journal
MENU ▼
Read by QxMD icon Read
search

FEMS Microbiology Ecology

journal
https://www.readbyqxmd.com/read/28087803/epiphytic-planctomycetes-communities-associated-with-three-main-groups-of-macroalgae
#1
Joana Bondoso, Filipa Godoy-Vitorino, Vanessa Balagué, Josep M Gasol, Jens Harder, Olga Maria Lage
Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis (DGGE) with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season...
January 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28087802/cytochrome-c-peroxidase-ccp-is-a-molecular-determinant-of-the-oxidative-stress-response-in-the-extreme-acidophilic-leptospirillum-sp-cf-1
#2
C Zapata, B Paillavil, R Chávez, P Álamos, G Levicán
Bioleaching processes are used to recover metals from sulfidic ores. Biofilm formation on ores is important for bioleaching because the attached microorganisms start the leaching process by concentrating ferric ions in the extracellular matrix. It has been shown that hydrogen peroxide is spontaneously generated on the surface of ores and that it negatively influences the growth and activity of microorganisms. However, the mechanism by which bioleaching microorganisms tolerate exogenous H2O2 as an adaptive trait remains elusive...
January 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28087801/occurrence-of-similar-mycoviruses-in-pathogenic-saprotrophic-and-mycorrhizal-fungi-inhabiting-the-same-forest-stand
#3
Eeva J Vainio, Taina Pennanen, Tiina Rajala, Jarkko Hantula
Fungal viruses (mycoviruses) are considered to be highly host specific, but phylogenetic analysis supports the occasional occurrence of horizontal transmission between species. We used an extensive sampling strategy to investigate whether similar viruses occur in more than one fungal species of the same forest habitat. Mycelial samples were collected from in-growth mesh bags (N = 259), fruiting bodies (N = 173) and cultured isolates (N = 68) at a forest site where the spatial distribution of viral infections in clonal individuals of the wood decay fungus H...
January 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28073802/assemblage-composition-of-fungal-wood-decay-species-has-major-influence-on-how-climate-and-wood-quality-modify-decomposition
#4
Parvathy Venugopal, Kaisa Junninen, Mattias Edman, Jari Kouki
The interactions among saprotrophic fungal species, as well as their interactions with environmental factors, may have a major influence on wood decay and carbon release in ecosystems. We studied the effects that decomposer diversity (species richness and assemblage composition) have on wood decomposition when the climatic variables and substrate quality vary simultaneously. We used two temperature (16 and 21(°)C) and two humidity (70% and 90%) levels at two wood qualities (wood from managed and old-growth forests) of Pinus sylvestris In a nine-month experiment, the effects of fungal diversity were tested using four wood-decaying fungi (Antrodia xantha, Dichomitus squalens, Fomitopsis pinicola and Gloeophyllum protractum) at assemblage levels one, two and four species...
January 10, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28011600/aspect-has-a-greater-impact-on-alpine-soil-bacterial-community-structure-than-elevation
#5
Jieyun Wu, Barbara J Anderson, Hannah L Buckley, Gillian Lewis, Gavin Lear
Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g., soil temperature, pH) and resource conditions (e...
December 22, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28011599/long-term-effects-of-aided-phytostabilization-on-microbial-communities-of-metal-contaminated-mine-soil
#6
Olatz Garaiyurrebaso, Carlos Garbisu, Fernando Blanco, Anders Lanzén, Iker Martín, Lur Epelde, José M Becerril, Sven Jechalke, Kornelia Smalla, Elisabeth Grohmann, Itziar Alkorta
Aided phytostabilization uses metal-tolerant plants, together with organic or inorganic amendments, to reduce metal bioavailability in soil while improving soil quality. The long-term effects of the following organic amendments were examined as part of an aided phytostabilization field study in an abandoned Pb/Zn mining area: cow slurry; sheep manure; paper mill sludge mixed with poultry manure. In the mining area, two heavily-contaminated vegetated sites, showing different levels of soil metal contamination (LESS and MORE contaminated site), were selected for this study...
December 22, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28011598/reconstructing-metabolic-pathways-of-a-member-of-the-genus-pelotomaculum-suggesting-its-potential-to-oxidize-benzene-to-carbon-dioxide-with-direct-reduction-of-sulfate
#7
Xiyang Dong, Johannes Dröge, Christine von Toerne, Sviatlana Marozava, Alice C McHardy, Rainer U Meckenstock
The enrichment culture BPL is able to degrade benzene with sulfate as electron acceptor and is dominated by an organism of the genus Pelotomaculum Members of Pelotomaculum are usually known to be fermenters, undergoing syntrophy with anaerobic respiring microorganisms or methanogens. By using a metagenomic approach, we reconstructed a high-quality genome (∼2.97 Mbp, 99% completeness) for Pelotomaculum candidate BPL. The proteogenomic data suggested: (1) anaerobic benzene degradation was activated by a yet unknown mechanism for conversion of benzene to benzoyl-CoA; (2) the central benzoyl-CoA degradation pathway involved reductive dearomatization by a class II benzoyl-CoA reductase followed by hydrolytic ring cleavage and modified β-oxidation; (3) the oxidative acetyl-CoA pathway was utilized for complete oxidation to CO2 Interestingly, the genome of Pelotomaculum candidate BPL has all the genes for a complete sulfate reduction pathway including a similar electron transfer mechanism for dissimilatory sulfate reduction as in other Gram-positive sulfate-reducing bacteria...
