Category Archives: Plant Root Soil microbiome

Microbiome digest, August 17, 2014

Posted on by

Childhood undernutrition and the gut microbiome, hibernating ground squirrels, Sphagnum, nematodes, and forensic discrimination of soils.

Human gut microbiome

An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome – Tahmeed Ahmed – Annals of the New York Academy of Sciences

“This paper summarizes work on mechanisms underlying the varied manifestations of childhood undernutrition and discusses current gaps in knowledge and challenges to our understanding of undernutrition and infection/immunity throughout the human life cycle, focusing on early childhood growth. ”

Animal microbiome

Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defense in the gut of 13-lined ground squirrels – Kimberly A. Dill-McFarland – Molecular Ecology

“We used 16S rRNA pyrosequencing and cecal tissue protein analysis to investigate the effects of hibernation on the mucosa-associated bacterial microbiota and host responses in 13-lined ground squirrels.”

Diversity of Bacteria Carried by Pinewood Nematode in USA and Phylogenetic Comparison with Isolates from Other Countries – Diogo Neves Proença – PLOS ONE

“The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. “

Plant microbiome

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions – Anastasia Bragina – Molecular Ecology

“We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation.”

Soil microbiome

Random Whole Metagenomic Sequencing for Forensic Discrimination of Soils – Anastasia S. Khodakova – PLOS ONE

“Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles”

Microbial Community Structure of Relict Niter-Beds Previously Used for Saltpeter Production – Takashi Narihiro – PLOS ONE

“In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). “

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda? – Peter O Alele – PLOS ONE

“Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. “

Soil-Borne Microbial Functional Structure across Different Land Uses – Eiko E. Kuramae – The Scientific World Journal

“In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio.”

Water microbiome

Temperature response of denitrification and anammox rates and microbial community structure in Arctic fjord sediments – Andy Canion – Environmental Microbiology

“Community structure in intact sediments and slurry incubations was determined using Illumina MiSeq SSU rRNA gene sequencing.”

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems – Marianne Simon – Environmental Microbiology

“We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm-size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France.”

Metagenomics

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” – Brian P. Hedlund- Extremophiles

“Unraveling the mysteries of these candidate phyla is a grand challenge in microbiology and is especially important in habitats where they are abundant, including some extreme environments and low-energy ecosystems.”

Metabolomics

Metabolic Modelling of Spatial Heterogeneity of Biofilms in Microbial Fuel Cells Reveals Substrate Limitations in Electrical Current Generation – Nadeera Jayasinghe – Biotechnology Journal

“The goal of this work is to develop a model that integrates genome-scale metabolic models with the model of biofilm environment. “

Bioinformatics

Rarefaction and extrapolation of phylogenetic diversity – Anne Chao – Methods in Ecology and Evolution

“We develop in this paper the “PD accumulation curve” (an extension of the species accumulation curve) to depict how PD increases with sampling size and sample completeness.”

Microbes in the news

Can’t Stick to That Diet? Blame Your Gut Bacteria – Nolan Feeney – Time

“The gut microbiome, the collection of all the microbes in our digestive tracts, may influence our food choices and behavior, suggests a new study that recently appeared in the journal BioEssays.”

How Clean Is Your Produce? Testing Fruit For Bacteria – WFMyNews2.com

“Ellis took samples of the fruits one by one and placed the samples on a petri dish. She then washed some of the lettuce and repeated the testing procedure on both the head of lettuce and the pre-washed bag of lettuce, in 72-hours the results were in.”

Bik’s Picks

9/11 dust cloud may have caused widespread pregnancy issues – ScienceDaily

“Pregnant women living near the World Trade Center during the 9/11 attacks experienced negative birth outcomes, according to a new paper.”

Volunteers on the scent of science with whale carcass – Peter Fimrite – SF Gate

“If there’s anything as enjoyable to Dan Sudran as sawing through the stinking blubber of a whale carcass and extracting bones from the gooey tissues, it would be showing the results to children.”

