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FEMS Microbiology Ecology

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https://www.readbyqxmd.com/read/27856622/in-vitro-fermentation-of-b-gos-impact-on-faecal-bacterial-populations-and-metabolic-activity-in-autistic-and-non-autistic-children
#1
Roberta Grimaldi, Drinalda Cela, Jonathan R Swann, Jelena Vulevic, Glenn R Gibson, George Tzortzis, Adele Costabile
Children with autism spectrum disorders (ASD) often suffer gastrointestinal problems consistent with imbalances in the gut microbial population. Treatment with antibiotics or pro/prebiotics has been postulated to regulate microbiota and improve gut symptoms, but there is a lack of evidence for such approaches, especially for prebiotics. This study assessed the influence of a prebiotic galactooligosaccharide (B-GOS) on gut microbial ecology and metabolic function using faecal samples from autistic and non-autistic children in an in vitro gut model system...
November 16, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27856621/trophic-state-and-geographic-gradients-influence-planktonic-cyanobacterial-diversity-and-distribution-in-new-zealand-lakes
#2
Susanna A Wood, Marcia Y Maier, Jonathan Puddick, Xavier Pochon, Anastasija Zaiko, Daniel R Dietrich, David P Hamilton
Cyanobacteria are commonly associated with eutrophic lakes, where they often form blooms and produce toxins. However they are a ubiquitous component of phytoplankton in lakes of widely varying trophic status. We hypothesised that cyanobacterial diversity would vary among lakes of differing trophic status, but that the relative importance of geographic and hydromorphological characteristics driving these patterns would differ across trophic groups. DNA from 143 New Zealand lakes that spanned a range of geographic, hydromorphological and trophic gradients was analysed using automated rRNA intergenic spacer analysis (ARISA) and screened for genes involved in cyanotoxin production...
November 16, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27856620/genomic-characterization-of-dehalococcoides-mccartyi-strain-11a5-reveals-a-circular-extrachromosomal-genetic-element-and-a-new-tetrachloroethene-reductive-dehalogenase-gene
#3
Siyan Zhao, Chang Ding, Jianzhong He
Dehalococcoides mccartyi exhibits versatile capabilities to respire halogenated compounds under anaerobic conditions. In this study, we report the assembly and annotation of the complete genome of a chloroethene dechlorinating D. mccartyi strain 11a5. Bearing a 1,461,973 base-pair chromosome, strain 11a5 distinguishes itself from other D. mccartyi strains by possessing a 5,940 base-pair circular extrachromosomal genetic element which contains a reductive dehalogenase homolog. The whole genome of strain 11a5 harbors 31 putative reductive dehalogenase genes...
November 16, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27827805/the-hot-oyster-levels-of-virulent-vibrio-parahaemolyticus-strains-in-individual-oysters
#4
Savannah Klein, Charles R Lovell
Vibrio parahaemolyticus is the leading cause of seafood-associated gastroenteritis and is most commonly transmitted by raw oysters. Consequently, detection of virulent strains of this organism in oysters is a primary concern for seafood safety. V. parahaemolyticus levels were determined in 110 individual oysters harvested from two sampling sites in South Carolina, USA. The majority of oysters (98%) contained low levels of presumptive V. parahaemolyticus However, two healthy oysters contained presumptive V. parahaemolyticus numbers that were unusually high...
November 7, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27827804/planktonic-protistan-communities-in-lakes-along-a-large-scale-environmental-gradient
#5
Maryia Khomich, Håvard Kauserud, Ramiro Logares, Serena Rasconi, Tom Andersen
Despite their obvious importance, our knowledge about the eukaryotic microbial diversity of inland waters is still limited and poorly documented. We applied 18S rDNA amplicon sequencing to provide a comprehensive analysis of eukaryotic diversity in 74 low-productivity lakes along a 750 km longitudinal transect (5.40-18.52°E) across southern Scandinavia. We detected a wide diversity of pelagic microbial eukaryotes, classified into 1882 operational taxonomic units (OTUs). The highest OTU richness was found in traditional phytoplankton groups like Dinoflagellata, Chrysophyceae, Chlorophyta and Cryptophyta...
November 7, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27815287/microbial-and-viral-like-rhodopsins-present-in-coastal-marine-sediments-from-four-polar-and-subpolar-regions
#6
J L López, M Golemba, E Hernández, M Lozada, H M Dionisi, J Jansson, J Carroll, L Lundgren, S Sjöling, W P Mac Cormack
Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis...
November 3, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27810879/bacterial-metacommunity-organization-in-a-highly-connected-aquatic-system
#7
Silke Langenheder, Jianjun Wang, Satu Maaria Karjalainen, Tiina M Laamanen, Kimmo T Tolonen, Annika Vilmi, Jani Heino
The spatial structure and underlying assembly mechanisms of bacterial communities have been studied widely across aquatic systems, focusing primarily on isolated sites, such as different lakes, ponds and streams. Here, our main aim was to determine the underlying mechanisms for bacterial biofilm assembly within a large, highly-connected lake system in Northern Finland using associative methods based on taxonomic and phylogenetic alpha- and beta-diversity and a large number of abiotic and biotic variables. Furthermore, null model approaches were used to quantify the relative importance of different community assembly processes...
