Tag Archives: invertebrates

Non-human microbiome, July 22

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Symbionts of tortoises, bees, diatoms, amoebae, and seaweed.

Reptile microbiome

Thesis: Population genetics and microbial communities of the gopher tortoise (Gopherus polyphemus) – Gaillard, Daniel Lyle – University of Sourthern Missisippi]

“Microbial communities did not show a correlation between community dissimilarity and geographic distance nor did they change in response to changes in plant communities at each site.”

Insect microbiome

Genomics and host specialization of honey bee and bumble bee gut symbionts – Waldan K. Kwong – PNAS

“We show that the simple microbiota of eusocial bees exhibits host specificity and that coresident species in the bee gut possess complementary capabilities for energy metabolism, implying their occupancy in distinct ecological niches.”

Diatom microbiome

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle – Takuro Nakayama – PNAS

“Here we present what is, to our knowledge, the first completely sequenced spheroid body genome from a rhopalodiacean diatom. Comparative analyses revealed that the endosymbiont is metabolically reduced, confirming its status as an obligate endosymbiont. “

Amoeba microbiome

Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae – Frederik Schulz – ISME Journal

“This symbiont, tentatively named ‘Candidatus Nucleicultrix amoebiphila’, is only moderately related to known bacteria (~90% 16S and 23S rRNA sequence similarity) and member of a novel clade of protist symbionts affiliated with the Rickettsiales and Rhodospirillales. “

Seaweed microbiota

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota
Marjolaine Martin – Applied and Environmental Microbiology

“A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci.”

Aquatic microbiology

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes – Alyse K. Hawley – PNAS

“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, a model ecosystem for studying microbial responses to changing levels of water column oxygen deficiency.”

EVENT: An Evening with the World’s Leading Marine Microbiologists – A Creative Collisions Initiative – Wednesday July 30, 2014 – Tech Museum San Jose, CA

“Mingle with the 16 Investigators of the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative”

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Non-human microbiome, July 21

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Microbiomes of water fleas, marine zooplankton, soil, rumen, and how a microbiome can help woodrats eat toxic plants.

Rumen microbiome

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

“A total of 1,666 OTU-specific probes were designed and synthesized on microarray slides (referred to as RumenBactArray) in a 6×5k format with each probe being represented in triplicate.”

Rodent microbiome

Gut microbes of mammalian herbivores facilitate intake of plant toxins – Kevin D. Kohl – Ecology Letters

“We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. “

Crustacean microbiome

Water fleas require microbiota for survival, growth and reproduction – Marilou P Sison-Mangus – ISME Journal

“We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts.”

Soil microbiome

Soil Properties and Spatial Processes Influence Bacterial Metacommunities within a Grassland Restoration Experiment – Cheryl A. Murphy – Restoration Ecology

“We found that soil bacterial communities were not influenced by plant restoration, but rather, by the local heterogeneity of soil environmental properties (16.9% of bacterial community variation) and pure spatial effects (11.1%).”

Environmental 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. “

Soil microbial community structure and activity along a montane elevational gradient on the Tibetan Plateau – Meng Xu – European Journal of Soil Biology

“We investigated the microbial community composition and functional patterns along an elevational gradient (3100–4600 m above sea level) on Mount Segrila using phospholipid fatty acids (PLFAs) and community level physiological profiles (CLPP). “

Oil pipeline microbiome

Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces – Tiffany R. Lenhart – The Journal of Bioadhesion and Biofilm Research

“Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed ‘cookies,’ revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. “

Plankton microbiome

Zooplankton diversity across three Red Sea reefs using pyrosequencing – John K. Pearman – Frontiers in Marine Science

“The diversity of metazoan plankton was investigated by targeting the 18S rRNA gene and clustering OTUs at 97% sequence similarity. A total of 754 and 854 metazoan OTUs were observed in the data set for the 1380F and 1389F primer sets respectively. “

Food microbiology

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity – Benjamin E. Wolfe – Cell

“Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. “

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Non-human microbiome, July 17

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Microbiomes of sparrows, stinkbugs, corals, grapevine, and archeological stones.

