Non-human microbiome, July 15

Murine skin commensals, nematodes, Bordeaux vines, polar soil, and water.

Mice microbiome

Adaptive immunity to murine skin commensals – Wei Shen – PNAS

“Here we report, for the first time, that commensal skin bacteria are recognized by major populations of T cells in skin-draining lymph nodes of mice.”

Nematode microbiome

Screen shot 2014-07-15 at 05.21PM, Jul 15NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes – Jeff L. Veesenmeyer – Molecular Microbiology

“Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression.”

Plant microbiome

Screen shot 2014-07-15 at 05.37PM, Jul 15Characterization of Pythium oligandrum populations that colonise the rhizosphere of vines from the Bordeaux region – Jonathan Gerbore – FEMS Microbiology Ecology

“The present study focused on one oomycete, Pythium oligandrum, well-known for its plant protection abilities, which thrives in microbial environment where bacteria and fungal communities are also present. “

Environmental microbial communities  (also see Human Gut digest)

Screen shot 2014-07-15 at 05.18PM, Jul 15Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity – Ashley Shade – mBio

“Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure.”

Soil microbiome

Screen shot 2014-07-15 at 05.38PM, Jul 15Environmental drivers of soil microbial community distribution at the Koiliaris Critical Zone Observatory – Myrto Tsiknia – FEMS Microbiology Ecology

“This study investigates the distribution of archaea, bacteria and fungi as well as the dominant bacterial phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes), and classes of Proteobacteria (α- and β-Proteobacteria) across the Koiliaris watershed by qPCR and associate them with environmental variables. “

SicilianoSoil fertility is associated with fungal and bacterial richness, whereas pH is associated with community composition in polar soil microbial communities – Steven D. Siciliano – Soil Biology and Biochemistry

“We quantified richness, evenness and taxonomic composition of both fungi and bacteria in 223 Arctic and Antarctic soil samples across 8 locations to test the global applicability of hypotheses concerning edaphic drivers of soil microbial communities that have been primarily developed from studies of bacteria in temperate and tropical systems.”

TianThe effect of irrigation with oil-polluted water on microbial communities in estuarine reed rhizosphere soils – Weijun Tian – Ecological Engineering

“PCR-denaturing gradient gel electrophoresis profiles revealed that the structure of the bacterial community was generally less affected, but the dominant flora was changed.”

Metatranscriptomic analysis of Arctic peat soil microbiota – Alexander Tveit – Applied and Environmental Microbiology

“A comparative analysis of mRNA enriched and non-enriched metatranscriptomes showed that mRNA enrichment resulted in a two-fold increase in the relative abundance of mRNA, but biased the relative distribution of mRNA. “

Screen shot 2014-07-15 at 07.15PM, Jul 15Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters – Alexandre B de Menezes – Environmental Microbiology

“Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community T-RFLPs as well as soil properties in paired woodland and pasture sites.”

Screen shot 2014-07-15 at 07.12PM, Jul 15 1Dynamic Succession of Soil Bacterial Community during Continuous Cropping of Peanut (Arachis hypogaea L.) – Mingna Chen – PLOS ONE

“In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation.”

Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members – Aurore Stroobants – Microbial Ecology

“In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat.”

Expression of copper-resistance genes in microbial communities under copper stress and oxic/anoxic conditions – Ludovic Besaury – Environmental Science and Pollution Research

“The abundance and expression of the copper-resistance genes cusA and copA, encoding respectively for a Resistance Cell Nodulation protein and for a P-type ATP-ase pump, was assessed along a gradient of copper concentration in microcosms prepared from Seine estuary mudflat sediment. “

Water microbiome

Screen shot 2014-07-15 at 05.40PM, Jul 15Distinct bacterial assemblages reside at different depths in Arctic multiyear sea ice – Ido Hatam – FEMS Microbiology Ecology

“Here, we determine whether bacterial communities: 1) differ with ice depth due to strong physical and chemical gradients, 2) are relatively homogenous within a layer, but differ between layers, or 3) do not vary with ice depth”

Screen shot 2014-07-15 at 05.41PM, Jul 15Microspatial gene expression patterns in the Amazon River Plume – Brandon M. Satinsky – PNAS

“The bacterial and archaeal communities associated with a phytoplankton bloom in Amazon River Plume waters at the outer continental shelf in June 2010 harbored ∼1.0 × 1013 genes and 4.7 × 1011 transcripts per liter that mapped to several thousand microbial genomes.”

Screen shot 2014-07-15 at 05.42PM, Jul 15Synchronous dynamics and correlations between bacteria and phytoplankton in a subtropical drinking water reservoir – Lemian Liu – FEMS Microbiology Ecology

“In this study, we evaluated the correlations between bacteria and phytoplankton communities, and determined the relative contribution of phytoplankton community succession to temporal variation of BCC in a subtropical drinking water reservoir (Tingxi Reservoir, southeast China).”

Screen shot 2014-07-15 at 07.12PM, Jul 15Metabolic and phylogenetic profile of bacterial community in Guishan coastal water (Pearl River Estuary), South China Sea – Xiaojuan Hu – Journal of Ocean University of China

“In the present study, the metabolic and phylogenetic profile of the bacterioplankton community in Guishan coastal water (Pearl River Estuary), South China Sea, at 12 sites (S1-S12) were explored by community-level physiological profiling (CLPP) with BIOLOG Eco-plate and denaturing gradient gel electrophoresis (DGGE).”


Bioreactor microbiomes

Screen shot 2014-07-15 at 05.39PM, Jul 15

Shifts in the Microbial Community, Nitrifiers and Denitrifiers in the Biofilm in a Full-scale Rotating Biological Contactor – Xingxing Peng – Environmental Science & Technology

“The microbial consortia were profiled using multiple approaches, including 454 high-throughput sequencing of the V3–V4 region of 16S rRNA gene, clone libraries, and quantitative polymerase chain reaction (qPCR). “

Enzymatic characterizationEnzymatic characterization of microbial isolates from lignocellulose waste composting: Chronological evolution – Juan Antonio López-González – Journal of Environmental Management

“Ammonification (72.04%), amylolysis (35.65%), hemicellulolyis (30.75%), and proteolysis (33.61%) were the more frequent activities among isolates, with mesophilic bacteria and fungi as the prevalent microbial communities.”


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