Tag Archives: reptiles

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

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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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