Microbial Diversi...
Follow
Find
510 views | +0 today
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.
Your new post is loading...
Your new post is loading...
Scooped by Thomas Haverkamp
Scoop.it!

Environmental Microbiology: Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay

Environmental Microbiology: Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay | Microbial Diversity and Ecology | Scoop.it
Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P. chrysosporium. During eighteen weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial OTUs varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after twelve weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P. chrysoporium, representing potential taxonomic bioindicators of the white-rot mycosphere.
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

The Amphibian Apprentice — Graphic representing the bacterial diversity at...

The Amphibian Apprentice — Graphic representing the bacterial diversity at... | Microbial Diversity and Ecology | Scoop.it
“Graphic representing the bacterial diversity at the class level encountered on the skin of 25 O. pumilio in Costa Rica. This image was produced by QIIME (Quantitative Insights into Microbial Ecology)...”
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

The ISME Journal - Two-stage microbial community experimental design

The ISME Journal - Two-stage microbial community experimental design | Microbial Diversity and Ecology | Scoop.it

Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene. Often, a collection of samples is then selected for subsequent metagenomic, metabolomic or other follow-up. Two-stage study design has long been used in ecology but has not yet been studied in-depth for high-throughput microbial community investigations. To avoid ad hoc sample selection, we developed and validated several purposive sample selection methods for two-stage studies (that is, biological criteria) targeting differing types of microbial communities. These methods select follow-up samples from large community surveys, with criteria including samples typical of the initially surveyed population, targeting specific microbial clades or rare species, maximizing diversity, representing extreme or deviant communities, or identifying communities distinct or discriminating among environment or host phenotypes. The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data. Specifically, all criteria were able to identify samples whose properties were accurately retained in 318 paired 16S amplicon and whole-community metagenomic (follow-up) samples from the Human Microbiome Project. Some selection criteria resulted in follow-up samples that were strongly non-representative of the original survey population; diversity maximization particularly undersampled community configurations. Only selection of intentionally representative samples minimized differences in the selected sample set from the original microbial survey. An implementation is provided as the microPITA (Microbiomes: Picking Interesting Taxa for Analysis) software for two-stage study design of microbial communities.

 

 

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Bacterial Communities in Soil Under Moss and Lichen-Moss Crusts

Bacterial Communities in Soil Under Moss and Lichen-Moss Crusts | Microbial Diversity and Ecology | Scoop.it

Biological soil crusts are symbiotic microbial communities formed by green algae, mosses, fungi, lichens, cyanobacteria and bacteria in different proportions. Crusts contribute to soil fertility and favour water retention and infiltration. However, little is known about the bacterial community structure in soil under the crusts. Soil was sampled under a moss crust (considered the MOSS group), lichen plus moss (considered the LICHEN group) and bare soil (considered the BARE group) and the microbial communities determined using nearly full 16S rRNA gene libraries. Bacteria belonging to seven different phyla were found and the Acidobacteria and Alphaproteobacteria were the dominant in each group. The crusts affected negatively the abundance of the Burkholderiales. The phylogenetic diversity and bacterial community membership were different in the LICHEN group compared to the BARE and MOSS groups, but not species richness and community structure. The beta diversity analysis also revealed a different bacterial community structure beneath the LICHEN and MOSS crusts, suggesting species-specific influence. This is a first insight into the effect of a biological soil crust on the bacterial community structure in an organic matter rich soil of a high altitude mountain forest.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database | Microbial Diversity and Ecology | Scoop.it

Quantitative PCR (qPCR) and community fingerprinting methods such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis are well suited techniques for the examination of microbial community structures. The use of phylum- and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared to domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria, Betaproteobacteria and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above mentioned groups and via screening of clone libraries from environmental soil samples and human fecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Taxonomic Relatedness Shapes Bacterial Assembly in Activated Sludge of Globally Distributed Wastewater Treatment Plants

