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Microbial Ecology

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https://www.readbyqxmd.com/read/27909750/repression-of-proteases-and-hsp90-chaperone-expression-induced-by-an-antiretroviral-in-virulent-environmental-strains-of-cryptococcus-neoformans
#1
Cleber Fernando Serafin, Ana Paula Paris, Claudete Rodrigues Paula, Rita Cássia Garcia Simão, Rinaldo Ferreira Gandra
This study evaluated the effect of the antiretroviral ritonavir on protease secretion in different strains of Cryptococcus neoformans isolated from the environment and investigated the expression of heat shock protein (Hsp90), classically described virulence factors in other yeast in the presence of the same antiretroviral. The presence of the enzyme was detected by the formation of a degradation of the halo around the colonies. The results were classified as follows: level 1 (without proteases), level 2 (positive for proteases), and level 3 (strongly positive for proteases)...
December 2, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27909749/diversity-of-total-bacterial-communities-and-chemoautotrophic-populations-in-sulfur-rich-sediments-of-shallow-water-hydrothermal-vents-off-kueishan-island-taiwan
#2
Li Wang, Man Kit Cheung, Rulong Liu, Chong Kim Wong, Hoi Shan Kwan, Jiang-Shiou Hwang
Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM)...
December 1, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27904921/survey-of-plant-growth-promoting-mechanisms-in-native-portuguese-chickpea-mesorhizobium-isolates
#3
Clarisse Brígido, Bernard R Glick, Solange Oliveira
Rhizobia may possess other plant growth-promoting mechanisms besides nitrogen fixation. These mechanisms and the tolerance to different environmental factors, such as metals, may contribute to the use of rhizobia inocula to establish a successful legume-rhizobia symbiosis. Our goal was to characterize a collection of native Portuguese chickpea Mesorhizobium isolates in terms of plant growth-promoting (PGP) traits and tolerance to different metals as well as to investigate whether these characteristics are related to the biogeography of the isolates...
December 1, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27900439/non-ribosomal-peptide-synthases-from-pseudomonas-aeruginosa-play-a-role-in-cyclodipeptide-biosynthesis-quorum-sensing-regulation-and-root-development-in-a-plant-host
#4
Omar González, Randy Ortíz-Castro, César Díaz-Pérez, Alma L Díaz-Pérez, Viridiana Magaña-Dueñas, José López-Bucio, Jesús Campos-García
Diverse molecules mediate cross-kingdom communication between bacteria and their eukaryotic partners and determine pathogenic or symbiotic relationships. N-acyl-L-homoserine lactone-dependent quorum-sensing signaling represses the biosynthesis of bacterial cyclodipeptides (CDPs) that act as auxin signal mimics in the host plant Arabidopsis thaliana. In this work, we performed bioinformatics, biochemical, and plant growth analyses to identify non-ribosomal peptide synthase (NRPS) proteins of Pseudomonas aeruginosa, which are involved in CDP synthesis...
November 30, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27900461/microbial-food-web-drivers-in-tropical-reservoirs
#5
Carolina Davila Domingues, Lucia Helena Sampaio da Silva, Luciana Machado Rangel, Leonardo de Magalhães, Adriana de Melo Rocha, Lúcia Meirelles Lobão, Rafael Paiva, Fábio Roland, Hugo Sarmento
Element cycling in aquatic systems is driven chiefly by planktonic processes, and the structure of the planktonic food web determines the efficiency of carbon transfer through trophic levels. However, few studies have comprehensively evaluated all planktonic food-web components in tropical regions. The aim of this study was to unravel the top-down controls (metazooplankton community structure), bottom-up controls (resource availability), and hydrologic (water residence time) and physical (temperature) variables that affect different components of the microbial food web (MFW) carbon stock in tropical reservoirs, through structural equation models (SEM)...
November 29, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27896376/reducing-the-bottleneck-in-discovery-of-novel-antibiotics
#6
Marcus B Jones, William C Nierman, Yue Shan, Bryan C Frank, Amy Spoering, Losee Ling, Aaron Peoples, Ashley Zullo, Kim Lewis, Karen E Nelson
Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform...
