Microbiome digest, September 22, 2014

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Temporal stability of the microbiomes of 85 adults, bacteria in breast milk, vaginal microbiome during pregnancy, water microbiomes, and Bik’s Picks.

Human microbiome general

Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – PeerJ PrePrints

“Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.”

Pregnancy and birth

It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant – Lars Bode – Advances in Nutrition

“This article is a summary of the symposium “It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant” held 29 April 2014 at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA.”

Microorganisms in the Female Genital Tract during Pregnancy: Tolerance versus Pathogenesis – Bruna de Andrade Ramos – American Journal of Reproductive Immunology

“We review the state of knowledge of microbe–host interactions in gestational tissues and highlight mechanisms that promote tolerance or pathogenesis.”

Determinants and pattern of care seeking for preterm newborns in a rural Bangladeshi cohort – Rashed Shah – BMC Health Services Research

“Only one-fifth (19.7%) of preterm newborns were taken to seek either preventive or curative health care.”

Human oral microbiome

Microbial signature profiles of periodontally healthy and diseased patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

“Subgingival biofilm was obtained from patients with periodontal health (27), gingivitis (11), chronic periodontitis (35) and aggressive periodontitis (24), and analysed for the presence of >250 species/phylotypes using HOMIM.”

Human gut microbiome

Review: Modulation of the Gut Microbiota by Nutrients with Prebiotic and Probiotic Properties – Céline Druart – Advances in Nutrition

“In this review, we describe how changes in the composition and/or activity of the gut microbiota by administration of nutrients with probiotic or prebiotic properties can modulate host gene expression and metabolism and thereby positively influence host adipose tissue development and related metabolic disorders.”

Mammal microbiome

Resistance to Antibiotics of Clinical Relevance in the Fecal Microbiota of Mexican Wildlife – Jurgi Cristóbal-Azkarate – PLOS ONE

“Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys, spider monkeys, tapirs and felids living freely in two regions of the Mexican state of Veracruz under different degrees of human influence.“

Bird microbiome

Do feather-degrading bacteria actually degrade feather colour? No significant effects of plumage microbiome modifications on feather colouration in wild great tits – Staffan Jacob – Naturwissenschaften

“Here, we tested whether (i) keratinolytic microorganisms can degrade feathers in vivo and thus modify the colour of feathers during the nesting period and (ii) whether feather microorganisms have a long-term effect on the investment in colouration of newly moulted feathers.”

Plant microbiome

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize – David Johnston-Monje – BMC Plant Biology

“The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping.“

Microbiota in Wheat Roots, Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems – Leszek Lenc – Journal of Phytopathology

“The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. “

Soil microbiome

Bacterial and Archaeal Communities in Bleached Mottles of Tropical Podzols –
K. J. Silva, P. Vidal-Torrado, M. R. Lambais – Microbial Ecology

“In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling.”

Water microbiome

Microplastic is an abundant and distinct microbial habitat in an urban river – Amanda McCormick – Environmental Science & Technology

“Results from high-throughput sequencing showed that bacterial assemblages colonizing microplastic within the river were less diverse and were significantly different in taxonomic composition compared to those from the water column and suspended organic matter.”

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity – Masanori Fujimoto – PLOS ONE

“The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry.”

Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes – Avinash Sharma – Annals of Microbiology

“Bacterial diversity of the Soldhar hot spring, located in the Chamoli district of Uttarakhand, India, was investigated using a clone library, denaturing gradient gel electrophoresis (DGGE) and functional genes.”

Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbial Ecology

“Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. “

A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing – Thangavelu Boopathi – Polar Biology

“In this study, freshwater microeukaryotes in an Arctic reservoir at Ny-Ǻlesund (Svalbard, Norway) were studied using the hypervariable V1–V3 small subunit rRNA and 454 pyrosequencing.”