Taxonomic Relatedness Shapes Bacterial Assembly in Activated Sludge of Globally Distributed Wastewater Treatment Plants | Microbial Diversity and Ecology | Scoop.it

Activated sludge (AS), which has been in use for 100 years, has been the most popular biological process in various wastewater treatment plants (WWTPs), in which bacteria plays central roles in pollutant removal. However, the potential relationship between bacteria taxa and the niches occupied by specific functional bacteria in AS are largely unknown. Here, correlation-based network analysis was applied to a 16S rRNA gene pyrosequencing dataset containing >760,000 sequences of 50 AS samples from globally distributed full-scale WWTPs. The results showed that (I) bacterial assembly in AS was nonrandomly arranged by taxonomic relatedness and (II) intra- and inter-phylum/class co-occurrence higher than expected by chance was induced by multiple deterministic processes, such as habitat filtering and competition. Moreover, based on bacterial occupancy, a prevalent core set of cosmopolitan functional bacteria (e.g., multiple nitrogen-cycling-related bacteria) was widely distributed in the AS of different WWTPs, showing strong ecological associations among them. Additionally, the AS network has statistical and structural characteristics similar to those of previously reported ecological networks, such as power-law connectivity distribution and nonrandomly connected properties. Overall, this work provides novel insights into the bacterial associations within activated sludge and sheds light on the ecological rules guiding bacterial assembly in WWTPs.

Thomas Haverkamp's insight:

Activated sludge (AS), which has been in use for 100 years, has been the most popular biological process in various wastewater treatment plants (WWTPs), in which bacteria plays central roles in pollutant removal. However, the potential relationship between bacteria taxa and the niches occupied by specific functional bacteria in AS are largely unknown. Here, correlation-based network analysis was applied to a 16S rRNA gene pyrosequencing dataset containing >760,000 sequences of 50 AS samples from globally distributed full-scale WWTPs. The results showed that (I) bacterial assembly in AS was nonrandomly arranged by taxonomic relatedness and (II) intra- and inter-phylum/class co-occurrence higher than expected by chance was induced by multiple deterministic processes, such as habitat filtering and competition. Moreover, based on bacterial occupancy, a prevalent core set of cosmopolitan functional bacteria (e.g., multiple nitrogen-cycling-related bacteria) was widely distributed in the AS of different WWTPs, showing strong ecological associations among them. Additionally, the AS network has statistical and structural characteristics similar to those of previously reported ecological networks, such as power-law connectivity distribution and nonrandomly connected properties. Overall, this work provides novel insights into the bacterial associations within activated sludge and sheds light on the ecological rules guiding bacterial assembly in WWTPs.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Microbiome of free-living amoebae isolated from drinking water

Microbiome of free-living amoebae isolated from drinking water | Microbial Diversity and Ecology | Scoop.it

Diversity of amoebae and associated bacteria were studied in drinking water.

To allow bacterial metagenomic a new cultural method was develop.

Hartmannella was the most represented genus of amoebae.

Among 54 genera of bacteria, 24 were never described in amoebae.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Bioconductor - CRISPRseek

“RT @Bioconductor: http://t.co/HYs56JOZuu CRISPRseek Design, scoring and annotating spacers for CRISPR-Cas9 system”
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Association of CRISPR elements with serotypes and virulence potential of Shiga toxin-producing Escherichia coli

more...
No comment yet.
Rescooped by Thomas Haverkamp from Virology and Bioinformatics from Virology.ca
Scoop.it!

