Non-human microbiome, August 14, 2014

Microbial diversity in lichen, rhizosphere microbiome, and a trip to the bottom of the “seaquence”.

Plant microbiome

Algal and Fungal Diversity in Antarctic Lichens – Chae Haeng Park – Journal of Eukaryotic Microbiology

“In the current study, we analyzed algal and lichen-associated fungal community structure in lichen species from King George Island, Antarctica by pyrosequencing of eukaryotic LSU and algal ITS domains of the nuclear rRNA gene.”

Nitrogen-transforming archaea and bacteria in tropical soils are affected under transgenic as compared to non-transgenic maize – Simone Raposo Cotta – Applied and Environmental Microbiology

“The data show that significant changes occurred in the abundances (revealed by qPCR) of ammonia-oxidizing bacterial and archaeal communities as a result of the maize host being genetically-modified.”

Soil microbiome

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site
Shinjini Mukherjee – ISME Journal

“Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. “

Water microbiome

Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria – Barbara Klippel – Extremophiles

“Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes.”

Voyage to the bottom of the ‘seaquence’ – Rachael Wash & Carmen Diaz Soria – Nature Reviews Microbiology

“This month’s Genome Watch highlights the use of deep sequencing metagenomics to identify bacteriophages that carry sulphur-oxidizing genes in deep-sea hydrothermal vent plumes.”

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Non-human microbiome, August 12, 2014

Insect, coral, plant, soil, sediment, and snow microbiome
Insect microbiome

Insect endosymbiont proliferation is limited by lipid availability – Jeremy K Herren – eLife

“In this study, we find that Spiroplasma proliferation specifically depletes host hemolymph diacylglyceride, the major lipid class transported by the lipoprotein, Lpp.”

Coral microbiome

Novel Tools Integrating Metabolic and Gene Function to Study the Impact of the Environment on Coral Symbiosis – Mathieu Pernice and Oren Levy – Frontiers Microbiology

“Here, we review the potential of recent technological advances in molecular biology and approaches using stable isotopes to fill critical knowledge gaps regarding coral symbiotic function. “

Plant microbiome

Towards a systems understanding of plant-microbe interactions – Akira Mine – Frontiers in Plant Science

“Recent advances in metagenomics of microbial communities associated with plants further point to the importance of systems approaches and open a research area of microbial community reconstruction. “

Amazonian Dark Earth and Plant Species from the Amazon Region Contribute to Shape Rhizosphere Bacterial Communities – Amanda Barbosa Lima – Microbial Ecology

The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata).”

Rhizosphere effect and salinity competing to shape microbial communities in Phragmites australis (Cav.) Trin. ex-Steud – Luigimaria Borruso – FEMS Microbiology Letters

“Microbiological analyses have been done by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and partial 16S rRNA gene 454 pyrosequencing. “

Soil and sediment microbiome

Diversity of Bacterial Communities Along a Petroleum Contamination Gradient in Desert Soils – Raeid M. M. Abed – Microbial Ecology

“We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution.”

16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns – Ethan A. Rundell – PLOS ONE

“A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers.”

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin – Adrien Vigneron – PLOS ONE

“Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches .. and correlated to comprehensive geochemical data.”

Isolation of Sphaerotilus-Leptothrix-strains from iron bacteria communities in Tierra del Fuego wetlands – B Schmidt – FEMS Microbiology Ecology

“The present work increases the number and diversity of cultivated SLG bacteria by obtaining isolates from biofilms and sediment samples of wetlands in Tierra del Fuego.”

Water and snow microbiome

Snow Surface Microbiome on the High Antarctic Plateau (DOME C) – Luigi Michaud – PLOS ONE

“In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including .. (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing.”

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Non-human microbiome, August 11, 2014

Microbiomes of Eurasian Magpie, mosquitoes, ticks, 218 insect species, sponges, plants, and olives.

Bird microbiome

Effect of Incubation on Bacterial Communities of Eggshells in a Temperate Bird, the Eurasian Magpie (Pica pica) – Won Young Lee – PLOS ONE

“In this study, we employed culture-independent methods, quantitative PCR and 16S rRNA gene pyrosequencing, to elucidate the effect of incubation on the bacterial abundance and bacterial community composition on the eggshells of the Eurasian Magpie (Pica pica).”

Arthropod microbiome

Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes
Grant L. Hughes – PNAS USA

“We show the native microbiota of Anopheles impede vertical transmission of Wolbachia. Antibiotic microbiome perturbation enables Wolbachia transmission in two Anopheles species.”

Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens – Yongjin Qiu – PLOS ONE

“Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. “

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host – Ji-Hyun Yun – Applied and Environmental Microbiology

In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes.

Sponge microbiome

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge – Ren-Mao Tian – Environmental Microbiology

“Here, we present and analyze the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy”

Plant microbiome

Foliage Friendships (behind paywall) – Peter Andrey Smith – Scientific American

“Microbial communities on a plant’s roots, stems and leaves may improve crop growth”

Effects of Fusarium oxysporum on rhizosphere microbial communities of two cucumber genotypes with contrasting Fusarium wilt resistance under hydroponic condition – Ju Ding – European Journal of Plant Pathology

“PCR-DGGE analysis of 16S rDNA fragments indicated that following FO inoculation, significant changes in the bacterial structure isolated from the root surfaces of susceptible plants were observed, such as an increased diversity index, a decreased evenness index, and the occurrence of several types of bacteria that decomposed organic substances.”

Food microbiology

Open-refrigerated retail display case temperature profile and its impact on product quality and microbiota of stored baby spinach – Liping Kou – Food Control

“All bags were immediately loaded in the display cases and the overall visual quality, tissue electrolyte leakage, total aerobic mesophilic bacteria and psychrotrophic bacteria were evaluated for each bag. “

Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production – Xi Zhang – Bioresouce Technology

“The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. “

Genetic diversity and dynamics of bacterial and yeast strains associated to Spanish-style green table-olive fermentations in large manufacturing companies – Helena Lucena-Padrós – International Journal of Food Microbiology

“We have genotyped a total of 1045 microbial isolates obtained along the fermentation time of Spanish-style green table olives from the fermentation yards (patios) of two large manufacturing companies in the province of Sevilla, south of Spain.”

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