Bird microbiome

Screen Shot 2014-07-17 at 5.14.56 PMGut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis – Leticia Mirón – Metagenomics

“This study is the first description of the diversity of bacteria along the whole intestine of a wild bird (Passer domesticus). Pyrosequencing of the 16S rRNA gene unveiled a high bacterial diversity, distributed in 11 bacterial phyla. “

Insect microbiome

StinkybugsSymbiont polyphyly, co-evolution, and necessity in pentatomid stinkbugs from Costa Rica – Kalia S. I. Bistolas – Frontiers in Microbiology

“The gut microbiota of 13 micro-allopatric tropical pentatomid species, from a Costa Rican lowland rainforest, was characterized and compared with insect and host plant phylogenies.”

Coral microbiome

CoralsReview: A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum – Chuya Shinzato – Frontiers in Microbiology

“Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. “

Plant microbiome

Screen Shot 2014-07-17 at 5.15.23 PMPyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere – Sohail Yousaf – Frontiers in Microbiology

“We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). “

Built Environment microbiome

Screen Shot 2014-07-17 at 5.15.49 PM 1Biological nanosilver particles for the protection of archaeological stones against microbial colonization – Ashraf M M Essa – International Biodeterioration & Biodegradation

“The stones treated with silicon polymer loaded with AgNPs showed an elevated antimicrobial potentiality against A. niger and S. parvullus.”

Water microbiome

Screen Shot 2014-07-17 at 5.16.30 PM16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization – Marie Ragon – Frontiers in Microbiology

“To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. “

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Non-human microbiome, July 2014

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Kittens! And squid, sponges, acid mine drainage in someone’s backyard, soils, and sediments.

Cat microbiome

KittensDeep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens – Oliver Deusch – PLOS ONE

“The present study… applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.”

Squid microbiome

Squid albaGene-Swapping Mediates Host Specificity among Symbiotic Bacteria in a Beneficial Symbiosis – Alba A. Chavez-Dozal – PLOS ONE

“Our results demonstrate that multiple bacterial genetic elements can determine V. fischeri strain specificity between two closely related squid hosts, indicating how important genetic variation is for regulating conspecific beneficial interactions that are acquired from the environment.”

Sponge microbiome 

Review: Diversity and biotechnological potential of microorganisms associated with marine sponges – Fuerst JA – Applied Microbiol Biotechnol (Direct link not working)

“Here, we review recent progress in our understanding of this genetic diversity, its retrieval via culture and genomic approaches, and its implications for chemical diversity and other biotechnology applications of sponge microorganisms and their genes.”

Soils and sediments

StroudMetal(loid) bioaccessibility dictates microbial community composition in acid sulfate soil horizons and sulfidic drain sediments – Jackie Stroud – Environmental Science & Technology

“Microbial community compositions were determined for three soil horizons and drain sediments within an anthropogenically-disturbed coastal acid sulfate landscape using 16S rRNA gene tagged 454 pyrosequencing.”

Screen shot 2014-07-14 at 12.34PM, Jul 14Geochemical and microbiological response to oxidant introduction into reduced subsurface sediment from the Hanford 300 Area, WA – Elizabeth M Percak-Dennett and Eric E. Roden – Environmental Science & Technology

“Together these results indicate the potential for heterotrophic carbon metabolism in the reduced sediments, consistent with the proliferation of known heterotrophic taxa (e.g. Pseudomonadaceae, Burkholderiaceae, Clostridiaceae) inferred from 16S rRNA gene pyrosequencing.”

Brantner AMDResponse of Soil-Associated Microbial Communities to Intrusion of Coal Mine-Derived Acid Mine Drainage – Justin S. Brantner and John M. Senko – Environmental Science & Technology

“Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment.”