Built Environment

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities? – Gary M. King – Journal of Microbiology

“I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems”

Phages and viruses

Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution – Elyse Stachler and Kyle Bibby – Environmental Science & Technology

“Here, 86 publically available metagenomes were surveyed to determine the presence and abundance of crAssphage in various environments, and to identify its utility for source tracking of human fecal pollution.”

Microbes in the news

Understanding the Microbiome and Its Impact on Human Health – Kristine Nally – HCPLive

“Instant polling at an educational session of the 2014 American Academy of Pain Management annual clinical meeting in Phoenix, AZ, revealed that only 40 percent of the approximately 350-person audience was “familiar” with the concept of a microbiome.”

Mining the microbiome for medicines – Set a thief… – The Economist

“Antibiotics are not the only things Dr Donia’s technique might turn up, for the bugs in the human microbiome spit out all sorts of other chemicals that could potentially be put to use as drugs.”

Techniques

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr and Elhanan Borenstein – MicroBEnet

“We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample.”

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science Insider

“The power of anonymous comments—and the liability of those who make them—is at the heart of a possible legal battle embroiling PubPeer, an online forum launched in October 2012 for anonymous, postpublication peer review.”

Time to Raise the Profile of Women and Minorities in Science – Brian Welle and Megan Smith – Scientific American

“Along these lines, over the past few years, we discovered some pretty ugly news about our beloved Google Doodles. “

Bik’s Picks

Immune system of newborn babies stronger than previously thought – Science Daily

“Contrary to what was previously thought, newborn immune T cells may have the ability to trigger an inflammatory response to bacteria, according to a new study.”

The Preservation Of Lonesome George – Sarah Fecht – PopSci.com

“Decades after the last giant tortoise was thought to have disappeared from the island of Pinta in the Galapagos, Lonesome George turned up in 1971 and became a conservation icon.”

 Great white sharks partly to blame for otter recovery stall – Peter Fimrite – SF Gate

“Most scientists agree that the number of animals, which are also known as southern sea otters, should be increasing, but hungry predators and a lack of food may be limiting their growth.”

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Animal microbiome digest, September 16, 2014

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 digest, September 15, 2014

Microbiomes of seals, sheep, pigs, raw milk, cheese, rubber, ocean, freshwater, acid mine drainage, deepsea basalt, and insects.

Mammal microbiome

Isolated faecal bacterial communities found for Weddell seals, Leptonychotes weddellii, at White Island, McMurdo Sound, Antarctica – Jonathan C. Banks – Polar Biology

“Here, we used 16S sequences obtained from clone libraries to characterise the faecal microbiota of Weddell seals breeding in McMurdo Sound and at White Island, Antarctica.”

Study of methanogen communities associated with different rumen protozoal populations – Alejandro Belanche – FEMS Microbiology Ecology

“Rumen protozoa were harvested from totally-faunated sheep and six protozoal fractions (plus free-living microbes) were generated by sequential filtration. “

Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine – Devin B. Holman and Martin R. Chénier – FEMS Microbiology Ecology

“In this study, the effect of two antibiotics on the swine gut microbiota over a 19-week monitoring period was investigated using Illumina-based sequencing.”

Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities – M. Kim – Journal of Applied Microbiology

“The utility of the RumenBactArray was tested using fractionated rumen samples obtained from sheep fed two different diets.”

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

“Fecal microbiota profiles were generated based on amplification and sequencing of the cpn60 universal target sequence from 89 samples from 18 pigs collected at −8, −5, −3 and 0 days post-inoculation, and at termination.”

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics – Hsiao-Pei Lu – Scientific Reports

“We analyzed bacterial communities of six distinct gut sites (the food bolus and mucus layer of the proximal small intestine, cecum and distal large intestine), using wild folivorous flying squirrels.”

Insect microbiome

Dynamics of midgut microflora and dengue virus impact on life history traits in Aedes aegypti – Casey L. Hill – Acta Tropica

“Here we investigated the effects of the midgut microbial environment and dengue infection on several fitness characteristics among three strains of the primary dengue virus vector mosquito Aedes aegypti. “

Anterior Foregut Microbiota of the Glassy-Winged Sharpshooter Explored Using Deep 16S rRNA Gene Sequencing from Individual Insects – Elizabeth E. Rogers – PLOS ONE

Here, a survey of microbiota associated with the GWSS anterior foregut was conducted.”

