations at different temperatures. It was found that: 1. With increasing temperature (4-40°C) a tenfold increase in aminopentol (associated with Crenothrix and Methylobacter spp. growth) occurred with only marginal increases in aminotriol and aminotetrol; 2...
August 3, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28772026/interactions-between-microbial-community-members
#6
Scott A Rice
No abstract text is available yet for this article.
August 3, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28714286/mosquitoes-can-harbour-yeasts-of-clinical-significance-and-contribute-to-their-environmental-dissemination
#7
Jovana Bozic, Aida Capone, Dario Pediconi, Priscilla Mensah, Alessia Cappelli, Matteo Valzano, Maria Vittoria Mancini, Patrizia Scuppa, Elena Martin, Sara Epis, Paolo Rossi, Guido Favia, Irene Ricci
There is still a lack of studies on fungal microbiota in mosquitoes, compared to the number available on bacterial microbiota. This study reports the identification of yeasts of clinical significance in laboratory mosquito species: Anopheles gambiae, Anopheles stephensi, Culex quinquefasciatus, Aedes albopictus and Aedes aegypti. Among the yeasts isolated, we focused on the opportunistic pathogen Candida parapsilosis, since there is a need to better understand breakthrough candidaemia with resistance to the usual antifungals, which requires careful consideration in the broad-spectrum therapy, as documented in many clinical reports...
July 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28703431/a-matter-of-hierarchy-activation-of-orfamide-production-by-the-posttranscriptional-gac-rsm-cascade-of-pseudomonas-protegens-cha0-through-expression-upregulation-of-the-two-dedicated-transcriptional-regulators
#8
Patricio Martín Sobrero, Andrés Muzlera, Julieta Frescura, Edgardo Jofré, Claudio Valverde
In this work, we surveyed the genome of P. protegens CHA0 in order to identify novel mRNAs possibly under the control of the Gac-Rsm cascade that might, for their part, serve to elucidate as-yet-unknown functions involved in the biocontrol of plant pathogens and/or in cellular processes required for fitness in natural environments. In view of the experimental evidence from former studies on the Gac-Rsm cascade, we developed a computational screen supported by a combination of sequence, structural, and evolutionary constraints that led to a dataset of 43 potential novel mRNA targets...
July 13, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28677342/the-fitness-costs-and-benefits-of-antibiotic-resistance-in-drug-free-microenvironments-encountered-in-the-human-body
#9
Ram Maharjan, Thomas Ferenci
The relationship between bacterial drug resistance and growth fitness is a contentious topic, but some antibiotic resistance mutations clearly have a fitness cost in the laboratory. Whether these costs translate to deleterious effects in natural habitats is less certain however. Previously, fitness effects of resistance mutations were mostly characterized in nutrient-rich, fast-growth conditions, which bacteria rarely encounter in natural habitats. Carbon, phosphate, iron or oxygen limitations are conditions met by bacterial pathogens in various compartments of the human body...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28677304/integrated-structural-biology-and-molecular-ecology-of-n-cycling-enzymes-from-ammonia-oxidizing-archaea
#10
Bradley B Tolar, Jonathan Herrmann, John R Bargar, Henry van den Bedem, Soichi Wakatsuki, Christopher A Francis
Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically-relevant ammonia oxidizers is unfortunately extremely limited...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28677262/high-resolution-phylogenetic-analysis-of-endomicrobia-reveals-multiple-acquisitions-of-endosymbiotic-lineages-by-termite-gut-flagellates
#11
Aram Mikaelyan, Claire L Thompson, Katja Meuser, Hao Zheng, Pinki Rani, Rudy Plarre, Andreas Brune
Bacteria of the class Endomicrobia form a deep-branching clade in the Elusimicrobia phylum. They are found almost exclusively in the intestinal tract of animals and are particularly abundant in many termites, where they reside as intracellular symbionts in the cellulolytic gut flagellates. Although small populations of putatively free-living lineages have been detected in faunated and flagellate-free hosts, the evolutionary origin of the endosymbionts is obscured by the limited amount of phylogenetic information provided by the 16S rRNA gene fragment amplified with Endomicrobia-specific primers...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28677247/major-phylum-level-differences-between-porefluid-and-host-rock-bacterial-communities-in-the-terrestrial-deep-subsurface
#12
Lily Momper, Brandi Kiel Reese, Laura Zinke, Greg Wanger, Magdalena R Osburn, Duane Moser, Jan P Amend
Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines, and sampling of deeply-sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply-circulating groundwater and corresponding host rock (at a depth of 1...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28675605/intrahost-milieu-modulates-production-of-outer-membrane-vesicles-vesicle-associated-shiga-toxin-2a-and-cytotoxicity-in-escherichia-coli-o157-h7-and-o104-h4
#13
Andreas Bauwens, Lisa Kunsmann, Monika Marejková, Wenlan Zhang, Helge Karch, Martina Bielaszewska, Alexander Mellmann
Outer membrane vesicles (OMVs) are important virulence tools of enterohaemorrhagic Escherichia coli (EHEC), but other biological functions of these nanostructures are unknown. We tested the hypothesis that modulation of OMV production enables EHEC to resist the intrahost environment during infection by investigating if simulated human gastrointestinal conditions affect OMV production in EHEC O157:H7 and O104:H4. All the conditions tested including a low pH, simulated ileal and colonic media, presence of mucin, intestinal epithelial cell lysate or antimicrobial peptides, as well as iron limitation, significantly increased OMV production by these pathogens...
July 4, 2017: Environmental Microbiology Reports
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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 analyse 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
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