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https://www.readbyqxmd.com/read/27904880/microbial-community-patterns-associated-with-automated-teller-machine-keypads-in-new-york-city
#1
Holly M Bik, Julia M Maritz, Albert Luong, Hakdong Shin, Maria Gloria Dominguez-Bello, Jane M Carlton
In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads...
November 2016: MSphere
https://www.readbyqxmd.com/read/27902886/lateral-gene-transfer-of-p-cresol-and-indole-producing-enzymes-from-environmental-bacteria-to-mastigamoeba-balamuthi
#2
Eva Nývltová, Robert Šuťák, Vojtěch Žárský, Karel Harant, Ivan Hrdý, Jan Tachezy
p-Cresol and indole are volatile biologically active products of the bacterial degradation of tyrosine and tryptophan, respectively. They are typically produced by bacteria in animal intestines, soil and various sediments. Here, we demonstrate that the free-living eukaryote Mastigamoeba balamuthi and its pathogenic relative Entamoeba histolytica produce significant amounts of indole via tryptophanase activity. Unexpectedly, M. balamuthi also produces p-cresol in concentrations that are bacteriostatic to non-p-cresol-producing bacteria...
November 30, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27902329/abundance-of-antibiotic-resistance-genes-in-environmental-bacteriophages
#3
Taruna Anand, Bidhan Ch Bera, Rajesh K Vaid, Sanjay Barua, Thachamvally Riyesh, Nitin Virmani, Mubarik Hussain, Raj K Singh, Bhupendra N Tripathi
The ecosystem is continuously exposed to a wide variety of antimicrobials through waste effluents, agricultural runoffs, animal related and anthropogenic activities, which contribute to spread of antibiotic resistance genes (ARGs). The contamination of ecosystems with ARGs may create increased opportunities for their transfer to naive microbes and eventually lead to entry into the human food chain. Transduction is a significant mechanism of horizontal gene transfer in natural environments, which has traditionally been underestimated as compared to transformation...
October 21, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27896478/soil-microbial-communities-buffer-physiological-responses-to-drought-stress-in-three-hardwood-species
#4
Steven A Kannenberg, Richard P Phillips
Trees possess myriad adaptations for coping with drought stress, but the extent to which their drought responses are influenced by interactions with soil microbes is poorly understood. To explore the role of microbes in mediating tree responses to drought stress, we exposed saplings of three species (Acer saccharum, Liriodendron tulipifera, and Quercus alba) to a four week experimental drought in mesocosms. Half of the pots were inoculated with a live soil slurry (i.e., a microbial inoculum derived from soils beneath the canopies of mature A...
November 28, 2016: Oecologia
https://www.readbyqxmd.com/read/27895629/genome-wide-discovery-of-putative-srnas-in-paracoccus-denitrificans-expressed-under-nitrous-oxide-emitting-conditions
#5
Hannah Gaimster, Lisa Chalklen, Mark Alston, John T Munnoch, David J Richardson, Andrew J Gates, Gary Rowley
Nitrous oxide (N2O) is a stable, ozone depleting greenhouse gas. Emissions of N2O into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. It is clear more effective mitigation strategies are required to reduce emissions. One way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume N2O. With this ultimate aim in mind we performed RNA-seq on a model soil denitrifier, Paracoccus denitrificans, cultured anaerobically under high N2O and low N2O emitting conditions, and aerobically under zero N2O emitting conditions to identify small RNAs (sRNAs) with potential regulatory functions transcribed under these conditions...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27892466/direct-evidence-for-microbial-derived-soil-organic-matter-formation-and-its-ecophysiological-controls
#6
Cynthia M Kallenbach, Serita D Frey, A Stuart Grandy
Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear...
November 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27891711/identifying-the-microbial-taxa-that-consistently-respond-to%C3%A2-soil-warming-across-time-and-space
#7
Angela M Oliverio, Mark A Bradford, Noah Fierer
Soil microbial communities are the key drivers of many terrestrial biogeochemical processes. However, we currently lack a generalizable understanding of how these soil communities will change in response to predicted increases in global temperatures and which microbial lineages will be most impacted. Here, using high-throughput marker gene sequencing of soils collected from 18 sites throughout North America included in a 100-day laboratory incubation experiment, we identified a core group of abundant and nearly ubiquitous soil microbes that shift in relative abundance with elevated soil temperatures...
November 7, 2016: Global Change Biology
https://www.readbyqxmd.com/read/27889181/brazilian-cerrado-soil-reveals-an-untapped-microbial-potential-for-unpretreated-polyethylene-biodegradation
#8
Julianna Peixoto, Luciano P Silva, Ricardo H Krüger
Discarded PE-based products pose a social and environmental threat because of their recalcitrance to degradation, a consequence of the unique set of PE's physicochemical properties. In this study we isolated nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado. These bacterial strains from the genera Comamonas, Delftia, and Stenotrophomonas showed metabolic activity and cellular viability after a 90-day incubation with PE as the sole carbon source. ATR/FTIR indicated that biodegraded PE undergone oxidation, vinylene formation, chain scission, among other chemical changes...