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs — small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.
Via Michael Wolfe
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

COST Action SUSTAIN - TALEN & CRISPR Training School / March 2014 Halle

COST Action SUSTAIN - TALEN & CRISPR Training School / March 2014 Halle | Microbial Diversity and Ecology | Scoop.it
The first training school of the action - TALEN & CRISPR Training School - is scheduled to take place on 24 - 28 March 2014 in Halle, Germany. The training school will be hosted by Dr. Jens Boch at the Martin Luther University in Halle. For more information about the training school, please refer to the presentation.
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Bacteria show surprising number of genetic paths to survival - Phys.Org

Bacteria show surprising number of genetic paths to survival - Phys.Org | Microbial Diversity and Ecology | Scoop.it
“Bioscience Technology Bacteria show surprising number of genetic paths to survival Phys.Org There may be much more genetic diversity within a single species of bacteria in an infected person than previously assumed.”
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Life at the Poles in the Age of Global Warming: Part 2

Life at the Poles in the Age of Global Warming: Part 2 | Microbial Diversity and Ecology | Scoop.it

SUMMARY
➤ Investigators continue to refine their projections of how global warming will affect microbial communities at the poles and how these communities, in turn, are likely either to promote or temper those warming trends.
➤ Ultraviolet radiation has a big impact on microbial life at the poles, and the role of DNA damage repair systems could prove critical for determining microbial population sizes.
➤ Changes in microbial communities at the poles could help to sequester carbon dioxide in soil and to fix more of this gas via photosynthesis.
➤ Despite many uncertainties, efforts to identify the microbial genetic potential in polar environments, including metabolic capabilities that may be triggered, are critical for predicting the fate of carbon cycling and subsequent global climate consequences.

 

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Bacterial and Fungal Diversity of Quaternary Cave Sediment Deposits

Bacterial and Fungal Diversity of Quaternary Cave Sediment Deposits | Microbial Diversity and Ecology | Scoop.it

The bacterial and fungal assemblages of clastic sediments collected from two caves located in north-western Romania were investigated by assessing ITS and 16S rRNA gene diversity. Bacterial members belonging to Chloroflexi, Nitrospirae, Proteobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, and fungal members of Ascomycota were identified. Except for Bacillus sp., all bacteria were related to uncultured or unknown species and the majority (86%) of the bacterial sequences from one of the caves had no close GenBank relatives. The bacterial sequences obtained clustered with species found in extreme environments. Half of the bacterial operational taxonomic units were clustered with clones isolated from deep subsurface sediments of a radioactively contaminated site in the USA. The present study represents the first attempt to identify microorganisms in Quaternary cave sediments.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Variability of subseafloor viral abundance at the geographically and geologically distinct continental margins.

Variability of subseafloor viral abundance at the geographically and geologically distinct continental margins. | Microbial Diversity and Ecology | Scoop.it

We studied the relationship between viral particle and microbial cell abundances in marine subsurface sediments from three geographically distinct locations in the continental margins (offshore of the Shimokita Peninsula of Japan, the Cascadia Margin off Oregon and the Gulf of Mexico), and found depth variations in viral abundances among these sites. Viruses in sediments obtained offshore the Shimokita and in the Cascadia Margin generally decreased with increasing depth, whereas those in sediments from the Gulf of Mexico were relatively constant throughout the investigated depths. In addition, the abundance ratios of viruses to microbial cells notably varied among the sites, ranging between 10-3 and 101. The subseafloor viral abundance offshore the Shimokita showed a positive relationship with the microbial cell abundance and the sediment porosity. In contrast, no statistically significant relationship was observed in the Cascadia Margin and the Gulf of Mexico sites, presumably due to the long-term preservation of viruses from enzymatic degradation within the low-porosity sediments. Our observations indicate that viral abundance in the marine subsurface sedimentary environment is regulated not only by in situ production but also by the balance of preservation and decay, which is associated with the regional sedimentation processes in the geological settings.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

A Unique Megaplasmid Contributes to Stress Tolerance and Pathogenicity of an Emergent Salmonella enterica Serovar Infantis Strain

A Unique Megaplasmid Contributes to Stress Tolerance and Pathogenicity of an Emergent Salmonella enterica Serovar Infantis Strain | Microbial Diversity and Ecology | Scoop.it

