Tag Archives: rhizosphere

Animal microbiome digest, September 16, 2014

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Microbiomes of baby elephants, baby macaques, cows, mice, honey bees, oysters, Panama forest trees, yoghurt, air, beer, and clothes. We also learn that oregano has no effect on piglet microbiome. Just in case you wondered.

Mammal microbiome

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes – Nele Ilmberger – PLOS ONE

“A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal.”

Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems – Amir Ardeshir – Science Translational Medicine

“We show that breast-fed and bottle-fed infant rhesus macaques develop markedly different immune systems, which remain different 6 months after weaning when the animals begin receiving identical diets.”

Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil – Sharon Ann Huws – Microbial Biotechnology

“Microbiome pyrosequences showed that 50% of the bacterial genera were core to all diets (found at least once under each dietary intervention)”

Metagenome of Mehsani Buffalo Rumen Microbiota: An Assessment of Variation in Feed-Dependent Phylogenetic and Functional Classification – Parmar N.R. – Journal of Molecular Microbiology and Biotechnology

“Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.”

Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing – Jakub Kreisinger – Molecular Ecology

“Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M.m.musculus and M.m. domesticus).”

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano – Katrin Stelter – Food and Nutrition Sciences

“The results showed no significant changes in microbiota in response to oregano. “

Insect microbiome

Buzz off, that’s my bee! – Gemma Langridge – Nature Reviews Microbiology

“These newly sequenced bee gut symbionts have revealed multiple genes that are candidates for determining host specificity. “

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics – Philipp Engel – PLOS Genetics

“In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. “

Bacterial Communities in the Gut and Reproductive Organs of Bactrocera minax (Diptera: Tephritidae) Based on 454 Pyrosequencing – Ailin Wang – PLOS ONE

“We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax.”

Invertebrate microbiome

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection – Ana Lokmer and Karl Mathias Wegner – ISME Journal

“We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. “

Plant microbiome

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest – Steven W. Kembel – PNAS

“In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. “

Litter decomposition and soil microbial community composition in three Korean pine (Pinus koraiensis) forests along an altitudinal gradient – Yong Zhou – Plant and Soil

“Single- and mixed-species litter decomposition rates were determined by the litterbag method and soil microbial community composition was characterized by PLFAs.”

Soil microbiome

Pyrosequencing assessment of rhizosphere fungal communities from a soybean field – Akifumi Sugiyama – Canadian Journal of Microbiology

“This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth.”

Water microbiome

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years – Jacob A Cram – ISME Journal

“Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time.”

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – Martin Eriksson – PeerJ PrePrints

“Pollution-Induced Community Tolerance (PICT) was observed for algae and cyanobacteria at 100 nM TCS and higher.”

Review: Master recyclers: features and functions of bacteria associated with phytoplankton blooms – Alison Buchan – Nature Reviews Microbiology

“In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling.”

Built environment microbiome

Diversity and dynamics of the indoor air microbiome in an urban subway network – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Targeting the 16S rDNA V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those seen associated on skin.”

Microbial Odor Profile of Polyester and cotton clothes after a fitness session – Chris Callewaert – Applied and Environmental Microbiology

“A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of DGGE fingerprinting. “

Food microbiology

Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling’? – Gabriele Berg – Microbial Biotechnology

“Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. “

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang of China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity of 22 home-made yoghurt samples from Zhaosu and Tekesi counties of Xinjiang in China were analyzed with pyrosequencing. “

Victory, life-sciences firm team up to detect bacteria that can spoil beer’s taste – Diane Mastrull – Philly.com

“The list is long of the perfect accompaniments to beer: hot dogs, pizza, peanuts, and pretzels, to name just a few. Most definitely not on that list: pediococcus and lactobacillus. Consider them beer buzzkills.”

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Non-human microbiome, August 19, 2014

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A very diverse mix today: kangaroo, rumen, Daphnia, ticks, corals, rice, switchgrass, drinking water, acid mine drainage, rocks, soil microbiomes.

Mammal microbiome

* Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing – Scott Godwin – ISME Journal

“Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos”

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling – Hailan Piao – Frontiers in Microbiology

“Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing.”