December 22, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28011597/exploring-the-methanogen-and-bacterial-communities-of-rumen-environments-solid-adherent-fluid-and-epimural
#8
Thijs De Mulder, Karen Goossens, Nico Peiren, Leen Vandaele, Annelies Haegeman, Caroline De Tender, Tom Ruttink, Tom Van de Wiele, Sam De Campeneere
The rumen microbiome occupies a central role in animal health and productivity. A better understanding of the rumen ecosystem is essential to increase productivity or decrease methane production. Samples were collected from the three main rumen environments: the solid adherent fraction, the liquid fraction and the epithelium. For the liquid and solid fraction, two alternative sample processing protocols were compared, resulting in a total of five sample types: crude solids (S), the eluted solid adherent fraction (Ad), free-living species in the crude rumen liquid (CRL), strained liquid samples (Lq) and epimural scrapings (Ep)...
December 22, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27986828/the-specific-and-exclusive-microbiome-of-the-deep-sea-bone-eating-snail-rubyspira-osteovora
#9
H S Aronson, A J Zellmer, S K Goffredi
Rubyspira osteovora is an unusual deep-sea snail from Monterey Canyon, CA. This group has only been found on decomposing whales and is thought to use bone as a novel source of nutrition. This study characterized the gut microbiome of R. osteovora, compared to the surrounding environment, as well as to other deep-sea snails with more typical diets. Analysis of 16S rRNA gene sequences revealed that R. osteovora digestive tissues hosted a much lower bacterial diversity (average Shannon index of 1.9; n = 12), compared to environmental samples (average Shannon index of 4...
December 15, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27986827/potential-of-semiarid-soil-from-caatinga-biome-as-a-novel-source-for-mining-lignocellulose-degrading-enzymes
#10
Gileno Lacerda Júnior, Melline Noronha, Sanderson Tarciso de Sousa, Lucélia Cabral, Daniela Domingos, Mírian Sáber, Itamar de Melo, Valéria Oliveira
The litterfall is the major organic material deposited in soil of Brazilian Caatinga biome, thus providing the ideal conditions for plant biomass-degrading microorganisms to thrive. Herein, the phylogenetic composition and lignocellulose degrading capacity have been explored for the first time from a fosmid library dataset of Caatinga soil by sequence-based screening. A complex bacterial community dominated by Proteobacteria and Actinobacteria was unraveled. SEED subsystems-based annotations revealed a broad range of genes assigned to carbohydrate and aromatic compounds metabolism, indicating microbial ability to utilize plant-derived material...
December 15, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27986826/the-contribution-of-genome-mining-strategies-to-the-understanding-of-active-principles-of-pgpr-strains
#11
Julia Paterson, Ghazaleh Jahanshah, Yan Li, Qi Wang, Samina Mehnaz, Harald Gross
Pathogenic microorganisms and insects affecting plant health are a major and chronic threat to food production and the ecosystem, worldwide. As agricultural production has intensified over the years, the use of agrochemicals has in turn increased. However, this extensive usage has had several detrimental effects, with a pervasive environmental impact and the emergence of pathogen resistance. In addition, there is an increasing tendency among consumers to give preference to pesticide-free food products. Biological control, through the employment of plant growth-promoting rhizobacteria (PGPR), is therefore considered a possible route to the reduction, even the elimination, of the use of agrochemicals...
