journal
MENU ▼
Read by QxMD icon Read
search

Environmental Microbiology Reports

journal
https://www.readbyqxmd.com/read/29052962/bacterial-catabolism-of-lignin-derived-aromatics-new-findings-in-a-recent-decade
#1
Naofumi Kamimura, Kenji Takahashi, Kosuke Mori, Takuma Araki, Masaya Fujita, Yudai Higuchi, Eiji Masai
Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalyzed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: i) funneling of a wide variety of lignin-derived aromatics into vanillate and syringate, ii) O demethylation of vanillate and syringate to form catecholic derivatives, and iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates...
October 20, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29052944/differential-expression-of-the-three-alcanivorax-borkumensis-sk2-genes-coding-for-the-p450-cytochromes-involved-in-the-assimilation-of-hydrocarbons
#2
Emma Sevilla, Luis Yuste, Renata Moreno, Fernando Rojo
Alcanivorax borkumensis, a marine bacterium highly specialized in degrading linear and branched alkanes, plays a key ecological role in the removal of marine oil spills. It contains several alternative enzyme systems for terminal hydroxylation of alkanes, including three P450 cytochromes (P450-1, P450-2 and P450-3). The present work shows cytochrome P450-1 to be expressed from the promoter of the upstream gene fdx. Promoter Pfdx was more active when C8 -C18 n-alkanes or pristane were assimilated than when pyruvate was available...
October 20, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28925557/analysis-of-multiple-haloarchaeal-genomes-suggests-that-the-quinone-dependent-respiratory-nitric-oxide-reductase-is-an-important-source-of-nitrous-oxide-in-hypersaline-environments
#3
Javier Torregrosa-Crespo, Pedro González-Torres, Vanesa Bautista, Julia M Esclapez, Carmen Pire, Mónica Camacho, María José Bonete, David J Richardson, Nicholas J Watmough, Rosa María Martínez-Espinosa
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Whilst the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors)...
September 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28925553/dispersal-and-inhibitory-roles-of-mannose-2-deoxy-d-glucose-and-n-acetylgalactosaminidase-on-the-biofilm-of-desulfovibrio-vulgaris
#4
Venkata G Poosarla, Thammajun L Wood, Lei Zhu, Daniel S Miller, Bei Yin, Thomas K Wood
Biofilms of sulfate-reducing bacteria (SRB) are often the major cause of microbiologically influenced corrosion. The representative SRB Desulfovibrio vulgaris has previously been shown to have a biofilm that consists primarily of protein. In this study, by utilizing lectin staining, we identified that the biofilm of D. vulgaris also consists of the matrix components mannose, fucose, and N-acetylgalactosamine (GalNAc), with mannose predominating. Based on these results, we found that the addition of mannose and the non-metabolizable mannose analog 2-deoxy-D-glucose inhibits the biofilm formation of D...
September 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28914491/nirs-type-denitrifying-bacterial-assemblages-respond-to-environmental-conditions-of-a-shallow-estuary
#5
Jessica A Lisa, Amal Jayakumar, Bess B Ward, Bongkeun Song
Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered "generalist" and "specialist" archetypes based on the distribution of archetypes within these assemblages...
September 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28914489/responses-of-microbial-decomposers-to-drought-in-streams-may-depend-on-the-environmental-context
#6
Sofia Duarte, Juanita Mora-Gómez, Anna M Romaní, Fernanda Cássio, Cláudia Pascoal
A consequence of drought in streams is the emersion of decomposing leaf litter, which may alter organic matter recycling. We assessed the effects of emersion on decomposition of black poplar leaves and associated microbes (microbial biomass, extracellular enzyme activities and microbial diversity) in two streams with distinct characteristics, in particular nutrients, temperature and oxygen levels. Leaf decomposition rates, fungal biomass and extracellular enzyme activities were lower in the most impacted stream (high nutrients and temperature, low oxygen)...