Screen shot 2014-07-14 at 12.36PM, Jul 14New carbohydrate-active enzymes identified by screening two metagenomic libraries derived from the soil of a winter wheat field – A. Stroobants – Journal of Applied Microbiology

“The aim of this work was to discover new β-glucosidases by constructing two metagenomic DNA libraries from soil samples collected in winter and spring from a field of winter wheat.”

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Non-human microbiome

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Microbiomes of frogs, kakapo birds, and very hot water springs. And a special on Ed DeLong.

Cow microbiome

RumenRumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains – Bareket Dassa – PLOS ONE

“Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen”

Reptile microbiome

Occurrence, Diversity, and Host Association of Intestinal Campylobacter, Arcobacter, and Helicobacter in Reptiles – Maarten J. Gilbert – PLOS ONE

“Based on PCR, Campylobacter, Arcobacter, and Helicobacter were detected in 69.3% of the reptiles; 82.5% of the chelonians, 63.8% of the lizards, and 58.0% of the snakes were positive for one or more of these genera.”

Amphibian microbiome

Frog taggingTagging Frogs with Passive Integrated Transponders Causes Disruption of the Cutaneous Bacterial Community and Proliferation of Opportunistic Fungi – Rachael E. Antwis – Applied and Environmental Microbiology

“We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase).”

Bird microbiome

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo – David W. Waite – Applied and Environmental Microbiology

“Amplicon pyrosequencing revealed a juvenile fecal microbiota enriched with particular lactic acid bacteria compared to the microbiota of adults, although the overall community structure did not differ significantly among kakapos of different ages. “

Multilocus Sequence Typing Confirms Wild Birds as the Source of a Campylobacter Outbreak Associated with the Consumption of Raw Peas – Patrick S. L. Kwan – Applied and Environmental Microbiology

“Novel STs clustered closely with isolates typically associated with wild birds and the environment but distinct from lineages commonly seen in human infections. “

 

Sponge microbiome

SpongeIn Situ Natural Product Discovery via an Artificial Marine Sponge – James J. La Clair – PLOS ONE

“Retrieving this artificial sponge from a tropical ecosystem after deployment for 320 hours afforded three actin–targeting jasplakinolide depsipeptides that had been discovered two decades earlier using traditional sponge specimen collection and isolation procedures.”

 

Water microbiology

Profile of Edward DeLong – Paul Gabrielsen – PNAS

“DeLong has learned that studying a reservoir of life as large and diverse as the ocean can lead to unexpected discoveries. “We’re continually being surprised,” he says.”

Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney – Mirjam Perner – Applied and Environmental Microbiology

“The SP metagenome reveals considerable differences in the taxonomic composition from those of other hydrothermal vent and subsurface samples; these could be better explained by temperature than by other available abiotic parameters. “

Methanotrophic bacteria in warm geothermal spring sediments identified using stable isotope probing – Christine E. Sharp – FEMS Microbiology Ecology

“Quantitative (q)PCR of pmoA genes identified the position of the heavy (13C-labelled) DNA fractions in density gradients, and 16S rRNA gene pyrotag sequencing of the heavy fractions was performed to identify the active methanotrophs.”

Bacterial and archaeal communities in long-term contaminated surface and subsurface soil evaluated through co-extracted RNA and DNA – Anu Mikkonen – FEMS Microbiology Ecology

“Soil RNA and DNA were co-extracted along a contamination gradient at a landfarming field with aged crude oil contamination to investigate pollution-dependent differences in 16S rRNA and rRNA gene pools”

rpoD Gene Pyrosequencing for the Assessment of Pseudomonas Diversity in a Water Sample from the Woluwe River – David Sánchez – Applied and Environmental Microbiology

“Culture-independent methods consisted of cloning and pyrosequencing of a Pseudomonas rpoD amplicon from total DNA extracted from the same sample and amplified with selective rpoD gene primers. “

Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems – Perrine Cruaud – Applied and Environmental Microbiology

“Thanks to statistical and diversity analyses as well as inference of operational taxonomic unit (OTU) networks, we show that (i) while DNA extraction methods do not seem to affect the results for some samples, they can lead to dramatic changes for others; and (ii) the choice of amplification and sequencing primers also considerably affects the microbial community detected in the samples.”