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand – Nicola M. Reid – FEMS Microbiology Ecology

“We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of 16S rRNA from five S. ruficeps colonies.”

Sponge and coral microbiome

Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum – Michel R. Z. Passarini – Journal of Basic Microbiology

“The present work aimed to investigate the diversity of bacteria and filamentous fungi of southern Atlantic Ocean marine sponge Dragmacidon reticulatum using cultivation-independent approaches.”

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.”

Plant microbiome

Micro-organisms in latex and natural rubber coagula of Hevea brasiliensis and their impact on rubber composition, structure and properties – M. Salomez – Journal of Applied Microbiology

“This review synthesizes the current knowledge on microbial populations in latex and natural rubber coagula of H. brasiliensis and the changes they induce on the biochemistry and technical properties of natural rubber during maturation.”

Soils, sediments, and rocks microbiomes

A role for biotic filtering in driving phylogenetic clustering in soil bacterial communities – Marta Goberna – Global Ecology and Biogeography

“Here, we used phylogeny-based methods to discern whether the coexistence of evolutionarily related soil bacteria results from abiotic and/or biotic filtering.”

Microbial community composition and in-silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbiology Ecology

“..we investigated biogeochemical parameters and microbial community composition in a bog, a fen and two SSF using high throughput barcoded sequencing of the small ribosomal subunit (SSU) variable region V4.”

Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts – S. Bengtson – Geobiology

“We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). “

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

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

Water microbiome

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

“Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location”

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model – Ferdi L. Hellweger – Science

“We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million–base-pair genomes in a global surface ocean circulation model. “

Microbial gardening in the ocean’s twilight zone: Detritivorous metazoans benefit from fragmenting, rather than ingesting, sinking detritus – Daniel J. Mayor – BioEssays

“Here we speculate that this apparently counterintuitive behaviour is an example of ‘microbial gardening’, a strategy that exploits the enzymatic and biosynthetic capabilities of microorganisms to facilitate the ‘gardener’s’ access to a suite of otherwise unavailable compounds that are essential for metazoan life.”

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

“… biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. “

Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing – Anna Klindworth – Marine Genomics

“In this study we re-analyzed samples from the initial study by total community RNA (metatranscriptomics) and 16S rRNA gene amplicon sequencing.”

Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity – Angeliki Marietou and Douglas H. Bartlett – Applied and Environmental Microbiology

“Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. “

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole – Noémie Pascault – 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.”

Food Microbiology

Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese – Ilaria De Pasquale – Applied and Environmental Microbiology

“Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese.”

Tracing the origin of raw milk from farm by using Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting of microbiota – Maria Feligini – Food Control

“A total of 64 markers within the range 279–756 bp were detected on the thirty-eight bulk milk samples, none of which was common to all the patterns. “

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Microbiome digest, August 28, 2014

Cool new study today by Jack Gilbert on the bacteria living in our homes, what happens to you microbiome after you die, (gut) microbiome and respiratory diseases, lots of water studies, and Bik’s Picks.

General  human microbiome 

* Your death microbiome could catch your killer – Anna Williams – NewScientist

“These “friendly” bacteria adhere to the lining of the gut and keep the microbial villains at bay by outcompeting them. After we die, however, our gut flora have a party.“

Human respiratory microbiome

The Microbiome and the Lung – Lijia Cui – Annals of the American Thoracic Society

“In this review, we provide an overview of the basics of microbiome studies.”

