Tag Archives: sponge

Non-human microbiome digest, September 29, 2014

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Microbiome of house mice, rumen, fish species in the same pond, sponges and corals, coastal sediments, and mycobacteria and amoeba in drinking water.

Mammal microbiome

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)”

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 microorganisms) were generated by sequential filtration. “

Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing – K. M. Singh – Molecular Biology Reports

“The rumen bacterial composition of both liquid and solid fraction was surveyed using pyrosequencing of the 16S rRNA gene.”

Bacterial Community Composition and Fermentation Patterns in the Rumen of Sika Deer (Cervus nippon) Fed Three Different Diets – Zhipeng Li – Microbial Ecology

“The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design.”

Fish microbiome

* Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? – X.M. Li – Journal of Applied Microbiology

“After 30 days of rearing, the intestinal microbiota of the two fish species was assessed by pyrosequencing of 16S rRNA genes.”

Tending a complex microbiota requires major immune complexity – Keaton Stagaman – Molecular Ecology

“In this issue of Molecular Ecology, Bolnick et al. (2014a) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake”

Insect microbiome

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 the 16S nucleotide sequence from five S. ruficeps colonies.”

Genetic groups and endosymbiotic microbiota of the Bemisia tabaci species complex in Japanese agricultural sites – A. Fujiwara – Journal of Applied Entomology

“Use of the cleaved amplified polymorphic sequence technique and mitochondrial cytochrome oxidase subunit I gene sequencing detected five genetic groups”

Sponge and Coral microbiome

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges – Cole G. Easson and Robert W. Thacker – Frontiers in Microbiology

“As part of the Earth Microbiome Project, we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range.”

* Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

“Using an amplicon pyrosequencing approach, the diversity of both nitrogen-fixing bacteria and of bacterial communities overall was assessed through analysis of nifH and 16S rRNA genes, respectively. “

Biogeography rather than association with cyanobacteria structures symbiotic microbial communities in the marine sponge Petrosia ficiformis  – Ilia Burgsdorf – Forntiers in Microbiology

“16S rRNA gene tag pyrosequencing data of the microbial communities revealed that Chloroflexi, Gammaproteobacteria and Acidobacteria dominated the bacterial communities of all sponges analyzed. “

Soil and sediments microbiome

Interactive effects of C, N and P fertilization on soil microbial community structure and function in an Amazonian rain forest – Nicolas Fanin – Functional Ecology

“Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. “

* The long-term adaptation of bacterial communities in metal-contaminated sediments. A metaproteogenomic study – David C. Gillan – Environmental Microbiology

“Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels .. were compared by shotgun metaproteogenomics.”

Effect of plankton-derived organic matter on the microbial community of coastal marine sediments – Paula Carpintero de Moraes – Journal of Experimental Marine Biology and Ecology

“Analyses of molecular fingerprints of bacterial communities by denaturing gel gradient electrophoresis (DGGE) showed differences in bacterial community composition between both treatments and control just after algae addition. “

Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms – Jesse P Harrison – BMC Microbiology

“Sequencing of cloned 16S rRNA genes demonstrated that these communities were dominated after 14 days by the genera Arcobacter and Colwellia “

Water microbiome

Picky, hungry eaters in the cold: persistent substrate selectivity among polar pelagic microbial communities – Andrew D. Steen and Carol Arnosti – Frontiers in Microbiology

“The purpose of this study was to investigate potential factors preventing hydrolysis of pullulan in Svalbard fjord waters. “

Saltwater intrusion history shapes the response of bacterial communities upon rehydration – Tiffanie M. Nelson – Science of The Total Environment

“Bacterial community composition before and after treatment were measured using next generation sequencing of bacterial DNA. “

Diversity of marine microbes in a changing Mediterranean Sea – Gian Marco Luna – Rendiconti Lincei

“This review aims at summarizing the knowledge on microbial diversity in the basin, by focusing on prokaryotes (bacteria and archaea) in pelagic and benthic habitats. “

* First evidence of amoebae – mycobacteria association in drinking water network – Vincent Delafont – Environmental Science & Technology

“Direct Sanger sequencing as well as pyrosequencing of environmental isolates demonstrated the frequent association of mycobacteria and FLA”

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Non-human microbiome digest, September 15, 2014

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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 29, 2014

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@MicrobiomDigest will be enjoying vacation for the next two weeks, so I won’t be able to post as much as usual. I might occasionally have some time and internet access at the same time, and post something, but don’t rely on this blog during that time for your daily Microbiome fix. But I will be back! Enjoy this last (short) one for now:
Human oral microbiome

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators – Vaia Galimanas – Microbiome

Human gut microbiome

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease – Noah W Palm – Cell

Modulation of immune development and function by intestinal microbiota – Agnieszka M. Kabat – Trends in Immunology