Arthropod microbiome

Bacterial epibionts of Daphnia: a potential route for the transfer of dissolved organic carbon in freshwater food webs – Ester M Eckert and Jakob Pernthaler – ISME Journal

“We analysed the activity and identity of bacterial epibionts in cultures of Daphnia galeata and of natural daphnid populations.”

Evaluation of microbial communities and symbionts in Ixodes ricinus and ungulate hosts (Cervus elaphus and Ovis aries) from shared habitats on the west coast of Norway
Erik G. Granquist – Ticks and Tick-borne Diseases

“Five different species; M. mitochondrii, W. pipientis, Borrelia spp., Rickettia spp. and A. phagocytophilum, were analyzed on a 7500 Fast Real-time PCR system (Life Technologies, Carlsbad, CA), and carried out in separate 96-wells reaction plates. “

Coral microbiome

New insights into Oculina patagonica coral diseases and their associated Vibrio spp. communities – Esther Rubio-Portillo – ISME Journal

“….we have analysed the seasonal patterns of the culturable Vibrio spp. assemblages associated with healthy and diseased O. patagonica colonies. “

Bloom of the cyanobacterium Moorea bouillonii on the gorgonian coral Annella reticulata in Japan – Hideyuki Yamashiro – Nature Scientific Reports

“In addition to the cyanobacterium–shrimp interaction, the new trait of anchoring by the cyanobacterium into gorgonian coral may contribute to persistence of this bloom.”

* Not just who, but how many: the importance of partner abundance in reef coral symbioses – Ross Cunning and Andrew C. Baker – Frontiers in Microbiology

“…we generate testable hypotheses regarding the importance of symbiont abundance by first discussing different metrics and their potential links to symbiosis performance and breakdown, and then describing how natural variability and dynamics of symbiont communities may help explain ecological patterns on coral reefs and predict responses to environmental change.”

Plant microbiome

Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots – Takashi Okubo – Microbes and Environments

“Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath.”

Reviving of the endophytic bacterial community as a putative mechanism of plant resistance – Olga Podolich – Plant and Soil

“Based on the published results, we suggest that the endophyte-mediated stress tolerance or disease resistance can develop, if the plant hosts a sufficient diversity of ‘protective’ endophytes. “

The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants – Vanessa C. Coats, Mary E. Rumpho – Frontiers in Microbiology

“This review discusses recent advances in invasive plant biology that have resulted from microbiome analyses as well as the microbial factors that direct plant fitness and adaptability in natural systems.”

Kelp forest size alters microbial community structure and function on Vancouver Island, Canada – Jessica Liz Clasen and Jonathan B. Shurin – Ecology

“We investigated the response of microbial communities to variation in kelp abundance between regions with and without sea otter populations along the west coast of Vancouver Island, British Columbia, Canada”

Soil, sediments, rocks

* Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest – Neslihan Taş – ISME Journal

“We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing.”

Integrated Metagenomics and Metatranscriptomics Analyses of Root-Associated Soil from Transgenic Switchgrass – Archana Chauhan – Genome Announcements

“Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts.”

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities – Marta Goberna – Ecology Letters

“We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. “

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments – Meiying Xu – ISME Journal

“Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants “

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbiology Ecology

“The presence and in vitro expression of homologues to 22 bacterial human virulence determinants amongst culturable soil bacteria was investigated.”

Endolithic bacterial communities in rock coatings from Kärkevagge, Swedish Lapland – Cassandra L. Marnocha – FEMS Microbiology Ecology

“Using 454 Roche pyrosequencing of the 16S rDNA gene, nine rock coating samples from three different coating mineralogies were sequenced.”

Biodegradation Potential of Organically Enriched Sediments under Sulfate- and Iron-Reducing Conditions as Revealed by the 16S rRNA Deep Sequencing – Tomoyuki Hori – Journal of Water and Environment Technology

“The effects of supplementation with sulfate and lepidocrocite (a crystalline Fe[III] oxide) on the structure and activity of the slurry microorganisms were examined by the combined physicochemical analyses and 16S rRNA deep sequencing. “

Soil bacterial diversity in degraded and restored lands of Northeast Brazil – Ademir Sérgio Ferreira Araújo – Antonie van Leeuwenhoek