Microbiome Diversity and Asthma and Allergy Risk – Antje Legatzki – Current Allergy and Asthma Reports

“In this review, we will discuss the available literature concerning the human microbiota and asthma and allergy development and occurrence. “

Gut microbiome

You waited for it: The journal Helicobacter has a Helicobacter special!
Gastric and Enterohepatic Helicobacters other than Helicobacter pylori
Armelle Ménard – Helicobacter

“Several studies highlighted the virulence of non-H. pylori species including H. cinaedi in humans and hyperlipidemic mice or H. macacae in geriatric rhesus monkeys with intestinal adenocarcinoma. “

Pregnancy and birth

Systemic Inflammation in the Extremely Low Gestational Age Newborn Following Maternal Genitourinary Infections – Raina N. Fichorova – American Journal of Reproductive Immunology

“Mothers of 914 infants born before 28th gestation week reported cervical/vaginal infection (CVI), and/or urine/bladder/kidney infection (UTI), or neither. Inflammation proteins measured in baby’s blood”

Animal models of microbiome research

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats – Ren, Zhigang – Transplantation

“cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR.”

Microbiology of the built environment

* Longitudinal analysis of microbial interaction between humans and the indoor environment – Simon Lax – Science

“Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. “

* Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015 – Jonathan Eisen – MicroBEnet

“to learn hands-on how to use these tools on their own data, to perform meta-analyses that combine built environment datasets“

Water microbiome

Microbial weeds in hypersaline habitats: the enigma of the weed-like Haloferax mediterranei – Aharon Oren and John E. Hallsworth – FEMS Microbiology Letters

“Here, we discuss the enigma of the less abundant Haloferax mediterranei, an archaeon that grows faster than any other, comparable extreme halophile.”

Bacterial profiling in brine samples of the Emalahleni Water Reclamation Plant, South Africa, using 454-pyrosequencing method – Sudharshan Sekar – FEMS Microbiology Letters

“A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. “

The role of dispersal mode and habitat specialisation in metacommunity structuring of aquatic macroinvertebrates in isolated spring fens – Vanda Rádková – Freshwater Biology

“We applied two species categorisations, common/rare and generalists/specialists, to disentangle the roles of dispersal capacity and habitat specialisation.”

Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary – Jiwen Liu – FEMS Microbiology Ecology

“Using 454 pyrosequencing, the present study examined the archaeal communities along a subtropical estuary, Pearl Estuary, China. “

Soil microbiome

The Effects of Radiation Pollution on the Population Diversities and Metabolic Characteristics of Soil Microorganisms – Meiying Gu – Water, Air, & Soil Pollution

“Microbial diversities were determined by using methods of cultured isolates and carbon source utilization on Biolog EcoPlate™. “

Bik’s Picks

A chocolate habit in ancient North America – Michael Bawaya – Science

“the findings suggest regular trade in cacao—and movements of the people who imbued it with significance—between ancient Mesoamericans and their northern neighbors, says Dorothy Washburn, an archaeologist at the University of Pennsylvania Museum of Archaeology and Anthropology “

Babies may be good at remembering, and forgetting – Laura Sanders – Science News

“over 20 percent of 5-year-olds and 8- to 9-year olds recounted events from their first year, some from the very first months of life.”

How the zebrafish gets its stripes: Uncovering how beautiful color patterns can develop in animals – Science Daily

Three major pigment cell types, black cells, reflective silvery cells, and yellow cells emerge during growth in the skin of the tiny juvenile fish and arrange as a multi-layered mosaic to compose the characteristic color pattern. “

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Non-human microbiome, August 26, 2014

Microbiomes of rabbits, exercising mice, fish, bees, beetles, forest soil after a hurricane (a simulated one!), water, and – why not – the whole world.

Mammal microbiome 

* Changes in Cecal Microbiota and Mucosal Gene Expression Revealed New Aspects of Epizootic Rabbit Enteropathy – Christine Bäuerl – PLOS ONE

“Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics), followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR.”

Effect of Intestinal Microbiota on Exercise Performance in Mice – Hsu, Yi-Ju – Journal of Strength & Conditioning Research

“We investigated the association of intestinal bacteria and exercise performance in specific pathogen-free (SPF), germ-free (GF), and Bacteroides fragilis (BF) gnotobiotic mice.”