Alaska’s Shrinking Glaciers Seen from Space – Kelly Dickerson – LiveScience

“Compared with a vintage satellite photo of the region, an image taken from space last year reveals just how much the glaciers have shrunk over the past 26 years.”

[hr]

Non-human microbiome, August 14, 2014

Posted on by

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.”

[hr]

Microbiome digest, August 13, 2014

Posted on by

Nose, glycan, butyrate, microbes on plastics, seawater microbial mats, and plants with microbes.

Respiratory microbiome

The nasal cavity microbiota of healthy adults – Christine M Bassis, Alice L Tang, Vincent B Young and Melissa A Pynnonen – Microbiome

“In our initial analysis, we compared the bacterial communities of the nasal cavity and the oral cavity from ten of these subjects.”

Gut microbiome

Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations – Omer Eilam – mBio

“Based on GlyDeR, we found a clear connection between microbial glycan degradation and human diet, and we suggest a method for the rational design of novel prebiotics.”

Microbial-Derived Butyrate: An Oncometabolite or Tumor-Suppressive Metabolite? -Scott J. Bultman, Christian Jobin – Cell Host & Microbe

“Dietary factors, microbial composition, and metabolism are intimately intertwined into a complex network whose activities influence important intestinal functions”

Review: Collateral Damage: Microbiota-Derived Metabolites and Immune Function in the Antibiotic Era – Christopher A. Lopez – Cell Host & Microbe

“A disruption of gut-associated microbial communities by antibiotic treatment can result in a depletion of microbiota-derived metabolites, thereby enhancing pathogen susceptibility, impairing immune homeostasis, and contributing to the rise of certain chronic inflammatory diseases”

Animal model of microbiome

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids
Sabina Lukovac – mBio

“The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids.”

Plant microbiome

Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors – Thomas R. Williams, Maria L. Marco – mBio

“We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce.”

Fundamental Plant Chemicals Rooted in Bacteria – Jenna Iacurci – Nature World News

“A fundamental chemical pathway that all plants use to create the essential amino acid phenylalanine has now been traced to two groups of ancient bacteria, a new study reports.”

Water microbiome

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters – Sonja Oberbeckmann – FEMS Microbial Ecology

“Denaturing Gradient Gel Electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location, and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. “

Molecular Ecology of Microbial Mats – Henk Bolhuis – FEMS Microbial Ecology

“Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring and hypersaline).”

Microbes in the news

Wearable structure of bacteria references antique animal bone corsets

“in terms of the material, it is grown from acetobacter xylinum, a strain of bacteria that produces a microbial cellulose textile as it consumes glucose.”

Bik’s Picks

Google Maps Dives Underwater – Scientific American

“Google has taken its ‘street view’ maps to a whole new level—namely, the ocean’s depths. “

[hr]

Non-human microbiome, August 12, 2014

Posted on by

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.”

[hr]

Non-human microbiome, August 11, 2014

Posted on by

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.”

[hr]

 

Microbiome digest, August 7, 2014

Posted on by

Microbiome and caries, colorectal cancer, and inflammatory bowel diseases. Microbiomes of fish, dogs, and mosses, microscopic life in an asphalt lake, and the Picks.

Human mouth microbiome

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing – Junko Obata – PLOS ONE

“In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the 16S rRNA gene.”

Human gut microbiome

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer – Joseph P. Zackular, Mary A.M. Rogers, Mack T. Ruffin IV, and Patrick D. Schloss – Cancer Prevention Research

“Analysis of the gut microbiome from stool samples revealed both an enrichment and depletion of several bacterial populations associated with adenomas and carcinomas.”

Manipulation of Microbiome, a Promising Therapy for Inflammatory Bowel Diseases – Dapeng Jin, Hongyu Zhang, and Jun Sun – Clinical & Cellular Immunology

“In this review, we summarize the current knowledge of how changes in microbiota may affect the pathogenesis of IBD. “

A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota – Bruce R. Hamaker, Yunus E. Tuncil – Journal of Molecular Biology

“the article encourages the building of a framework of information to manipulate the colon microbiota in a predicted way for improved health”

 

Human microbiome after death

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans – Ismail Can – Journal of Microbiological Methods

“We compared the effectiveness of two methods by amplifying the 16S rRNA genes and sequencing the amplicons from four cadavers”

Animal models of human microbiome

Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats
S.M. O’Mahony – Neuroscience

“Neonatal antibiotic treatment leads to an increase in visceral sensitivity in adulthood in rats.”