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Human and other microbiomes, July 2

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Fungi in the mouth, microbiome in celiac disease, viruses in bats, fecal microbiota of penguins, and bacteria in water and concrete.

Human oral microbiome

Screen Shot 2014-07-02 at 10.35.22 PMMolecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region – Shinsuke Ieda – PLOS ONE

“In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions.”

Human respiratory microbiome

Screen Shot 2014-07-02 at 10.35.47 PMLetter: No Clinical Association of Live Attenuated Influenza Virus with Nasal Carriage of Bacteria or Acute Otitis Media – Kathleen L. Coelingh, Robert B. Belshe – mBio

“We write this note to clarify the article “Live Attenuated Influenza Vaccine Enhances Colonization of Streptococcus pneumoniae and Staphylococcus aureus in Mice” by Mina et al. (1) in order that patients or clinicians not misinterpret the study’s clinical relevance.”

Human gut microbiome

Review: Screen Shot 2014-07-02 at 10.16.45 PMIntestinal Microbiota and Probiotics in Celiac Disease – Luís Fernando de Sousa Moraes – Clinical Microbiology Reviews

“This review aims to discuss the characteristics of the microbiota in CD subjects and the use of probiotics as a novel therapy for CD. “

Bat microbiome

Screen Shot 2014-07-02 at 10.36.24 PMBat Distribution Size or Shape as Determinant of Viral Richness in African Bats – Gaël D. Maganga – PLOS ONE

“We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. “

Bird microbiome

Screen Shot 2014-07-02 at 10.36.58 PMInfluence of Fasting during Moult on the Faecal Microbiota of Penguins – Meagan L. Dewar – PLOS ONE

“Therefore, the present study aimed to examine the microbial composition and diversity of the GI microbiota of fasting little (Eudyptula minor) and king penguins (Aptenodytes patagonicus) penguins during early and late moult.”

Invertebrate microbiome

Screen Shot 2014-07-02 at 10.37.27 PMBacterial Community Composition in the Gut Content and Ambient Sediment of Sea Cucumber Apostichopus japonicus Revealed by 16S rRNA Gene Pyrosequencing – Fei Gao – PLOS ONE

“The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. “

Plant microbiome

Screen Shot 2014-07-02 at 10.37.55 PMSelecting Microbial Strains from Pine Tree Resin: Biotechnological Applications from a Terpene World – Cristina Vilanova – PLOS ONE

“The taxonomic and functional diversity of the cultivated, resin-tolerant fraction of the whole microbiota were unveiled by high-throughput sequencing, which resulted in the detection of more than 40 bacterial genera among the terpene-degrading microorganisms, and a range of genes involved in the degradation of different terpene families.”

Water and concrete microbiology

Screen Shot 2014-07-02 at 10.38.23 PMCoupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species – Alexander J. Probst – PLOS ONE

“Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current.”

Screen Shot 2014-07-02 at 10.38.41 PMMicrobial Quality and Phylogenetic Diversity of Fresh Rainwater and Tropical Freshwater Reservoir – Rajni Kaushik – PLOS ONE

“The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. “

Screen Shot 2014-07-02 at 10.29.38 PMBacteria and concrete-a love-hate relationship – Embriette Hyde

“Sometimes bacteria appear to harm concrete, sometimes they appear to help it.”

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General microbiome digest, July 1

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Diet and gut microbiome (again), Campylobacter in chicken is not a commensal, microbiomes of fish, insects, corals, plant, and hospitals, and women in science.