December 15, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27940647/gaia-and-her-microbiome
#12
John F Stolz
The Gaia Hypothesis, proposed 50 years ago, posits that the Earth's biosphere, atmosphere, hydrosphere, and lithosphere interact as a cybernetic system, maintaining the long-term habitability of the planet. The resulting chemical composition of the atmosphere, oceans, and crust is unique as compared to the other planets of our solar system, and due to the presence of life. Together these components comprise the biosphere, the life support system of the planet, with most of the essential processes carried out by microbes...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27940646/an-improved-protocol-with-a-highly-degenerate-primer-targeting-copper-containing-membrane-bound-monooxygenase-cummo-genes-for-community-analysis-of-methane-and-ammonia-oxidizing-bacteria
#13
Jian-Gong Wang, Fei Xia, Jemaneh Zeleke, Bin Zou, Sung-Keun Rhee, Zhe-Xue Quan
The copper-containing membrane-bound monooxygenase (CuMMO) family comprises key enzymes for methane or ammonia oxidation: particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO). To comprehensively amplify CuMMO genes, a two-step PCR strategy was developed using a newly designed tagged highly degenerate primer (degeneracy = 4608). Designated THDP-PCR, the technique consists of primary CuMMO gene-specific PCR followed by secondary PCR with a tag as a single primer. No significant bias in THDP-PCR amplification was found using various combinations of template mixtures of pmoA/amoA genes from different microbes...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27940645/biogeography-of-soil-thaumarchaeota-in-relation-to-soil-depth-and-land-usage
#14
Xinda Lu, Brent Seuradge, Josh D Neufeld
Although thaumarchaeota are important contributors to ammonia oxidation in terrestrial habitats, distributions of ammonia oxidizers along soil depth profiles are poorly understood, especially in relation to distinct land usages. Leveraging the close proximity of forest, field, and agricultural plots at the RARE: Charitable Research Reserve, we examined soil thaumarchaeotal biogeography at three different depths (0-15, 15-30, and 30-45 cm) from plots within areas of contrasting land usage. Data from high-throughput sequencing of thaumarchaeotal 16S rRNA gene sequences demonstrated that OTU richness was affected significantly by depth and land-use type...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27940644/rhizosphere-microbiomes-of-potato-cultivated-in-the-high-andes-show-stable-and-dynamic-core-microbiomes-with-different-responses-to-plant-development
#15
Stefan Pfeiffer, Birgit Mitter, Andreas Oswald, Brigitte Schloter-Hai, Michael Schloter, Stéphane Declerck, Angela Sessitsch
The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3,245 to 4,070 m.a.s.l., differing in soil characteristics, climate, and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27940643/marine-heatwaves-and-optimal-temperatures-for-microbial-assemblage-activity
#16
Ian Joint, Dan A Smale
The response of microbial assemblages to instantaneous temperature change was measured in a seasonal study of the coastal waters of the western English Channel. On 18 occasions between November 1999 and December 2000, bacterial abundance was assessed and temperature responses determined from the incorporation of (3)H leucine, measured in a temperature gradient from 5-38°C. Q10 values varied, being close to 2 in spring and summer but were >3 in autumn. There was a seasonal pattern in the assemblage optimum temperature (Topt), which was out of phase with sea surface temperature...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27940642/new-insights-into-the-role-of-the-porcine-intestinal-yeast-kazachstania-slooffiae-in-intestinal-environment-of-weaned-piglets
#17
Vladimir Urubschurov, Kirsten Büsing, Gertraude Freyer, Daniel P R Herlemann, Wolfgang-Bernhard Souffrant, Annette Zeyner
Kazachstania slooffiae is a porcine intestinal yeast which role in the intestinal environment is largely unexplored. Therefore, the impact of K. slooffiae on growth performance, intestinal microbial metabolites and the microbiota of weaned piglets was investigated in this study. Forty-eight German Landrace pigs were weaned at day 27 or 28 of life and grouped into one control and three treatment groups. During the five-week experiment, piglets had ad libitum access to feed and water. On day 5, 6 and 7 post weaning, pigs were orally supplemented with either placebo, or K...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27915286/presence-of-diverse-rhizobial-communities-responsible-for-nodulation-of-common-bean-phaseolus-vulgaris-in-south-african-and-mozambican-soils
#18
Mwazuma K Zinga, Sanjay K Jaiswal, Felix D Dakora
The diversity and phylogeny of root-nodule bacteria isolated from common bean grown in Mozambique and different provinces of South Africa was studied by restriction fragment length polymorphism and phylogenetic analysis. The combined restriction banding pattern of 16S rRNA and nifH profile-generated dendrogram grouped all test isolates into four major clusters with XXI restriction group and three clusters with the VIII restriction groups. Location-based clustering was observed with the 16S-RFLP analysis. Phylogenetic analysis of 16S rRNA, glnII, gyrB and gltA sequences showed that common bean was nodulated specifically by Rhizobium etli in Mozambican soils, and by diverse of group of Rhizobium species in South African soils (e...
December 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27915285/depth-dependent-influence-of-different-land-use-systems-on-bacterial-biogeography
#19
Brent J Seuradge, Maren Oelbermann, Josh D Neufeld
Despite progress in understanding microbial biogeography of surface soils, few studies have investigated depth-dependent distributions of terrestrial microorganisms in subsoils. We leveraged high-throughput sequencing of 16S rRNA genes obtained from soils collected from the RARE: Charitable Research Reserve (Cambridge, Ontario, Canada) to assess the influence of depth on bacterial communities across various land-use types. Although bacterial communities were strongly influenced by depth across all sites, the magnitude of this influence was variable and demonstrated that land-use attributes also played a significant role in shaping soil bacterial communities...
December 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27915284/dna-extraction-protocols-may-influence-biodiversity-detected-in-the-intestinal-microbiome-a-case-study-from-wild-prussian-carp-carassius-gibelio
#20
Elena N Kashinskaya, Karl B Andree, Evgeniy P Simonov, Mikhail M Solovyev
In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTU's, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species...
December 2, 2016: FEMS Microbiology Ecology
journal
journal
30018
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"