Dog microbiome

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque – Ian J Davis, Christopher Bull, Alexander Horsfall, Ian Morley and Stephen Harris – BMC Microbiology

“Using a quantitative polymerase chain reaction (qPCR) directed approach a range of microbiological media were screened and optimized to enrich for previously uncultivated target species. A systematic screening methodology was then employed to isolate the species of interest. ‘

Fish microbiome

Characterization of Microbiota Composition and Presence of Selected Antibiotic Resistance Genes in Carriage Water of Ornamental Fish – Lenka Gerzova – PLOS ONE

“In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents.”

Insect microbiome

The mosquito microbiota influences vector competence for human pathogens – Nathan J Dennison, Natapong Jupatanakul, George Dimopoulos – Current Opinion in Insect Science

“Understanding the interaction between the vector, its microbiota and transmitted pathogens will provide novel opportunities to limit disease transmission.”

Plant microbiome

Bacterial-biota dynamics of eight bryophyte species from different ecosystems
Faisal Hammad Mekky Koua – Saudi Journal of Biological Sciences

“..we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan.”

Soil and water microbiome

Two Neumann U students discover new types of viruses – CatholicPhilly.com

“They collected arthrobacter (a bacteria present in soil) from under trees and near lakes, found and filtered out the phages that were present, and then studied phage anatomy and life cycles.”

Water droplets in oil are microhabitats for microbial life – Rainer U. Meckenstock – Science

“In Pitch Lake, Trinidad and Tobago—the world’s largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. “

Microbiome of the built environment

Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings – Jörg D. Ettenauer – PLOS ONE

“In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques.”

Metagenomics

High-resolution metagenomics – Eran Mick & Rotem Sorek – Nature Biotechnology

In this issue, Nielsen et al. present a powerful method for interpreting metagenomic data at the level of individual genomes without relying on reference sequences of cultured isolates, which can be generated for only a small fraction of microbial life.

Microbes in the News

The Quantified Microbiome Self – Carl Zimmer – National Geographic

“But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.”

Science and Career

Ph.D.’s, come out of the closet! – Lina Nilsson – Science

“If you promise not to tell Fisher’s Ph.D. adviser (or mine), I’ll let you in on this well-hidden truth: Fisher isn’t planning to pursue an academic career.”

Bik’s Picks

Stress during pregnancy can be passed down through generations, rat study shows – Science Daily

“Scientists investigating pregnancies in four generations of rats show that inherited epigenetic effects of stress could affect pregnancies for generations.”

This Is Your Brain on Fish – James Hamblin – The Atlantic

“Thicker, stronger, and more resilient. Once a week is all it takes, new research says.”

10 Great Novels That Will Make You More Passionate About Science – Charlie Jane Anders – io9

“A lot of the best science fiction features scientists who solve problems and make breakthroughs.”

Scientist looking forward to weekend of binge-experimenting – The Allium

“Imperial college Scientist Dr. Lou Pole announced earlier today that he was going to spend the entirety of this weekend binge-experimenting.”

[hr]

 

Non-human microbiome, August 5, 2014

Posted on by

Microbiome papers on giraffes, sheeps, sponges and corals, soybean, soil, seawater, and fungi found in vacuum cleaner dust.

Mammal microbiome

The giraffe (Giraffa camelopardalis) rumen microbiome – Michael Roggenbuck, Cathrine Sauer, Morten Poulsen, Mads F. Bertelsen, Søren Johannes Sørensen – FEMS Microbiology Ecology

“Here we investigated the microbial community of 7 wild-caught giraffes (Giraffa camelopardalis), 3 of which were fed natural browse and 4 were fed Boskos pellets, leafy alfalfa hay and cut savanna browse, by characterizing the 16S rRNA gene diversity using 454 FLX high throughput sequencing. “

Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep – Sandra Kittelmann – PLOS ONE

“Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields”

Invertebrate microbiome

Host-specific microbial communities in three sympatric North Sea sponges – Mohd Azrul Naim, Jose A. Morillo, Søren J. Sørensen, Waleed Abu Al-Soud, Hauke Smidt and Detmer Sipkema – FEMS Microbiology Ecology

“In this study we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments.”