November 14, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27885927/the-quest-for-industrial-enzymes-from-microorganisms
#9
Shotaro Yamaguchi
Satoshi Ōmura, Professor Emeritus at Kitasato University, was awarded the Nobel Prize for his discovery of a substance of tremendous value to mankind from a microorganism. As a researcher who regularly deals with enzymes produced by microorganisms and a person engaged in microorganism-based business, Professor Ōmura's Nobel Prize fills me with great pride and joy. It is perhaps not surprising that this Nobel Prize-winning research would emerge from Asia, specifically Japan, where people live in harmony with nature rather than try to conquer it...
January 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/27881166/using-the-social-amoeba-dictyostelium-to-study-the-functions-of-proteins-linked-to-neuronal-ceroid-lipofuscinosis
#10
REVIEW
Robert J Huber
Neuronal ceroid lipofuscinosis (NCL), also known as Batten disease, is a debilitating neurological disorder that affects both children and adults. Thirteen genetically distinct genes have been identified that when mutated, result in abnormal lysosomal function and an excessive accumulation of ceroid lipofuscin in neurons, as well as other cell types outside of the central nervous system. The NCL family of proteins is comprised of lysosomal enzymes (PPT1/CLN1, TPP1/CLN2, CTSD/CLN10, CTSF/CLN13), proteins that peripherally associate with membranes (DNAJC5/CLN4, KCTD7/CLN14), a soluble lysosomal protein (CLN5), a protein present in the secretory pathway (PGRN/CLN11), and several proteins that display different subcellular localizations (CLN3, CLN6, MFSD8/CLN7, CLN8, ATP13A2/CLN12)...
November 24, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27878943/microbial-community-composition-but-not-diversity-changes-along-succession-in-arctic-sand-dunes
#11
Anbu Poosakkannu, Riitta Nissinen, Minna Männistö, Minna-Maarit Kytöviita
We tested the generality of increasing diversity of fungi and bacteria along arctic sand dune succession. Microbial communities were examined by high-throughput sequencing of 16S rRNA genes (bacteria) and internal transcribed spacer (ITS) regions (fungi). We studied four microbial compartments (inside leaf, inside root, rhizosphere and bulk soil) and characterized microbes associated with a single plant species (Deschampsia flexuosa) across two sand dune successional stages (early and late). Bacterial richness increased along succession in bulk soil and leaf endosphere...
November 23, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27878084/effect-of-different-root-endophytic-fungi-on-plant-community-structure-in-experimental-microcosms
#12
Carlos A Aguilar-Trigueros, Matthias C Rillig
Understanding the effects of root-associated microbes in explaining plant community patterns represents a challenge in community ecology. Although typically overlooked, several lines of evidence point out that nonmycorrhizal, root endophytic fungi in the Ascomycota may have the potential to drive changes in plant community ecology given their ubiquitous presence, wide host ranges, and plant species-specific fitness effects. Thus, we experimentally manipulated the presence of root endophytic fungal species in microcosms and measured its effects on plant communities...
November 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/27872569/new-antimicrobial-anthraquinone-6-6-1-bis-1-5-7-trihydroxy-3-hydroxymethylanthraquinone-isolated-from-streptomyces-sp-isolate-eri-26
#13
V Duraipandiyan, Naif Abdullah Al-Dhabi, S Ignacimuthu
The present report is about Streptomyces sp. isolate ERI-26 isolated from the soil sample of Nilgiri forest, Western Ghats. The methanol extract of ERI-26 showed good antimicrobial activity against tested microbes. The antimicrobial novel anthraquinones were purified by bioactivity-guided fractionation using a silica gel column and preparative HPLC. The compound was characterized and identified by UV, IR, NMR and MASS spectral data. The compound named as 6,6(1)-bis (1,5,7-trihydroxy-3-hydroxymethylanthraquinone), showed significant antimicrobial activities against tested microbes...