Human gut microbiome

Screen shot 2014-07-01 at 06.07PM, Jul 01Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health – T Kelder – Nutrition & Diabetes

“We assessed fecal microbiota composition and host response patterns of metabolic and inflammatory markers in 10 apparently healthy men subjected to a high-fat high-caloric diet (HFHC, 1300 kcal/day extra) for 4 weeks. “

Pregnancy and birth

Screen shot 2014-07-01 at 06.08PM, Jul 01 1Gestational Age and Age at Sampling Influence Metabolic Profiles in Premature Infants
Reese H. Clark – Pediatrics

“Metabolic profiles (15 amino acids and 35 acylcarnitines) were obtained by using standard newborn techniques on infants born between 23 and 31 completed weeks of gestation.”

Screen shot 2014-07-01 at 06.08PM, Jul 01Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing – Jason M. Knight – Nature Scientific Reports

“we have developed a novel, noninvasive, molecular approach that utilizes next generation RNA sequencing on stool samples containing intact epithelial cells for the purpose of quantifying intestinal gene expression.”

Screen shot 2014-07-01 at 06.09PM, Jul 01Cesarean Section and Rate of Subsequent Stillbirth, Miscarriage, and Ectopic Pregnancy: A Danish Register-Based Cohort Study – Sinéad M. O’Neill – PLOS Medicine

“This study found that cesarean section is associated with a small increased rate of subsequent stillbirth and ectopic pregnancy.”

Bird microbiome

Screen shot 2014-07-01 at 06.10PM, Jul 01Campylobacter jejuni Is Not Merely a Commensal in Commercial Broiler Chickens and Affects Bird Welfare – Suzanne Humphrey – mBio

“Through experimental infection of four commercial breeds of broiler chickens, we show that breed has a significant effect on C. jejuni infection and the immune response of the animals, although these factors have limited impact on the number of bacteria in chicken ceca. “

Fish microbiome

Screen shot 2014-07-01 at 06.10PM, Jul 01 1Quorum quenching bacteria Bacillus sp. QSI-1 protect zebrafish (Danio rerio) from Aeromonas hydrophila infection – Weihua Chu – Nature Scientific Reports

“In this study, the effect of Bacillus sp. QSI-1 as an efficient quorum quencher on virulence factors production and biofilm formation of fish pathogen Aeromonas hydrophila was investigated. ”

Insect microbiome

Screen shot 2014-07-01 at 06.11PM, Jul 01Evolutionary origin of insect–Wolbachia nutritional mutualism – Naruo Nikoh – PNAS

“In the bedbug’s Wolbachia genome, we identified a gene cluster encoding the complete synthetic pathway for biotin (vitamin B7), which is not present in other Wolbachia genomes and is presumably acquired via lateral transfer from a coinfecting endosymbiont. “

Corals and sponges microbiome

Screen shot 2014-07-01 at 06.12PM, Jul 01Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors – Linda W. Kelly – PNAS

“The present study investigated the community structure and metabolic potential of microbes inhabiting coral reefs located across an extensive area in the central Pacific. “

Plant microbiome

Screen shot 2014-07-01 at 06.13PM, Jul 01The role of sulfur and phosphorus mobilizing bacteria in biochar induced growth promotion of Lolium perenne – A Fox – FEMS Microbiology Ecology

“16S rRNA gene based rhizobacteria community analysis revealed a significant biochar treatment effect. Abundance of nematodes feeding on bacteria was also significantly increased in the biochar treatments.”

Functional diversification within bacterial lineages promotes wide functional overlapping between taxonomic groups in a Mediterranean soil forest – J Curiel Yuste – FEMS Microbiology Ecology

“We investigated the relationship between taxonomy and functioning of soil bacterial communities in soils from a Mediterranean Holm-oak forest using a high throughput DNA pyrosequencing technique. “

Soil, sewage and sludge microbiome

Screen shot 2014-07-01 at 06.15PM, Jul 01Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage – Justin S Brantner and John M Senko – Environmental Science & Technology

” Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment. “

Transformation Products and Human Metabolites of Triclocarban and Triclosan in Sewage Sludge Across the United States – Benny F. G. Pycke – Environmental Science & Technology

“Here, we report on the levels of eight transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in raw and treated sewage sludge.”