September 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28892310/genetic-diversity-of-marine-anaerobic-ammonium-oxidizing-bacteria-as-revealed-by-genomic-and-proteomic-analyses-of-candidatus-scalindua-japonica
#7
Mamoru Oshiki, Keisuke Mizuto, Zen-Ichiro Kimura, Tomonori Kindaichi, Hisashi Satoh, Satoshi Okabe
Anaerobic ammonium-oxidizing (anammox) bacteria affiliated with the genus 'Candidatus Scalindua' are responsible for significant nitrogen loss in oceans, and thus their ecophysiology is of great interest. Here, we enriched a marine anammox bacterium, 'Ca. S. japonica' from a Hiroshima bay sediment in Japan, and comparative genomic and proteomic analyses of 'Ca. S. japonica' were conducted. Sequence of the 4.81-Mb genome containing 4019 coding regions of genes (CDSs) composed of 47 contigs was determined. In the proteome, 1762 out of 4019 CDSs in the 'Ca...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28892305/high-level-resistance-of-melissococcus-plutonius-clonal-complex-3-strains-to-antimicrobial-activity-of-royal-jelly
#8
Daisuke Takamatsu, Aya Osawa, Keiko Nakamura, Mikio Yoshiyama, Masatoshi Okura
Melissococcus plutonius is the causative agent of European foulbrood of honey bee larvae. Among its three genetically distinct groups (CC3, CC12 and CC13), CC3 strains have been suggested to be more virulent at the colony level. Honey bee larvae are fed royal or worker jellies by adult bees, and these jellies exhibit antimicrobial activity. Since M. plutonius orally infects larvae via brood food, we herein investigated the resistance of M. plutonius to the antimicrobial activity of royal jelly (RJ). The results obtained revealed that M...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28892304/redefining-the-sponge-symbiont-acquisition-paradigm-sponge-microbes-exhibit-chemotaxis-towards-host-derived-compounds
#9
Jessica Tout, Carmen Astudillo-García, Michael W Taylor, Gene W Tyson, Roman Stocker, Peter J Ralph, Justin R Seymour, Nicole S Webster
Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28892291/ectosymbiotic-endomicrobia-a-transition-stage-towards-intracellular-symbionts
#10
Andreas Brune
No abstract text is available yet for this article.
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28892290/is-microbial-terroir-related-to-geographic-distance-between-vineyards
#11
Toshiko Miura, Roland Sánchez, Luis E Castañeda, Karina Godoy, Olga Barbosa
While there are substantial studies suggesting that characteristics of wine are related to regional microbial community composition (microbial terroir), there has been little discussion about what factors affect variation in regional microbial community composition. In this study, we compared the microbial community composition of leaves and berries of a grape variety (Carmenere) from six different Chilean vineyards within 35 km of each other. In order to determine relationships between spatial proximity and microbial compositional dissimilarity, we sequenced amplicons of the internal transcribed spacer (ITS) region for fungi and 16S rRNA gene for bacteria...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28892269/bacteria-utilising-plant-derived-carbon-in-the-rhizosphere-of-triticum-aestivum-change-in-different-depths-of-an-arable-soil
#12
Marie Uksa, Franz Buegger, Silvia Gschwendtner, Tillmann Lueders, Susanne Kublik, Timo Kautz, Miriam Athmann, Ulrich Köpke, Jean Charles Munch, Michael Schloter, Doreen Fischer
Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28836743/hydrography-shapes-amoa-containing-thaumarcheota-in-the-coastal-waters-off-central-chile
#13
Anthony D Bertagnolli, Osvaldo Ulloa
Thaumarchaea are often abundant in low oxygen marine environments, and recent kinetic studies indicate a capacity for aerobic ammonia oxidation at vanishingly low oxygen levels (nM). However, molecular diversity surveys targeting this group to high sequencing coverage are limited, and how these populations are coupled to changes in dissolved oxygen remains unknown. In this study, the ammonia monooxygenase subunit A (amoA) gene was sequenced from samples collected in the Chilean coast (36.5 °S), a system prone to recurrent seasonal hypoxia and anoxia, at several depths over one year, to read depths that saturated coverage statistics...
August 24, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28836742/thriving-or-surviving-evaluating-active-microbial-guilds-in-baltic-sea-sediment
#14
Laura A Zinke, Megan M Mullis, Jordan T Bird, Ian P G Marshall, Bo Barker Jørgensen, Karen G Lloyd, Jan P Amend, Brandi Kiel Reese
Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes...
August 24, 2017: Environmental Microbiology Reports
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
#15
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-versus-18s-amf-specific-primers-reveal-similar-amf-based-diversity-patterns-in-roots-and-soils-of-three-mountain-vineyards
#16
Andrea Berruti, Alessandro Desirò, Stefano Visentin, Odoardo Zecca, Paola 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
#17
Estrella Duque, Abdelali Daddaoua, Baldo F Cordero, Jesús De la Torre, Maria 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 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
#18
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-signatures-as-a-function-of-temperature-related-growth-survival-cell-death-and-preservation-in-the-geological-record
#19
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: (i) With increasing temperature (4°C-40°C) a 10-fold increase in aminopentol (associated with Crenothrix and Methylobacter spp. growth) occurred with only marginal increases in aminotriol and aminotetrol; (ii) A further increase in temperature (50°C) saw selection for the thermophile Methylocaldum and mixtures of aminopentol and C-3 methylated aminopentol, again, with no increase in aminotriol and aminotetrol...
August 3, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28772026/interactions-between-microbial-community-members
#20
Scott A Rice
No abstract text is available yet for this article.
August 3, 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"