November 28, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27889811/bacterial-diversity-patterns-differed-in-two-developing-ecosystems
#7
Shankar G Shanmugam, Zenaida V Magbanua, Mark A Williams, Kamlesh Jangid, William B Whitman, Daniel G Peterson, William L Kingery
Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and diversity change as a result of local environmental gradients that develop during pedogenesis. Geographic factors were studied between and within locations spanning two scales: (1) regionally between 0...
November 26, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27888292/seasonal-and-spatial-variations-of-saltmarsh-benthic-foraminiferal-communities-from-north-norfolk-england
#8
Salha A Saad, Christopher M Wade
Time series foraminiferal data were obtained from samples collected from three sites at Brancaster Overy Staithe, Burnham Overy Staithe and Thornham on the North Norfolk coast over a 1-year period. At each collection point, six environmental variables-temperature, chlorophyll, sand, mud, pH and salinity-were also measured. The principle aim of this study was to examine the benthic foraminiferal fauna in regard to the temporal variability of foraminiferal abundance, seasonal trend, dominant species, species diversity and the impact of environmental variables on the foraminiferal communities in the top 1 cm of sediment over a 1-year time series...
November 26, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27888291/whole-genome-enrichment-provides-deep-insights-into-vibrio-cholerae-metagenome-from-an-african-river
#9
L Vezzulli, C Grande, G Tassistro, I Brettar, M G Höfle, R P A Pereira, D Mushi, A Pallavicini, P Vassallo, C Pruzzo
The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania)...
November 25, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27878347/detection-and-diversity-of-the-nitrite-oxidoreductase-alpha-subunit-nxra-gene-of-nitrospina-in-marine-sediments
#10
Sundas Rani, Hyeon-Woo Koh, Sung-Keun Rhee, Hirotsugu Fujitani, Soo-Je Park
Nitrite-oxidizing bacteria (NOB) are chemolithoautotrophs that catalyze the oxidation of nitrite to nitrate, which is the second step of aerobic nitrification. In marine ecosystems, Nitrospina is assumed to be a major contributor to nitrification. To date, two strains of Nitrospina have been isolated from marine environments. Despite their ecological relevance, their ecophysiology and environmental distribution are understudied owing to fastidious cultivation techniques and the lack of a sufficient functional gene marker...
November 22, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27878346/salinity-affects-the-composition-of-the-aerobic-methanotroph-community-in-alkaline-lake-sediments-from-the-tibetan-plateau
#11
Yongcui Deng, Yongqin Liu, Marc Dumont, Ralf Conrad
Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied...
November 22, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27872949/symbiont-diversity-of-aphis-toxoptera-citricidus-hemiptera-aphididae-as-influenced-by-host-plants
#12
Aline Sartori Guidolin, Fernando Luis Cônsoli
Aphids are well known for their association with endosymbiont bacteria. Almost all aphids harbor Buchnera aphidicola as an obligate symbiont and several other bacteria as facultative symbionts. Associations of facultative symbionts and aphids are quite variable in terms of diversity and prevalence across aphid species. Facultative symbionts can have a major impact on aphid bioecological traits. A number of factors shape the outcome of the facultative symbiont-aphid association, including aphid clone, bacterial genotype, geography, and host plant association...
November 21, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27853840/phyllosphere-metaproteomes-of-trees-from-the-brazilian-atlantic-forest-show-high-levels-of-functional-redundancy
#13
M R Lambais, S E Barrera, E C Santos, D E Crowley, A Jumpponen
The phyllosphere of the Brazilian Atlantic Forest has been estimated to contain several million bacterial species that are associated with approximately 20000 plant species. Despite the high bacterial diversity in the phyllosphere, the function of these microorganisms and the mechanisms driving their community assembly are largely unknown. In this study, we characterized the bacterial communities in the phyllospheres of four tree species of the Atlantic Forest (Mollinedia schottiana, Ocotea dispersa, Ocotea teleiandra, and Tabebuia serratifolia) and their metaproteomes to examine the basic protein functional groups expressed in the phyllosphere...