November 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27810878/prebiotic-potential-of-l-sorbose-and-xylitol-in-promoting-the-growth-and-metabolic-activity-of-specific-butyrate-producing-bacteria-in-human-fecal-culture
#8
Tadashi Sato, Shiro Kusuhara, Wakae Yokoi, Masahiko Ito, Kouji Miyazaki
Dietary low-digestible carbohydrates (LDCs) affect gut microbial metabolism, including the production of short-chain fatty acids. The ability of various LDCs to promote butyrate production was evaluated in in vitro human fecal cultures. Fecal suspensions from five healthy males were anaerobically incubated with various LDCs. L-sorbose and xylitol markedly promoted butyrate formation in cultures. Bacterial 16S rRNA gene-based denaturing gradient gel electrophoresis analyses of these fecal cultures revealed a marked increase in the abundance of bacteria closely related to the species Anaerostipes hadrus or Anaerostipes caccae, or both, during enhanced butyrate formation from L-sorbose or xylitol...
November 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27810876/impact-of-cystic-fibrosis-disease-on-archaea-and-bacteria-composition-of-gut-microbiota
#9
Francesco Miragoli, Sara Federici, Susanna Ferrari, Andrea Minuti, Annalisa Rebecchi, Eugenia Bruzzese, Vittoria Buccigrossi, Alfredo Guarino, Maria Luisa Callegari
Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among cystic fibrosis patients of 10-22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included fourteen homozygotes and fourteen heterozygotes with the delF508 mutation, and two heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea, and sulfate-reducing bacteria...
November 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27810875/seasonal-and-geographical-distribution-of-near-surface-small-photosynthetic-eukaryotes-in-the-western-north-pacific-determined-by-pyrosequencing-of-18s-rdna
#10
Takafumi Kataoka, Haruyo Yamaguchi, Mayumi Sato, Tsuyoshi Watanabe, Yukiko Taniuchi, Akira Kuwata, Masanobu Kawachi
In this study, we investigated the distribution of small photosynthetic eukaryotes in the near-surface layer of the western North Pacific at four stations, including two oceanic stations where the subarctic Oyashio and subtropical Kuroshio currents influence a transition region and the bay mouth and head of the Sendai Bay, from April 2012 to May 2013. Flow cytometry was applied to sort small photosynthetic eukaryotes (< 5 μm), and high-throughput sequencing of 18S rDNA was performed. Our taxonomic analysis showed that 19/195 operational taxonomic units (OTUs) were frequently distributed among all sites...
November 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27810874/cyanobacterial-populations-in-biological-soil-crusts-of-the-northwest-negev-desert-israel-effects-of-local-conditions-and-disturbance
#11
Martin Hagemann, Manja Henneberg, Vincent J M N L Felde, Simon M Berkowicz, Hagai Raanan, Nadin Pade, Peter Felix-Henningsen, Aaron Kaplan
Biological soil crusts (BSCs) fulfill numerous ecological functions in arid and semiarid areas. Cyanobacteria are important BSC organisms, which are responsible for carbon fixation, N2-fixation, and binding of soil via extracellular polysaccharides. The cyanobacterial populations were characterized in different sampling plots established in three experimental stations along a rainfall gradient within NW Negev Desert, Israel. Cyanobacterial crust thickness and osmolyte accumulation therein decreased in plots with lower moisture...
November 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27810873/the-ecology-of-anaerobic-degraders-of-btex-hydrocarbons-in-aquifers
#12
Tillmann Lueders
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed...
November 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27789537/successive-soybean-monoculture-cropping-assembles-rhizosphere-microbial-communities-for-the-soil-suppression-of-soybean-cyst-nematode
#13
M Imran Hamid, Muzammil Hussain, Yunpeng Wu, Xiaoling Zhang, Meichun Xiang, Xingzhong Liu
One of the mechanisms of disease suppressiveness in soils is long-term monoculture cropping to dissuade pathogen infestation. However, the linkage between monoculturing and microbial community assemblage in the rhizosphere for disease suppression remains unclear. To decipher this potential relationship, soil samples were collected from seven locations in northeastern China, where long-term monoculture (LTM, 6-38 yr) and short-term monoculture (STM, ≤ 5 yr) cropping of soybean showed varying degrees of soil suppressiveness to the soybean cyst nematode (SCN; Heterodera glycines)...