Of all known Salmonella enterica serovars, S. Infantis is one of the most commonly isolated and has been recently emerging worldwide. To understand the recent emergence of S. Infantis in Israel we performed extensive comparative analyses between pre-emergent and the clonal emergent S. Infantis populations. We demonstrate the fixation of adaptive mutations in the DNA gyrase (gyrA) and nitroreductase (nfsA) genes, conferring resistance to quinolones and nitrofurans, respectively and the carriage of an emergent-specific plasmid, designated pESI. This self-transferred episome is a mosaic megaplasmid (∼280 kb), which increases bacterial tolerance to environmental mercury (mer operon), oxidative stress and provides further resistance to tetracycline, sulfamethoxazole and trimethoprim, most likely due to the presence of tetRA, sulI and dfrA genes, respectively. Moreover, pESI carries the yersiniabactin siderophore system and two novel chaperone-usher fimbriae. In-vitro studies established that pESI conjugation into a plasmidless S. Infantis strain results in superior biofilm formation, adhesion and invasion to avian and mammalian host cells. In-vivo mouse infections demonstrated higher pathogenicity and increased intestinal inflammation caused by a S. Infantis strain harboring pESI compared to the plasmidless parental strain. Our results indicate that the presence of pESI that was found only in the emergent population of S. Infantis in Israel contributes significantly to antimicrobials tolerance and pathogenicity of its carrier. It is highly likely that pESI plays a key role in the successful spread of the emergent clone that replaced the local S. Infantis community in short time of only 2-3 years.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Soil microbial diversity and C turnover modified by tillage and cropping in Laos tropical grassland - Springer

Agricultural practices should modify the diversity of soil microbes. However, the precise relationships between soil properties and microbial diversity are poorly known. Here, we study the effect of agricultural management on soil microbial diversity and C turnover in tropical grassland of north-eastern Laos. Three years after native grassland conversion into agricultural land, we compared soils from five land use management systems: one till versus two no-till rotational cropping systems, one no-till improved pasture and the natural grassland. Soils were incubated in microcosms during 64 days at optimum temperature and humidity. Bacterial and fungal diversity were evaluated by metagenomic 454-pyrosequencing of 16S and 18SrRNA genes, respectively. Changes in soil respiration patterns were evaluated by monitoring 12C- and 13C-CO2 release after soil amendment with 13C-labelled wheat residues. Results show that residue mineralization increased with bacterial richness and diversity in the tilled treatment 7 days after soil amendment. Native soil organic C mineralization and priming effect increased with fungal richness and diversity in improved pasture and natural grassland. No-till cropping systems represented intermediate situations between tillage and pasture systems. Our findings evidence the potential of controlling soil microbial diversity by agricultural practices to improve soil biological properties. We suggest the promotion of no-till systems as a fair compromise between the need for agriculture intensification and soil ecological processes preservation.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Genomes from Metagenomics

Thomas Haverkamp's insight:

A short but usefull perspective paper on the issues encountered when assembling microbial genomes from complex communities.

more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

Lactobacillus buchneri genotyping using CRISPR diversity.

more...
No comment yet.
Rescooped by Thomas Haverkamp from WHAT THINGS ARE GMO FOODS OR SUPPORTERS OF MONSANTO? Weather Disasters
Scoop.it!

Natural GMOs Part 186. Bacteria use GE to protect against transgenic DNA. Rodolphe Barrangou gives best research review talk of 2013 -- on CRISPR-Cas systems

Highly recommended
viewing or
readingThis is the way a great review talk is done in science. Concise clear and inspiring revelation of important advances.