 

Worms, bacteria, and micronutrients: an elegant model of our diet – Lutfu Safak Yilmaz, Albertha J.M. Walhout – Trends in Genetics

 

Mammal microbiome

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics (in flying squirrels) – Hsiao-Pei Lu – Scientific Reports

Social influences on the gut microbiome of developing monkeys – W.Z. Amaral – Brain, Behavior, and Immunity

 

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? – AE Naas – mBio

 

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

 

Sponges and corals

The versatile nature of coral-associated viruses – Bettarel Yvan – Environmental Microbiology

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

Rocks and Water Microbiome

Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering – F. Seiffert – Procedia Earth and Planetary Science

Microbial diversity and biogeochemical cycling in soda lakes – Dimitry Y. Sorokin – Extremophiles

Food microbiome

Switzerland Puts Secret Bacteria In Cheese To Catch Knockoffs – Sarah Zhang – Gizmodo

Bioinformatics

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data – Yuan Zhang – PLOS Computational Biology

Metabolomics

Taking your breath away: metabolomics breathes life in to personalized medicine
Nicholas J.W. Rattray – Trends in Biotechnology

Phages and Viruses

Identifying and analyzing bacteriophages in human fecal samples: what could we discover? – Maite Muniesa1 & Juan Jofre – Future Medicine

Microbes in the news

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours — Rachel Feltman – Washington Post

A touching story: The ancient conversation between plants, fungi and bacteria – David Tenenbaum – News UW Madison

Bik’s Picks

The universal ‘anger face’: Each element makes you look physically stronger and more formidable – Science Daily

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

Report: Ice Bucket Challenge Causing Ecological Mayhem in California – The Allium (Satire)

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Non-human microbiome, August 26, 2014

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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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Non-human microbiome, August 11, 2014

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Microbiomes of Eurasian Magpie, mosquitoes, ticks, 218 insect species, sponges, plants, and olives.

Bird microbiome

Effect of Incubation on Bacterial Communities of Eggshells in a Temperate Bird, the Eurasian Magpie (Pica pica) – Won Young Lee – PLOS ONE

“In this study, we employed culture-independent methods, quantitative PCR and 16S rRNA gene pyrosequencing, to elucidate the effect of incubation on the bacterial abundance and bacterial community composition on the eggshells of the Eurasian Magpie (Pica pica).”

Arthropod microbiome

Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes
Grant L. Hughes – PNAS USA

“We show the native microbiota of Anopheles impede vertical transmission of Wolbachia. Antibiotic microbiome perturbation enables Wolbachia transmission in two Anopheles species.”

Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens – Yongjin Qiu – PLOS ONE

“Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. “

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host – Ji-Hyun Yun – Applied and Environmental Microbiology

In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes.

Sponge microbiome

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge – Ren-Mao Tian – Environmental Microbiology

“Here, we present and analyze the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy”

Plant microbiome

Foliage Friendships (behind paywall) – Peter Andrey Smith – Scientific American

“Microbial communities on a plant’s roots, stems and leaves may improve crop growth”

Effects of Fusarium oxysporum on rhizosphere microbial communities of two cucumber genotypes with contrasting Fusarium wilt resistance under hydroponic condition – Ju Ding – European Journal of Plant Pathology

“PCR-DGGE analysis of 16S rDNA fragments indicated that following FO inoculation, significant changes in the bacterial structure isolated from the root surfaces of susceptible plants were observed, such as an increased diversity index, a decreased evenness index, and the occurrence of several types of bacteria that decomposed organic substances.”

Food microbiology

Open-refrigerated retail display case temperature profile and its impact on product quality and microbiota of stored baby spinach – Liping Kou – Food Control

“All bags were immediately loaded in the display cases and the overall visual quality, tissue electrolyte leakage, total aerobic mesophilic bacteria and psychrotrophic bacteria were evaluated for each bag. “

Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production – Xi Zhang – Bioresouce Technology

“The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. “

Genetic diversity and dynamics of bacterial and yeast strains associated to Spanish-style green table-olive fermentations in large manufacturing companies – Helena Lucena-Padrós – International Journal of Food Microbiology

“We have genotyped a total of 1045 microbial isolates obtained along the fermentation time of Spanish-style green table olives from the fermentation yards (patios) of two large manufacturing companies in the province of Sevilla, south of Spain.”

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Non-human microbiome, August 5, 2014

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

Mammal microbiome

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

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

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

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

Invertebrate microbiome

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

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

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

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

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

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

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

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

Plant microbiome

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

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

Soil microbiome

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

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

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

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

Seawater microbiome

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

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

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

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

Microbiome of the Built Environment

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

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

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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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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 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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