Host-specific microbial communities in three sympatric North Sea sponges– Mohd Azrul Naim – FEMS Microbiology Ecology

“In this study we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. “

Disturbance to conserved bacterial communities in the cold water gorgonian coral Eunicella verrucosa – Emma Ransome – FEMS Microbial Ecology

“The bacterial communities associated with healthy and diseased colonies of the cold water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. “

Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia – Dawoon Jung – FEMS Microbial Ecology

“The I-tip was developed as an in situ cultivation device that allows microorganisms to enter and natural chemical compounds to diffuse, thereby permitting the microorganisms to grow utilizing chemical compounds in their natural environment. “

Plant microbiome

Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar – Jingang Liang – PLOS ONE

“Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved.”

Soil microbiome

Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance – Leise Riber, Pernille Hasse Busk Poulsen, Waleed Abu Al-Soud, Lea Benedicte Skov Hansen, Lasse Bergmark, Asker Brejnrod, Anders Norman, Lars Hestbjerg Hansen, Jakob Magid andSøren Johannes Sørensen – FEMS Microbiology Immunology

“Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil-bacterial community structure was investigated using 16S-rRNA amplicon pyrosequencing.”

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing – Yongcui Deng – PLOS ONE

“Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. “

Seawater microbiome

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes – Alyse K. Hawley, Heather M. Brewer, Angela D. Norbeck, Ljiljana Paša-Tolić, and Steven J. Hallam – PNAS USA

“Here we use metagenomic and metaproteomic methods to chart in situ metabolic networks linking key microbial players driving carbon and nutrient cycling in a seasonally stratified fjord, Saanich Inlet”

Sequencing on the Seven Seas – Rina Shaikh-Lesko – The Scientist

“Researchers have installed an advanced genomics lab facility aboard a boat to create a floating molecular testing facility for marine life sciences”

Microbiome of the Built Environment

Characterization of Fungal Communities in House Dust Samples Collected From Central Portugal—A Preliminary Survey – Ana C.A. Sousa – Journal of Toxicology and Environmental Health

“A total of 28 samples were obtained from vacuum cleaner deposits from households located in central Portugal. DNA was extracted from dust samples and fungal communities were analyzed using a culture-independent polymerase chain reaction (PCR)– denaturing gradient gel electrophoresis (DGGE) approach. “

[hr]

Non-human microbiome, July 29

Posted on by

Microbiomes of chickens with Marek’s disease, fish, fungus-growing termites, ticks, leeches, mosses, soil and acid mine drainage.

Chicken microbiome

Marek’s Disease Virus Influences the Core Gut Microbiome of the Chicken During the Early and Late Phases of Viral Replication – Sudeep Perumbakkam – FEMS Microbiology Ecology

“In this study, dysbiosis induced by MDV on the core gut flora of chicken was assessed using next generation sequence (NGS) analysis. “

Fish microbiome

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata) – Konstantinos A. Kormas – Microbiology Open

“There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. “

Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism? – Sébastien Boutin – PLOS ONE

“we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. “

Arthropod microbiome

Identifying the core microbial community in the gut of fungus-growing termites – Saria Otani – Molecular Ecology

“The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus-growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. “

Characterization of the Bacterial Communities of Life Stages of Free Living Lone Star Ticks (Amblyomma americanum) – Amanda Jo Williams-Newkirk – PLOS ONE

“We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5–3.”

Leech microbiome

Hitchhiking of host biology by beneficial symbionts enhances transmission –
Brittany M. Ott – Nature Scientific Reports

“we show that the A. veronii population within secretions originates from the host digestive tract and proliferates synchronously with shedding frequency, demonstrating the coupling of partner biology.”