Built Environment Microbiome

Screen shot 2014-07-01 at 06.14PM, Jul 01Rethinking Sterile: The Hospital Microbiome – Carrie Arnold – Environ Health Perspect

“Gilbert, an environmental microbiologist at Argonne National Laboratory, and his platoon of graduate students, postdocs, and research assistants descended on the hospital several times each day, even before it opened to the public. Armed with cotton swabs, they focused their efforts on the floors devoted to surgery and oncology. “

Bioinformatics

Screen shot 2014-07-01 at 06.15PM, Jul 01 1A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples – Samia N. Naccache – Genome Research

“Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. “

Metagenomics

Metagenomic scaffolds enable combinatorial lignin transformation
Cameron R. Strachan – PNAS

“In this study, we devised a previously unidentified biosensor responsive to lignin transformation products. We used this biosensor in a functional screen to recover metagenomic scaffolds sourced from coal bed bacterial communities. “

Arsenic metabolism

Sealing rice field boundaries in Bangladesh: a pilot study demonstrates reductions in water use, arsenic loading to field soils, and methane emissions from irrigation water – Rebecca B Neumann – Environmental Science & Technology

“Irrigation of rice fields in Bangladesh with arsenic-contaminated and methane-rich groundwater loads arsenic into field soils and releases methane into the atmosphere. We tested the water-savings potential of sealing field bunds (raised boundaries around field edges) as a way to mitigate these negative outcomes.”

Localised Flux-Maxima of Arsenic, Lead and Iron around Root Apices in Flooded Lowland Rice – Paul Nicholas Williams – Environmental Science & Technology

“Here we use new diffusive gradients in thin-film (DGT)/planar optode sandwich sensors deployed in situ on rice roots to demonstrate a new geochemical niche of greatly enhanced As, Pb and Fe(II) mobilization into solution immediately adjacent to the root tips characterized by O2 enrichment and low pH. “

Dengue

Screen shot 2014-07-01 at 06.16PM, Jul 01Baicalin, a metabolite of baicalein with antiviral activity against dengue virus – Ehsan Moghaddam – Nature Scientific Reports

“Here, we examined the anti-DENV properties of baicalin in vitro, and described the inhibitory potentials of baicalin at different steps of DENV-2 (NGC strain) replication.”

Antibiotic resistance

Review: The expression of antibiotic resistance genes in antibiotic-producing bacteria – Stefanie Mak – Molecular Microbiology

“Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. “

General microbiology

Screen shot 2014-07-01 at 06.20PM, Jul 01Bacterial sugar utilization gives rise to distinct single-cell behaviors – Taliman Afroz – Molecular Microbiology

“Here, we performed single-cell analyses to probe the behavior of representative pathways in the model bacterium Escherichia coli. “

Identification of essential Alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems – Patrick D. Curtis and Yves V. Brun – Molecular Microbiology

“These results show that while essential cell functions are conserved across varying genetic distance, much of a given organism’s essential gene pool is specific to that organism.”

Science and career

Screen shot 2014-07-01 at 06.22PM, Jul 01Elite male faculty in the life sciences employ fewer women – Jason M. Sheltzer and Joan C. Smith – PNAS

“To explore the current causes of women’s underrepresentation in biology, we collected publicly accessible data from university directories and faculty websites about the composition of biology laboratories at leading academic institutions in the United States. “

Screen shot 2014-07-01 at 06.01PM, Jul 01Americans Think We Have the World’s Best Colleges. We Don’t. – Kevin Carey – New York Times

“We see K-12 schools and colleges differently because we’re looking at two different yardsticks: the academic performance of the whole population of students in one case, the research performance of a small number of institutions in the other.”