Via Poppen Report
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

CRISPR-Cas: A powerful new tool for precise genetic engineering

CRISPR-Cas: A powerful new tool for precise genetic engineering | Microbial Diversity and Ecology | Scoop.it
Viruses cannot only cause illnesses in humans, they also infect bacteria. Those protect themselves with a kind of ‘immune system’ which – simply put – consists of specific sequences in the genetic material of the bacteria and a suitable enzyme. It detects foreign DNA, which may originate from a virus, cuts it up and thus makes the invaders harmless. Scientists from the Helmholtz Centre for Infection Research (HZI) in Braunschweig have now shown that the dual-RNA guided enzyme Cas9 which is involved in the process has developed independently in various strains of bacteria. This enhances the potential of exploiting the bacterial immune system for genome engineering. Even though it has only been discovered in recent years the immune system with the cryptic name ‘CRISPR-Cas’ has been attracting attention of geneticists and biotechnologists as it is a promising tool for genetic engineering. CRISPR is short for Clustered Regularly Interspaced Palindromic Repeats, whereas Cas simply stands for the CRISPR-associated protein. Throughout evolution, this molecule has developed independently in numerous strains of bacteria. This is now shown by Prof Emmanuelle Charpentier and her colleagues at the Helmholtz Centre for Infection Research (HZI) who published their finding in the international open access journal Nucleic Acids Research. The CRISPR-Cas-system is not only valuable for bacteria but also for working in the laboratory. It detects a specific sequence of letters in the genetic code and cuts the DNA at this point. Thus, scientists can either remove or add genes at the interface. By this, for instance, plants can be cultivated which are resistant against vermins or fungi. Existing technologies doing the same thing are often expensive, time consuming or less accurate. In contrast to them the new method is faster, more precise and cheaper, as fewer components are needed and it can target longer gene sequences. Additionally, this makes the system more flexible, as small changes allow the technology to adapt to different applications. “The CRISPR-Cas-system is a very powerful tool for genetic engineering,“ says Emmanuelle Charpentier, who came to the HZI from Umeå and was awarded with the renowned Humboldt Professorship in 2013. “We have analysed and compared the enzyme Cas9 and the dual-tracrRNAs-crRNAs that guide this enzyme site-specifically to the DNA in various strains of bacteria.” Their findings allow them to classify the Cas9 proteins originating from different bacteria into groups. Within those the CRISPR-Cas systems are exchangeable which is not possible between different groups. This allows for new ways of using the technology in the laboratory: The enzymes can be combined and thereby a variety of changes in the target-DNA can be made at once. Thus, a new therapy for genetic disorders caused by different mutations in the DNA of the patient could be on the horizon. Furthermore, the method could be used to fight the AIDS virus HIV which uses a receptor of the human immune cells to infect them. Using CRISPR-Cas, the gene for the receptor could be removed and the patients could become immune to the virus. However, it is still a long way until this aim will be reached. Still those examples show the huge potential of the CRISPR-Cas technology. “Some of my colleagues already compare it to the PCR,” says Charpentier. This method, developed in the 1980s, allows scientists to ‘copy’ nucleic acids and therefore to manifold small amounts of DNA to such an extent that they can be analysed biochemically. Without this ground-breaking technology a lot of experiments we consider to be routine would have never been possible. Charpentier was not looking for new molecular methods in the first place. “Originally, we were looking for new targets for antibiotics. But we found something completely different,” says Charpentier. This is not rare in science. In fact some of the most significant scientific discoveries have been made incidentally or accidentally. Reference: Ines Fonfara, Anaïs Le Rhun, Krzysztof Chylinski, Kira Makarova, Anne-Laure Lécrivain, Janek Bzdrenga, Eugene V. Koonin, Emmanuelle Charpentier: Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Research, 2013, DOI: 10.1093/nar/gkt1074
more...
No comment yet.
Scooped by Thomas Haverkamp
Scoop.it!

A little trim for your genes

A little trim for your genes | Microbial Diversity and Ecology | Scoop.it
“You can almost hear the molecular scissors going *snip* *snip*. (New on #scienceonyou: A little trim for your genes.”
Thomas Haverkamp's insight:
A nice blog post on an interesting new method for gene therapy.
more...
No comment yet.