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Microbial Diversity and Ecology
This Scoop is a collection of internet publications, tweets, and newly published papers in the wide field of Microbial diversity and ecology. I try to curate these here to show relevant news items for people interested in this field. Feel free to suggest or comment on any of my postings.
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Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods

Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods | Microbial Diversity and Ecology | Scoop.it
Assessing microbial diversity requires analysis of all three domains of life, including eukaryotic microbes. We examined the diversity of two ecologically important clades of microbial eukaryotes, ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), by comparing pyrosequencing to Sanger-sequenced clone libraries and microscopy. Using samples from a large temperate estuary (Long Island Sound, USA), we gained three major insights. First, richness estimates varied by up to one order of magnitude either using different criteria for pyrosequence processing or among pyrosequencing, cloning and microscopy, while taxon identification was almost always coherent. Error-correcting algorithms for pyrosequences (“denoising”) reduced discrepancies in richness but also removed known morphospecies from the data. Second, although most of the pyrosequenced Operational Taxonomic Units (OTUs) distributed within known orders and families, we found evidence of a previously uncharacterized or unknown clade even in these ciliate lineages that have a rich history of morphological description. Third, pyrosequencing allowed the detection of OTUs that were either dominant or extremely rare in different samples. Our findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of pyrosequence processing for using this method to address ecological questions.
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Archaeal Assemblages Inhabiting Temperate Mixed Forest Soil ...

Archaeal Assemblages Inhabiting Temperate Mixed Forest Soil ... | Microbial Diversity and Ecology | Scoop.it
“This study explored the persistence and spatial distribution of a diverse Archaeal assemblage inhabiting a temperate mixed forest ecosystem. Persistence under native conditions was measured from 2001 to 2010, 2011, and ...”
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A Quest for Even Safer Drinking Water

A Quest for Even Safer Drinking Water | Microbial Diversity and Ecology | Scoop.it
Researchers are mapping the microscopic fauna in our underground water systems, to better understand how some organisms eke out a living in dark, cool pipes loaded with chlorine.
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A nice article in the nytimes about the work of the lab of Norman Pace on microbes in tap water. It is different from what leaves the water cleaning plant!
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Tiny Organisms Thrive Well Below Earth's Surface : DNews

Tiny Organisms Thrive Well Below Earth's Surface : DNews | Microbial Diversity and Ecology | Scoop.it
Despite making up an estimated 6 percent of all life on Earth, researchers know almost nothing about these deep-dwellers.
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Positive correlations between genomic %AT and genome size within strains of microbial species - Bohlin - Environmental Microbiology Reports - Wiley Online Library

Positive correlations between genomic %AT and genome size within strains of microbial species - Bohlin - Environmental Microbiology Reports - Wiley Online Library | Microbial Diversity and Ecology | Scoop.it
Genomic %AT has been found to correlate negatively with genome size in microbes. While microbes with large genomes are often GC-rich and free-living, AT-rich bacteria tend to be host-associated with smaller genomes. With over 2000 fully sequenced microbial genomes available, we explored the relationship between genomic %AT, genome size, relative entropy (a measure of accumulated random mutations) and fraction of genome islands (GI) in microbial species with the genomes of more than 10 strains available. A negative correlation with genome size was found in 6 out of 12 phyla and a positive correlation in only 2. At the species level, we found a remarkable trend of positive correlations between genomic %AT and genome size in 8 out of 20 species, while only 4 showed a negative correlation. Estimated chromosomal fractions of GI's were found to correlate positively with genome size in the strains of 14 out of 18 species and genomic %AT in the strains of 7 species (2 correlated negatively). Although GI's may explain most of the positive correlations between genomic %AT and size observed within the strains of the microbial species, Chlamydia trachomatis seem to be an exception, therefore these findings needs to be further explored.
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Molecular Characterization and Analysis of Bacterial Diversity in Aleurocanthus woglumi (Hemiptera: Aleyrodidae)

Molecular Characterization and Analysis of Bacterial Diversity in Aleurocanthus woglumi (Hemiptera: Aleyrodidae) | Microbial Diversity and Ecology | Scoop.it
“Neeti Pandey, Ambika Singh, Vipin Singh Rana, and R. Rajagopal (2013) Molecular Characterization and Analysis of Bacterial Diversity in Aleurocanthus woglumi (Hemiptera: Aleyrodidae) Environmental Entomology: Vol.”
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The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing : Scientific Reports : Nature Publishing Group

The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing : Scientific Reports : Nature Publishing Group | Microbial Diversity and Ecology | Scoop.it
“Indoor microbial communities play an important role in everyday human health, especially in the intensive care units (ICUs) of hospitals.”
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H5N1: Beijing smog contains witches' brew of microbes

H5N1: Beijing smog contains witches' brew of microbes | Microbial Diversity and Ecology | Scoop.it
“Chinese researchers have now used genome sequencing to identify about 1,300 different microbial species in an exceptionally soupy smog that hit Beijing in January 2013. Reassuringly, most of the microbes they found are ...”
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Going back to the roots: the microbial ecology of the rhizosphere

Going back to the roots: the microbial ecology of the rhizosphere | Microbial Diversity and Ecology | Scoop.it
The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.
Via Olivier ANDRE
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Harnessing Metagenomics To Study Microbial Ecology in Soils