November 16, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27844108/transcriptional-responses-of-the-bacterium-burkholderia-terrae-bs001-to-the-fungal-host-lyophyllum-sp-strain-karsten-under-soil-mimicking-conditions
#14
Irshad Ul Haq, Francisco Dini-Andreote, Jan Dirk van Elsas
In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between both partner organisms was absent, whereas in the final stage (T3-day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime...
November 14, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27838765/temporal-changes-rather-than-long-term-repeated-burning-predominately-control-the-shift-in-the-abundance-of-soil-denitrifying-community-in-an-australian-sclerophyll-forest
#15
Xian Liu, C R Chen, J M Hughes, W J Wang, Tom Lewis
To understand the temporal dynamics of soil bacterial denitrifying community in response to long-term prescribed burning and its resilience and recovery following a fire, a wet sclerophyll forest study site under two treatments (2 yearly burning (2YB) and no burning (NB)) and with 40-year-old burning history was used. Similar temporal patterns in the abundance of total (16S rRNA) and denitrifying (narG, nirK, nirS, nosZ) bacteria between two burning treatments revealed strong temporal influences. The magnitude of burning impacts on the abundance of 16S rRNA and denitrification genes was smaller compared with the impact of sampling time, but significant burning and temporal impacts were recorded for all (P < 0...
November 12, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27838764/soil-carbon-fixation-rates-and-associated-bacterial-diversity-and-abundance-in-three-natural-ecosystems
#16
Tin Mar Lynn, Tida Ge, Hongzhao Yuan, Xiaomeng Wei, Xiaohong Wu, Keqing Xiao, Deepak Kumaresan, San San Yu, Jinshui Wu, Andrew S Whiteley
CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of (14)C ((14)C-MBC) differed among the soils from three ecosystems, accounting for 14...
November 12, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27837253/characterization-of-nosema-ceranae-genetic-variants-from-different-geographic-origins
#17
B Branchiccela, D Arredondo, M Higes, C Invernizzi, R Martín-Hernández, I Tomasco, P Zunino, K Antúnez
In recent years, large-scale colony losses of honey bees (Apis mellifera) have been reported and the infection with the microsporidia Nosema ceranae has been involved. However, the effect of N. ceranae at the colony level and its role in colony losses vary in different geographic areas. This difference may be related to the presence of multiple N. ceranae genetic variants resulting in different biological consequences. In this study, we analyzed the genetic diversity of 75 N. ceranae samples obtained from 13 countries and Hawaii through inter-sequence single repetition (ISSR) and evaluated if two of these genetic variants triggered different immune responses when infecting Apis mellifera iberiensis...
November 12, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27837252/polar-lipids-analysis-of-cultured-phytoplankton-reveals-significant-inter-taxa-changes-low-influence-of-growth-stage-and-usefulness-in-chemotaxonomy
#18
José Pedro Cañavate, Isabel Armada, Ismael Hachero-Cruzado
The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed...
November 11, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27833995/cultivation-versus-molecular-analysis-of-banana-musa-sp-shoot-tip-tissue-reveals-enormous-diversity-of-normally-uncultivable-endophytic-bacteria
#19
Pious Thomas, Aparna Chandra Sekhar
The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes)...
November 10, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27832305/constructed-wetlands-revisited-microbial-diversity-in-the-omics-era
#20
REVIEW
Olga Sánchez
Constructed wetlands (CWs) constitute an interesting alternative option to conventional systems for wastewater treatment. This technology is based on the utilization of the concerted activity of microorganisms for the removal of contaminants. Consequently, knowledge on the microbial assemblages dwelling CWs and the different environmental factors which can alter their activities is crucial for understanding their performance. In the last decades, the use of molecular techniques to characterize these communities and more recently, application of -omics tools, have broaden our view of microbial diversity and function in wastewater microbiology...
November 10, 2016: Microbial Ecology
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