November 2016: Saudi Journal of Biological Sciences
https://www.readbyqxmd.com/read/27871140/metabolic-response-of-agrobacterium-tumefaciens-5a-to-arsenite
#14
Monika Tokmina-Lukaszewska, Zunji Shi, Brian Tripet, Timothy R McDermott, Valérie Copié, Brian Bothner, Gejiao Wang
Wide-spread abundance in soil and water, coupled with high toxicity have put arsenic at the top of the list of environmental contaminants. Early studies demonstrated that both concentration and the valence state of inorganic arsenic (arsenite, As(III) vs. arsenate As(V)) can be modulated by microbes. Using genetics, transcriptomic and proteomic techniques, microbe-arsenic detoxification, respiratory As(V) reduction, and As(III) oxidation have since been examined. The effect of arsenic exposure on whole-cell intracellular microbial metabolism, however, has not been extensively studied...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27871135/fire-modifies-the-phylogenetic-structure-of-soil-bacterial-co-occurrence-networks
#15
Eduardo Pérez-Valera, Marta Goberna, Karoline Faust, Jeroen Raes, Carlos García, Miguel Verdú
Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27870059/transfer-of-13-c-between-paired-douglas-fir-seedlings-reveals-plant-kinship-effects-and-uptake-of-exudates-by-ectomycorrhizas
#16
Brian J Pickles, Roland Wilhelm, Amanda K Asay, Aria S Hahn, Suzanne W Simard, William W Mohn
Processes governing the fixation, partitioning, and mineralization of carbon in soils are under increasing scrutiny as we develop a more comprehensive understanding of global carbon cycling. Here we examined fixation by Douglas-fir seedlings and transfer to associated ectomycorrhizal fungi, soil microbes, and full-sibling or nonsibling neighbouring seedlings. Stable isotope probing with 99% (13) C-CO2 was applied to trace (13) C-labelled photosynthate throughout plants, fungi, and soil microbes in an experiment designed to assess the effect of relatedness on (13) C transfer between plant pairs...
November 21, 2016: New Phytologist
https://www.readbyqxmd.com/read/27864737/significance-of-diazotrophic-plant-growth-promoting-herbaspirillum-sp-gw103-on-phytoextraction-of-pband-zn-by-zea-mays-l
#17
Loganathan Praburaman, Sung-Hee Park, Min Cho, Kui-Jae Lee, Jeong-Ae Ko, Sang-Sub Han, Sang-Hyun Lee, Seralathan Kamala-Kannan, Byung-Taek Oh
Microbe-assisted phytoremediation has been considered a promising measure for the remediation of heavy metal-polluted soil. The aim of this study was to assess the effect of diazotrophic plant growth-promoting Herbaspirillum sp. GW103 on growth and lead (Pb) and zinc (Zn) accumulation in Zea mays L. The strain GW103 exhibited plant growth-promoting traits such as indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic deaminase. Treatment of Z. mays L. plants with GW103 significantly increased 19, 31, and 52% of plant biomass and 10, 50, and 126% of chlorophyll a contents in Pb, Zn, and Pb + Zn-amended soils, respectively...
November 18, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27862698/warming-of-subarctic-tundra-increases-emissions-of-all-three-important-greenhouse-gases-carbon-dioxide-methane-and-nitrous-oxide
#18
Carolina Voigt, Richard E Lamprecht, Maija E Marushchak, Saara E Lind, Alexander Novakovskiy, Mika Aurela, Pertti J Martikainen, Christina Biasi
Rapidly rising temperatures in the Arctic might cause a greater release of greenhouse gases (GHGs) to the atmosphere. To study the effect of warming on GHG dynamics, we deployed open-top chambers in a subarctic tundra site in Northeast European Russia. We determined carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O) fluxes as well as the concentration of those gases, inorganic nitrogen (N) and dissolved organic carbon (DOC) along the soil profile. Studied tundra surfaces ranged from mineral to organic soils and from vegetated to unvegetated areas...
November 14, 2016: Global Change Biology
https://www.readbyqxmd.com/read/27862537/pervasive-yet-idiosyncratic-epistatic-pleiotropy-during-adaptation-in-a-behaviourally-complex-microbe
#19
P C Zee, J Liu, G J Velicer
Understanding how multiple mutations interact to jointly impact multiple ecologically important traits is critical for creating a robust picture of organismal fitness and the process of adaptation. However, this is complicated by both environmental heterogeneity and the complexity of genotype-to-phenotype relationships generated by pleiotropy and epistasis. Moreover, little is known about how pleiotropic and epistatic relationships themselves change over evolutionary time. The soil bacterium Myxococcus xanthus employs several distinct social traits across a range of environments...
October 19, 2016: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/27861770/termites-promote-resistance-of-decomposition-to-spatiotemporal-variability-in-rainfall
#20
Michiel P Veldhuis, Francisco J Laso, Han Olff, Matty P Berg
The ecological impact of rapid environmental change will depend on the resistance of key ecosystems processes, which may be promoted by species that exert strong control over local environmental conditions. Recent theoretical work suggests that macrodetritivores increase the resistance of African savanna ecosystems to changing climatic conditions, but experimental evidence is lacking. We examined the effect of large fungus-growing termites and other non-fungus-growing macrodetritivores on decomposition rates empirically with strong spatiotemporal variability in rainfall and temperature...
November 16, 2016: Ecology
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