Dr. Bik’s picks

Screen shot 2014-07-01 at 06.23PM, Jul 01Herbivore diet breadth mediates the cascading effects of carnivores in food webs – Michael S. Singer – PNAS

“Accounting for phylogenetic nonindependence of herbivores and plants, we show for the first time (to our knowledge) that dietary specialization of herbivore species is associated with reduced bird predation across an herbivore phylogeny, and that dietary specialization of herbivores increases the antipredator effects of camouflage and aposematism.”

Screen shot 2014-07-01 at 06.23PM, Jul 01 1Evolution of the ribosome at atomic resolution – Anton S. Petrov – PNAS

“Comparing eukaryotic and prokaryotic ribosomes allows us to identify 3D insertion fingerprints of the expansion segments. Similar fingerprints allow us to analyze the common core and detect ancestral expansion segments within it. “

Plastic mapPlastic debris in the open ocean – Andrés Cózar – PNAS

“In this work, we synthetize data collected across the world to provide a global map and a first-order approximation of the magnitude of the plastic pollution in surface waters of the open ocean.”

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Non-human microbiome, June 24

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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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Non-human microbiome, June 18

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Microbiomes of horses, sheep, chicken, plants in Chili, built environment and rocks.

General microbiomes of animals

Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection? – Sarah Temmam – Int J Mol Sci

“In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases.”

Horse microbiome

Screen Shot 2014-06-18 at 9.39.22 PMFaecal Microbiome of the Thoroughbred Racehorse and Its Response to Dietary Amylase Supplementation – Proudman C – Equine Veterinary Journal

“Amplicons for the V1-V3 region of the 16S rDNA gene were multiplexed and sequenced on the 454 resulting in ∼25,000 reads per sample. Differences in bacterial community structure were detected by linear discriminant analysis.”

Sheep microbiome

Screen Shot 2014-06-05 at 8.48.40 PMMethane yield phenotypes linked to differential gene expression in the sheep rumen microbiome – Weibing Shi – Genome Research

“Deep metagenomic and metatranscriptomic sequencing demonstrated the presence of methanogens both in the highest and lowest methane-producing sheep, with a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. “

Chicken microbiome

ChickenSpatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens – J. H. Choi – Poultry Science

“Bacterial communities in the different regions of gastrointestinal tract (GIT) of broiler chickens were analyzed by pyrosequencing approach to understand microbial composition and diversity. “

Squid microbiome

SquidThe real threat posed by discover of antibiotic- resistent bacteria found in squid – Robert Lawrence and Patrick Baron, Baltimore – Washington Post

“The Food and Drug Administration can, and should, do more to limit the misuse of antibiotics in the production of food animals, whether terrestrial or aquatic, in order to reduce the risk of accelerating antibiotic resistance.”

Plant microbiome

Bacterial community structure and detection of putative plant growth-promoting rhizobacteria associated with plants grown in Chilean agro-ecosystems and undisturbed ecosystems – Milko A. Jorquera – Biology and Fertility of Soils

“Soil microorganisms with phytase- and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activities are widely studied as plant growth-promoting rhizobacteria (PGPR). Here, we explored the bacterial community structure and occurrence of putative PGPR in plants grown in agro-ecosystems and undisturbed ecosystems from northern, central, and southern Chile.”

Built Environment Microbiome

housesmicroBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere – Holly M. Bik, David A. Coil, Jonathan A. Eisen – PLOS Biology

“The microbiology of the Built Environment network (microBEnet: http://www.microbe.net/) was formed as an experiment in interdisciplinary community building, with an overarching goal to facilitate and nurture the development of a new research field: the microbiology of the built environment (MBE). “

Water microbiome

Review: Emerging Strategies and Integrated Systems Microbiology Technologies for Biodiscovery of Marine Bioactive Compounds – Javier Rocha-Martin – Marine Drugs

“Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts.”

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists – María Gomariz – ISME Journal

“Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE.”

Soil and rock microbiome

Mineral Microniches Control the Diversity of Subsurface Microbial Populations – Aaron A. Jones – Geomicrobiology Journal

“These results suggest that adaptations to specific rocks are retained even when the organism is displaced in time and space from an ancestral rock habitat.”