Fish microbiome

Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches – Taiga Asakura – PeerJPrePrints

“We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments.”

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing – Tongtong Li – Microbial Ecology

“In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. “

Insect microbiome

* Microbial Communities of Three Sympatric Australian Stingless Bee Species – Sara D. Leonhardt – PLOS ONE

“Here, we characterized the microbiota of three Australian stingless bee species (Apidae: Meliponini) of two phylogenetically distant genera (Tetragonula and Austroplebeia). “

Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis – Matteo Montagna – Insect Science

“The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs).”

Invertebrate microbiome

Antioxidant Activity of Bacteria Associated with the Marine Sponge Tedania anhelans – Dhivya Balakrishnan – Indian Journal of Microbiology

In the present study, several Bacillus sp. with just 97 % similarity with its closest match in Gen Bank were isolated, and found to show free radical scavenging activity”

Soil and sediment microbiome

Effects of a simulated hurricane disturbance on forest floor microbial communities – Sharon A. Cantrell – Forest Ecology and Management

“We studied the independent and interactive hurricane effects of canopy openness and debris deposition on the relative abundance and diversity of microorganisms in soil and leaf litter using ester link fatty acids methyl esters (EL-FAME) analysis, and terminal restriction fragment length polymorphism (TRFLP) profile.”

Spatiotemporal changes in arbuscular mycorrhizal fungal communities under different nitrogen inputs over a 5-year period in intensive agricultural ecosystems on the North China Plain – Wei Liu – FEMS Microbiology Ecology

“Terminal restriction fragment length polymorphism and clone sequencing were used to analyse the AMF community. “

A Long-Term Cultivation of an Anaerobic Methane-Oxidizing Microbial Community from Deep-Sea Methane-Seep Sediment Using a Continuous-Flow Bioreactor – Masataka Aoki – PLOS ONE

“Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor.”

Water microbiome

Characterization of Wastewater Treatment Plant Microbial Communities and the Effects of Carbon Sources on Diversity in Laboratory Models – Sangwon Lee – PLOS ONE

“…using PhyloChip 16S-rRNA-gene targeting microarrays, we compared the compositions of sampled communities to those of inocula propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources”

* Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa) – Rosine E. Tiodjio – Nature Scientific Reports

“Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. “

Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods – Ping Li – Ecotoxicology

“A survey of bacterial and archaeal community structure was carried out in 10 shallow tube wells in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by 16S rRNA gene based two-step nested PCR-DGGE, clone libraries and 454 pyrosequencing. “

* Biogeographic Congruency among Bacterial Communities from Terrestrial Sulfidic Springs – Brendan Headd – Frontiers in Microbiology

“Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. “

The whole world microbiome

* The Earth Microbiome project: successes and aspirations – Jack A Gilbert, Janet K Jansson, and Rob Knight – BMC Biology

“ ‘Knight and Gilbert literally talk about sampling the entire planet. It is ludicrous and not feasible – yet they are doing it’”

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Microbiome digest, August 17, 2014

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.”

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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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Non-human microbiome, July 9

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. “

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Non-human microbiome, June 25

Mongolian Gerbils, soil microbiome affects plant flowering time, soybeans, and seawater viruses.

Mammalian microbiome

Screen shot 2014-06-25 at 01.26PM, Jun 25Helicobacter pylori Induced Gastric Immunopathology Is Associated with Distinct Microbiota Changes in the Large Intestines of Long-Term Infected Mongolian Gerbils – Markus M. Heimesaat – PLOS ONE

“Comprehensive cultural analyses revealed that severe gastric diseases such as atrophic pangastritis and precancerous transformations were accompanied by elevated luminal loads of E. coli and enterococci in the caecum and together with Bacteroides/Prevotella spp. in the colon of H. pylori WT, but not MUT infected gerbils as compared to naïve animals. “

Plant microbiome

Screen shot 2014-06-25 at 01.27PM, Jun 25Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field – Akifumi Sugiyama – PLOS ONE

“Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. “

Screen shot 2014-06-25 at 06.41PM, Jun 25Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative – Maggie R. Wagner – Ecology Letters

Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. “

Water microbiology

Screen shot 2014-06-25 at 01.27PM, Jun 25 1Anthropogenic Litter in Urban Freshwater Ecosystems: Distribution and Microbial Interactions – Timothy Hoellein – PLOS ONE

“To assess microbial interactions with AL, we incubated AL and natural substrates in 3 freshwater ecosystems, quantified biofilm metabolism as gross primary production (GPP) and community respiration (CR), and characterized biofilm bacterial community composition via high-throughput sequencing of 16S rRNA genes.”

Screen shot 2014-06-25 at 01.28PM, Jun 25Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea – Christian Winter – PLOS ONE

“The identifiable richness and relative abundance in both viromes were dominated by archaeal and bacterial viruses accounting for 92.3% of the relative abundance in the Atlantic Ocean and for 83.6% in the Mediterranean Sea. “

Screen shot 2014-06-25 at 01.28PM, Jun 25 1The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing – Patrick J. Keeling – PLOS Biology

“The MMETSP relies primarily on cultured organisms, and this introduces a different set of biases, most obviously, favoring organisms that are photosynthetic. “

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Non-human microbiome, June 24

Lots of marine microbiotas for you today, from corals, sponges, bivalves, to seawater and sediments.

Coral, sponges and other invertebrate microbiome

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata – Collin J Closek – ISME Journal

“We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. “

Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR – Kristina Bayer – FEMS Microbiology Ecology

“Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. “

Comparative modifications in bacterial gill-endosymbiotic populations of the two bivalves Codakia orbiculata and Lucina pensylvanica during bacterial loss and reacquisition – Nathalie H. Elisabeth – FEMS Microbiology Ecology

“We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. I”

Plant microbiology

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest – Rebecca C Mueller – ISME Journal

“We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation.”

Soil microbiology

High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation – Dawei Ren – ISME Journal

“Our results show a high prevalence of synergy in biofilm formation in multispecies consortia isolated from a natural bacterial habitat and suggest that interspecific cooperation occurs.”

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments – Tim Engelhardt – ISME Journal

“Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (~14 Ma old) and the most oligotrophic subsurface sediments of the world’s oceans (South Pacific Gyre (SPG)).”

Water and sediment microbiology

Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers, denitrifiers, and anammox bacteria in sediments of estuarine tidal flats – Anjing Yang – Annals of Microbiology

“The alpha diversities (Shannon and Simpson indices) and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA), denitrifier and anammox bacteria (AMB) were revealed using denaturing gradient gel electrophoresis and clone library analysis of amoA, nosZ and 16S rRNA gene markers. “

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill – Olivia U Mason – ISME Journal

“The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. “

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin – Maria-Cristina Ciobanu – ISME Journal

“Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. “

The niche of an invasive marine microbe in a subtropical freshwater impoundment – K David Hambright – ISME Journal

“Using a long-term field study of the ‘invasive’ marine haptophyte Prymnesium parvum, we characterize the environmental niche of P. parvum in a subtropical impoundment in the southern United States.”

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin – Maria G Pachiadaki – ISME Journal

“This first metatranscriptome analysis of DHAB samples provides significant insights into shifts in metabolic activities of microorganisms as physicochemical conditions change from deep Mediterranean sea water to brine.”

Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany
Sebastian Opitz – FEMS Microbiology Ecology

“We followed the abundance and compared the diversity of ammonia oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months”

Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient – Joe D Taylor – FEMS Microbiology Ecology

“Biofilms were sampled from three sites exposed to seawater with different pH/CO2 levels and diversity determined using high-throughput sequencing of 16S rRNA genes. “

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype
J Cameron Thrash – ISME Journal

“Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets.”

A microarray for assessing transcription from pelagic marine microbial taxa
Irina N Shilova – ISME Journal

“Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. “

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