Plant microbiome

Forestry impacts on the hidden fungal biodiversity associated with bryophytes – Marie L. Davey – FEMS Microbiology Ecology

“Shoots of Hylocomium splendens were collected in Picea abies dominated forests of different ages, and their associated fungal communities were surveyed by pyrosequencing of ITS2 amplicons. “

Soil microbiology

Review: Functional soil microbiome: Belowground solutions to an aboveground problem
Venkatachalam Laksmanan – Plant Physiology

“This update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.”

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment – Jose A. Siles – PLOS ONE

“Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community.”

Water and drainage microbiome

Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and others drivers along an acid mine drainage – A. Volant – FEMS Microbiology Ecology

“biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and highthrouput sequencing.”

[hr]

Non-human microbiome

Posted on by

Microbiome of sheep, Drosophila on cherries, wild and sugar beets, sauerkraut, sake, and cheese. Sounds like a good meal.
Sheep microbiome

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community – Gabriel de la Fuente – PLOS ONE

“We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP).”

Insect microbiome

The bacterial communities of Drosophila suzukii collected from undamaged cherries
James Angus Chandler – PeerJ

“Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. “

Evaluating Insect-Microbiomes at the Plant-Insect Interface – Clare L. Casteel, Allison K. Hansen – Journal of Chemical Ecology

“In this review, we critically evaluate the requirements for insect-associated microbes to develop synergistic relationships with their hosts, and we mechanistically discuss how some of these insect-associated microbes can target or modify host plant defenses.”

Saccharide breakdown and fermentation by the honey bee gut microbiome
Authors – Fredrick J. Lee – Environmental microbiology

“In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome.”

Plant microbiome

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima – ancestor of all beet crops – and modern sugar beets – Christin Zachow – Frontiers in Microbiology

“Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions.”

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process – Daniela Bulgari – BMC Microbiology

“Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. “

Water microbiology

Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover – Christopher Staley – Frontiers in Microbiology

“In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches.”

Potential drivers of microbial community structure and function in Arctic snow – Lorrie Maccario – Frontiers in Microbiology

“We applied a metagenomic approach to nine snow samples taken over two months during the spring season. Fungi, Bacteroidetes and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season.”

Soil microbiology

Nutrient addition dramatically accelerates microbial community succession – Knelman JE – PLOS ONE

“We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization.”

Food microbiology

Sauerkraut: bacteria making food – S.E. Gould – Lab Rat – Scientific American

“As the bacteria required for sauerkraut fermentation are found on the cabbage leaves, it’s a very easy and healthy dish to produce. All you need is cabbage! “

Indigenous bacteria and fungi drive traditional kimoto sake fermentations
Nicholas A. Bokulich – Applied and Environmental Microbiology

“Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus subsp. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. “

Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis – V. Delcenserie – Journal of Dairy Science

“The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. “

[hr]

 

Non-human microbiome, July 9

Posted on by

Amphibians and fungi, microbes in the interface of plants and soil, and methane production by starving SAR11.

Amphibian microbiome

Screen Shot 2014-07-09 at 10.11.22 PMAmphibians acquire resistance to live and dead fungus overcoming fungal immunosuppression – Taegan A. McMahon – Nature

“Here we demonstrate that three species of amphibians can acquire behavioural or immunological resistance to B. dendrobatidis. “

Plant and soil microbiome

Screen Shot 2014-07-09 at 10.11.40 PMRoot exudates mediated interactions belowground – Feth el Zahar Haichar – Soil Biology and Biochemistry

“The root exudates may have a direct impact on carbon and nitrogen cycling, as they exhibit a rhizosphere priming effect towards soil organic matter degraders, and may inhibit nitrification process by soil nitrifying microorganisms. “

Water microbiology

Methane productions SAR11Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria – Paul Carini – Nature Communications

“Here we show that Pelagibacterales sp. strain HTCC7211, an isolate of the SAR11 clade of marine α-proteobacteria, produces methane from MPn, stoichiometric to phosphorus consumption, when starved for phosphate. “

[hr]