Harnessing Metagenomics To Study Microbial Ecology in Soils | Microbial Diversity and Ecology | Scoop.it
“Through soil metagenomics research, we can address fundamental questions about soil microbial ecology. For example, is there functional microbial redundancy in soil? Soil microbial community compositions differ in ...”
Via Andreas Sjödin
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The microbial communities of inactive Oslofjord pockmark sediments - Part 1

The microbial communities of inactive Oslofjord pockmark sediments - Part 1 | Microbial Diversity and Ecology | Scoop.it
“Last Friday I added another article to my publication list. The publication was in the PLOS ONE journal and caries the title: Linking microbiology and Geology: inactive pockmarks affect sediment mi...”
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My own blog post about my paper...
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Connectedness, human use of buildings shape indoor bacterial communities - Science Codex

Connectedness, human use of buildings shape indoor bacterial communities - Science Codex | Microbial Diversity and Ecology | Scoop.it
“Science Codex Connectedness, human use of buildings shape indoor bacterial communities Science Codex The location, connectedness, and human use patterns in a building may influence the types of bacteria they house, according to a study published in...”
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PLOS ONE: Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

PLOS ONE: Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure | Microbial Diversity and Ecology | Scoop.it
Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.
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This is my own paper. Enjoy it.
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Archaeal Community Structures in the Solfataric Acidic Hot Springs ...

Archaeal Community Structures in the Solfataric Acidic Hot Springs ... | Microbial Diversity and Ecology | Scoop.it
“In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured ...”
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Protein Adaptations in Archaeal Extremophiles

Protein Adaptations in Archaeal Extremophiles | Microbial Diversity and Ecology | Scoop.it
“Archaea is a peer-reviewed, open access journal that publishes original research articles as well as review articles dealing with all aspects of research on the archaea, including bioinformatics, biotechnology, environmental adaptation, enzymology,...”
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BGD - Abstract - Diversity and distribution of amoA-type nitrifying ...

“The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria, ...”
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Reconstructing the Microbial Diversity and Function of Pre ...

Reconstructing the Microbial Diversity and Function of Pre ... | Microbial Diversity and Ecology | Scoop.it
“Below ground activity is only just beginning to be understood in grassland systems. Below find a summary of some work to understand microbial communities in grasslands. Reconstructing the Microbial Diversity and Function ...”
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Characterising microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two-dimensional distributions of porewater solutes - Pagès - Environmental Microbi...

Characterising microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two-dimensional distributions of porewater solutes - Pagès - Environmental Microbi... | Microbial Diversity and Ecology | Scoop.it
“Characterising microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and... http://t.co/VZZWFCLeDZ”;
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Microbial Diversity: How does an obligately intracellular symbiont ...

“The first paper I'll tackle (Schneider et al) asks if Wolbachia strains exist as diverse quasi-species within a host and reveals that diversity using host transfer techniques. In "Uncovering Wolbachia Diversity upon Artificial Host ...”
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Interesting blog about diversity in Wolbachia.
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Microbial Diversity: What's the DEal? Differential Expression using ...

Microbial Diversity: What's the DEal? Differential Expression using ... | Microbial Diversity and Ecology | Scoop.it
“We've been looking for ways to analyze transcriptomes correctly, with sufficient power, not too many type I and II errors, and not much fuss. For those relatively unfamiliar with performing differential expression analyses on ...”
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Bacterial Diversity in Butterflies Changes Drastically During Metamorphosis

Bacterial Diversity in Butterflies Changes Drastically During Metamorphosis | Microbial Diversity and Ecology | Scoop.it
“For the first time ever, a team led by the University of Colorado Boulder has sequenced the internal bacterial makeup of the three major life stages of a butterfly species, a project that showed so...”
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MOTHUR 1.27 - Bioinformatics Platform of Microbial Ecology ...

MOTHUR 1.27 - Bioinformatics Platform of Microbial Ecology ... | Microbial Diversity and Ecology | Scoop.it
“ MOTHUR is bioinformatics package which includes functions from DOTUR, SONS, TreeClimber, S-Libshuff and Unifrac. MOTHUR aims to be a comprehensive software package that allows users to use a single piece of ...”
Via Biswapriya Biswavas Misra
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PLOS ONE: Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar, the Alimentary Tract and Stored Food of Honey Bees (Apis mellifera)

PLOS ONE: Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar, the Alimentary Tract and Stored Food of Honey Bees (Apis mellifera) | Microbial Diversity and Ecology | Scoop.it
Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.
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Two of History's Deadliest Plagues Were Linked, With Implications for Another ... - National Geographic

Two of History's Deadliest Plagues Were Linked, With Implications for Another ... - National Geographic | Microbial Diversity and Ecology | Scoop.it
“National Geographic Two of History's Deadliest Plagues Were Linked, With Implications for Another ...”
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Unknown aquatic sponge bacteria, a chemical factory

Unknown aquatic sponge bacteria, a chemical factory | Microbial Diversity and Ecology | Scoop.it
“A new, unknown strain of bacteria produces most of the bioactive substances that the stony sponge Theonella swinhoei exudes.”
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Another group of bacteria having a very interesting metabolic repetoire.
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