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Non-human microbiome, June 17

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You waited for it: the Cannabis microbiome! But also microbiotas of salmon, a quail, coral, sponges, water, and ice.

Bird microbiome

Cultivable Bacterial Microbiota of Northern Bobwhite (Colinus virginianus): A New Reservoir of Antimicrobial Resistance? – Hongwen Su – PLOS ONE

“Firmicutes was the most commonly encountered phylum (57%) followed by Actinobacteria (24%), Proteobacteria (17%) and Bacteroidetes (0.02%). Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations.”

Fish microbiome

Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system – K.Z. Zarkasi – Journal of Applied Microbiology

“Salmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. “

Coral and sponge microbiome

Community Shifts in the Surface Microbiomes of the Coral Porites astreoides with Unusual Lesions – Julie L. Meyer – PLOS ONE

“The presence of lesions in P. astreoides coincided with a decrease in the relative abundance of Endozoicomonas, rather than the appearance of specific pathogenic taxa.”

Bacterial suspects identified in Caribbean coral deaths – NewScientist

“Three bacteria seem to be responsible for a disease that has killed most of the Caribbean’s reef-building corals.”

Effects of salinity on antibiotic production in sponge-derived Salinispora actinobacteria – Y.K. Ng – Journal of Applied Microbiology

“Fingerprint data were generated from extracts of S. arenicola broth cultures grown in media of varying salt (NaCl) concentrations.”

Plants microbiome

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome – Max E. Winston – PLOS ONE

“Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity.”

The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar – Michal Samuni-Blank – PLOS ONE

“ We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient.”

Microbial community structure during fluoranthene degradation in the presence of plants – S. Storey – Journal of Applied Microbiology

“Bacterial and fungal community composition in the rhizosphere was significantly different from that in nonrhizospheric and unplanted samples.”

Soil microbiome

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community – Yizhuang Zhou – Scientific Reports

“Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes.”

Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas – Belén Carbonetto – PLOS ONE

“The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas.”

 

Dust microbiome

Richness and Diversity in Dust Stormborne Biomes at the Southeast Mediterranean – Itzhak Katra – Scientific Reports

“In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared.”

Bioreactors

The maximum specific hydrogen-producing activity of anaerobic mixed cultures: definition and determination – Yang Mu – Scientific Reports

“ Our results demonstrate that this novel SHAm assay was a rapid, accurate and simple methodology for determining the hydrogen-producing activity of anaerobic mixed cultures.”

Methanogenic community changes, and emissions of methane and other gases, during storage of acidified and untreated pig slurry – S.O. Petersen – Journal of Applied Microbiology

“Pig slurry from two farms, acidified by different techniques or untreated, was stored for 83 days in a pilot-scale facility. Methanogens were characterized before and after storage by T-RFLP and qPCR targeting mcrA.”

Water and ice

The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics – Alexander I. Culley – mBio

“In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics.”

Variations of algal communities cause darkening of a Greenland glacier – Stefanie Lutz – FEMS Microbiology Ecology

“We have assessed the microbial ecology on the surface of Mittivakkat glacier in SE-Greenland during the exceptional high melting season in July 2012 when the so far most extreme melting rate for the Greenland Ice Sheet has been recorded.”

Pyrosequencing reveals correlations between extremely acidophilic bacterial communities with hydrogen sulphide concentrations, pH and inert polymer coatings at concrete sewer crown surfaces – E. Pagaling – Journal of Applied Microbiology

“Pyrosequencing and cloning showed that Mycobacterium and Acidithiobacillus dominated the acidophilic microbial communities. Methylacidiphilum was also dominant in samples where methane was detected.”

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration – I. Douterelo – Journal of Applied Microbiology

“Selected samples were analysed by cloning and sequencing of the 16S rRNA gene. Fingerprinting analysis revealed significant changes in the bacterial community structure over time (P < 0·05). “

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