“In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. “

* Biogeochemical environments of streambed-sediment pore waters with and without arsenic enrichment in a sedimentary rock terrain, New Jersey Piedmont, USA
A.C. Mumford – Science of the Total Environment

“The 16S rRNA gene and the As(V) respiratory reductase gene, arrA, were amplified from DNA extracted from streambed pore water at both sites and analyzed, revealing that distinct bacterial communities that corresponded to the redox conditions were present at each site. “

Water, wastewater, sludge microbiome

* A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing – Kailong Huang – Ecotoxicology and Environmental Safety

“In order to comprehensively investigate bacterial virulence in drinking water, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential pathogenic bacteria and virulence factors (VFs) in a full-scale drinking water treatment and distribution system. “

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole – Pascault Noémie – FEMS Microbiology Ecology

“Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously-exposed sites than in pristine sites.”

Disturbance and temporal partitioning of the activated sludge metacommunity – David C Vuono – ISME Journal

“Bacterial small subunit (SSU) rRNA genes were surveyed from sludge samples resulting in a sequence library of >417 000 SSU rRNA genes. “

Review: Environmental bacteriophages: viruses of microbes in aquatic ecosystems – Télesphore Sime-Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology,”

* Inter-species interconnections in acid mine drainage microbial communities
Luis R. Comolli and Jill F. Banfield – Frontiers in Microbiology

“Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. “

A study on the microbial community structure in oil reservoirs developed by water flooding – Lin Junzhang – Journal of Petroleum Science and Engineering

“This study was performed to identify the microbial community structures in 10 different types of water-flooded oil reservoirs on Sinopec Shengli Oil Field. “

Microbes of the built environment

* Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions – Kasthuri Venkateswaran – Microbes and Environments

“In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.”

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives – Nobuyasu Yamaguchi – Microbes and Environments

“In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed.”

Food microbiology

Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing
Zhihong Sun – Journal of Dairy Science

“This is the first study on the bacterial and fungal community diversity in 17 tarag samples (naturally fermented dairy products) through a metagenomic approach involving high-throughput pyrosequencing. “

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Microbiome digest, August 18, 2014

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Mushroom microbiome, mice fed T7 phages, and uBiome got some money.

Plant microbiome

Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing – M. Kim – Journal of Applied Microbiology

“The bacterial communities in soil samples collected from inside, beneath and outside the T. matsutake fairy ring were investigated using barcoded pyrosequencing. “

Rhizospheric fungal community structure of a Bt brinjal and a near isogenic variety – A.K. Singh – Journal of Applied Microbiology

“..this study concludes that genetic modification of brinjal crop has minor effect on the fungal community.”

Phages and viruses

Observation of inflammatory responses in mice orally fed with bacteriophage T7 – K. Park – Journal of Applied Microbiology

“A histopathological analysis of tissue samples from the stomach, small intestine and colon revealed no significant pathological change.”

Microbes in the news

GW High students to name bacterium – Maria Hernandez – Pacific Sunday News

“Students from George Washington High School got the opportunity to name a bacterium that was discovered during a historic underwater expedition to the Mariana Trench, which was led by filmmaker James Cameron in 2012.”

uBiome Raises $4.5M From Angel Investors, Andreessen Horowitz To Crowdsource Microbiome Research – Julian Chokkattu – Techcrunch

“uBiome also has the largest private dataset of human microbiome samples in the world, giving participants a quick way to compare what’s in their microbiome to a large group.”

Bik’s Picks

All Things Considered podcast (3 min): Often On The Move, Restless Elephants Are Tough To Count — And Keep Safe – Gregory Warner – NPR

“The reason elephants are so hard to protect is the same that makes them so hard to count: They roam — exceptionally far.”

Mapping Cell Fate Conversion via CellNet, a Network Biology Tool – Kevin Mayer – GenEngNews

“The differentiation of engineered stem cells may be imagined as a subway journey, where the genetic equivalents of missing a transfer or getting off at the wrong stop can take your stem cells far off course.”

Camouflage sheet inspired by octopus – Jonathan Webb – BBC Science

“Based on the camouflage abilities of octopuses and cuttlefish, engineers in the US have built a flexible material that changes colour to match its surroundings.”

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Non-human microbiome, August 14, 2014

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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

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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

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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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