October 27, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27789536/optical-properties-of-dissolved-organic-matter-relate-to-different-depth-specific-patterns-of-archaeal-and-bacterial-community-structure-in-the-north-atlantic-ocean
#14
Elisa Guerrero-Feijóo, Mar Nieto-Cid, Eva Sintes, Vladimir Dobal-Amador, Víctor Hernando-Morales, Marta Álvarez, Vanessa Balagué, Marta M Varela
Abundance, activity and prokaryotic community composition were studied in the euphotic, intermediate and deep waters off the Galician coast (NW Iberian margin) in relation to the optical characterization of dissolved organic matter (DOM). Microbial (Archaea and Bacteria) community structure was vertically stratified. Among the Archaea, Euryarchaeota, especially Thermoplasmata, was dominant in the intermediate waters and decreased with depth, whereas marine Thaumarchaeota, especially Marine Group I, was the most abundant archaeal phyla in the deeper layers...
October 27, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27789535/drivers-of-yeast-community-composition-in-the-litter-and-soil-of-a-temperate-forest
#15
Tereza Mašínová, Barbara Doreen Bahnmann, Tomáš Větrovský, Michal Tomšovský, Kristina Merunková, Petr Baldrian
Fungi represent a group of soil microorganisms fulfilling important ecological functions. Although several studies have shown that yeasts represent a significant proportion of fungal communities, our current knowledge is based mainly on cultivation experiments. In this study, we used amplicon sequencing of environmental DNA to describe the composition of yeast communities in European temperate forest and to identify the potential biotic and abiotic drivers of community assembly. Based on the analysis of ITS2 PCR amplicons, yeasts represented a substantial proportion of fungal communities ranging from 0...
October 27, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27797967/polar-and-alpine-microbiology-earth-s-cryobiosphere
#16
EDITORIAL
Josef Elster, Rosa Margesin, Dirk Wagner, Max Häggblom
No abstract text is available yet for this article.
October 18, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27797966/distribution-and-function-of-carbamate-hydrolase-genes-ceha-and-mcd-in-soils-the-distinct-role-of-soil-ph
#17
Constantina Rousidou, Dionysis Karaiskos, Despoina Myti, Evangelos Karanasios, Panagiotis Karas, Maria Tourna, Emmanuel A Tzortzakakis, Dimitrios G Karpouzas
Synthetic carbamates constitute a significant pesticide group with oxamyl being a leading compound in the nematicides market. Oxamyl degradation in soil is mainly microbially mediated. However the distribution and function of carbamate hydrolase genes (cehA, mcd, cahA) associated with the soil biodegradation of carbamates is not yet clear. We studied oxamyl degradation in 16 soils from a potato monoculture area in Greece, where oxamyl is regularly used. Oxamyl showed low persistence (DT50s 2.4-26.7 days). q-PCR detected the cehA and mcd genes in 10 and 3 soils respectively...
October 18, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27797965/seasonality-of-freshwater-bacterioplankton-diversity-in-two-tropical-shallow-lakes-from-the-brazilian-atlantic-forest
#18
Marcelo P Ávila, Peter A Staehr, Francisco A R Barbosa, Edmar Chartone-Souza, Andréa M A Nascimento
Bacteria are highly important for the cycling of organic and inorganic matter in freshwater environments, however, little is known about the diversity of bacterioplankton in tropical systems. Studies on carbon and nutrient cycling in tropical lakes suggest a very different seasonality from that of temperate climates. Here, we used 16S rRNA gene next generation sequencing (NGS) to investigate seasonal changes in bacterioplankton communities of two tropical lakes, which differed in trophic status and mixing regime...
October 18, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27797964/an-in-situ-inventory-of-fungi-and-their-associated-migrating-bacteria-in-forest-soils-using-fungal-highways-columns
#19
Anaele Simon, Vincent Hervé, Andrej Al-Dourobi, Eric Verrecchia, Pilar Junier
Soils are complex ecosystems in which fungi and bacteria co-exist and interact. Fungal highways are a kind of interaction by which bacteria use fungal hyphae to disperse in soils. Despite the fact that fungal highways have been studied in laboratory models, the diversity of fungi and bacteria interacting in this way in soils is still unknown. Fungal highway columns containing two different culture media were used as a selective method to study the identity of fungi and bacteria able to migrate along their hyphae in three forest soils...
October 18, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27797963/molecular-characterization-of-the-psinb-plasmid-of-the-arsenite-oxidizing-metallotolerant-sinorhizobium-sp-m14-insight-into-the-heavy-metal-resistome-of-sinorhizobial-extrachromosomal-replicons
#20
Krzysztof Romaniuk, Lukasz Dziewit, Przemyslaw Decewicz, Sebastian Mielnicki, Monika Radlinska, Lukasz Drewniak
Sinorhizobium sp. M14 is an As(III)-oxidizing, psychrotolerant strain, capable of growth in the presence of extremely high concentrations of arsenic and many other heavy metals. Metallotolerant abilities of the M14 strain depend upon the presence of two extrachromosomal replicons, pSinA (∼ 109 kb) and pSinB (∼ 300 kb). The latter was subjected to complex analysis. The performed analysis demonstrated that the plasmid pSinB is a narrow-host-range repABC-type replicon, which is fully stabilized by the phd-vapC-like toxin-antitoxin stabilizing system...
October 18, 2016: FEMS Microbiology Ecology
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