In an ideal world, we would have time to read every great paper coming out in all the microbiology journals each month.  Instead we have to focus our reading on the topics that directly impact our research. But reading papers from other fields can often help us to find new methods or generate ideas for our projects that we wouldn’t have thought of on our own.

 To make scanning the monthly journals a little bit easier for you, today’s blog is a first in what will be a regular series of articles highlighting some of the exciting research going on in microbiology. After scanning the January and February publications on Highwire, I picked a few headlines that I thought the community would find particularly interesting.

There are so many to choose from that I could write all day about the great papers coming out from our customers but I had to narrow it down for the sake of brevity. Most of my picks will lean towards methods papers that may be helpful to our readers, and also research into novel areas of microbiology or “firsts”.  In some cases, papers are chosen to highlight a particular lab group.

These were my top picks covering January and February:

1.  A Rapid and Specific Method for Quantifying Streptomyces Competitive Dynamics in Complex Soil Communities
Daniel C. Schlatter, Deborah A. Samac, Mesfin Tesfaye, and Linda L. Kinkel
Appl. Envir. Microbiol., Jan 2010; 10.1128/AEM.02320-09.

The authors developed a sensitive (down to 0.01 pg of DNA, which is 1 genome equivalent for Streptomyces) and specific qPCR assay for determination of two species of Streptomyces that co-exist but compete with each other in soil. The assay was designed using the short hyper-variable region of the 16S rRNA gene. SYBR Green primers were designed for S. lavendulae and S. scabies using species-specific forward primers and a single conserved reverse primer from the hypervariable region. Because of the background detected from indigenous Streptomyces in soil, a probe based assay was developed using species-specific forward and reverse primers and a Streptomyces specific dual-labeled probe (FAM and NFQ). The specificity of the assay was validated by spiking in S. lavendulae and S. scabies either together or separately into autoclaved soil and in field samples containing 15 different strains of Streptomyces. The assay provides a model for developing qPCR based microbial tracking assays in samples with very complex communities, such as soil

2. Sample pooling masks PCR-based estimates of soil microbial richness and community structure
Daniel K. Manter, Tiffany L. Weir, and Jorge M. Vivanco
Appl. Envir. Microbiol., Feb 2010; 10.1128/AEM.03017-09

Due to the richness of microbial communities in soil, profiling of the  dominant community structure is typically done by taking multiple samples of soil from a plot and combining them to provide a samples that is representative of the soil.  But does pooling of soil or DNA prior to PCR have an impact on the results of community diversity? This paper shows that it does. In this report,  ARISA (atomated ribosomal intergenic spacer analysis) technique was used to analyze the differences in community profiles from three different types of soils processed three different ways. The three strategies were: 1) soil samples were unpooled, extracted, and analyzed individually, 2) DNA extraction from multiple samples were pooled prior to PCR, and 3) soil samples were pooled prior to DNA extraction and then DNA isolated from a large quantity of soil.    Their results showed that pooling soil or DNA prior to PCR results in missed detection of fungal and bacterial phylotypes compared to unpooled samples which revealed a number of amplicons unique to individual samples. Loss of fungal community richness was impacted greater by pooling than bacterial community richness.  This effect differed between sites related to the evenness of the community in the different soils. The authors make some suggestions for best practices in sampling and pooling based on your project goals and soil type.

3. First Autochthonous Case of Rhinocladiella mackenziei Cerebral Abscess Outside the Middle East
Hamid Badali, Jagdish Chander, Shaifali Bansal, Atul Aher, Surendra S. Borkar, Jacques F. Meis, and G. Sybren De Hoog
J. Clin. Microbiol., Feb 2010; 48: 646 – 649.

Cerebral phaeohyphomycosis is a rare infection of a melanized fungi that causes brain abscesses that typically leads to death. The fungi in the order Chaetothyriales, of which Rhinocladiella is a member, are neurotropic in humans, and R. mackenziei causes 100% mortality in even immunocompetent hosts. The organism has never been isolated from the environment and has only been identified patients in the middle east.  This report describes the first case of R. mackenziei infection in a person outside the area of endemicity.  The details of the microscopy and culture techniques used to diagnose the patient are described.

4. Identification of a Two-Component Regulatory Pathway Essential for Mn(II) Oxidation in Pseudomonas putida GB-1
Kati Geszvain and Bradley M. Tebo
Appl. Envir. Microbiol., Feb 2010; 76: 1224 – 1231.

Oxidation of manganese by bacterial species via a family of enzymes known as multicopper oxidases (MCO) serve important potential functions including the binding of trace metals, making Mn oxidizing bacteria good candidates for bioremediation of heavy metal contaminated sites. Pseudomonas putida GB-1 is a Mn oxidizing strain that is easy to work with in the lab and contains an MCO family of enzymes. Their surprising results found that oxidation in this strain was not due to the MCO but involved a sensor histidine kinase (mnxS1) and a response regulator gene (mnxR). Environmental signals, such as nutritional state, growth phase, or oxygen concentration, result in autophosphorylation of mnxS1 and subsequently the transfer of the phosphoryl group to the mnxR transcription factor, inducing downstream effects on genes transcribed by σ⁵⁴ -RNA polymerase dependent promoters.  Their results provide the Mn oxidation field a powerful tool for studying the signals that trigger oxidation.

5. Up-regulation of integrin expression in lung adenocarcinoma cells caused by bacterial infection: in vitro study
Sean Gravelle, Rebecca Barnes, Nicole Hawdon, Lee Shewchuk, Joseph Eibl, Joseph S. Lam, and Marina Ulanova
Innate Immunity, Feb 2010; 16: 14 – 26.

Integrins are heterodimeric transmembrane proteins that interact with extracellular matrix proteins and are important for repair of damaged tissue, regulating inflammatory responses, and tissue remodeling. Integrin receptor expression changes in pulmonary epithelium under pathological conditions, including damage or neoplasia in the lung. One organism that causes severe pulmonary infections in immunocompromised people is Pseudomonas aeruginosa. This study examined whether infection with P. aeruginosa alters integrin expression. Using flow cytometry and RT-qPCR, their results demonstrated a rapid up-regulation of integrins in response to internalization of live, virulent, piliated and LPS containing bacteria. The authors propose a model for integrin signalling in response to infection by P. aeruginosa.

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This small sampling of papers covers a wide range of new and exciting research in microbiology. 

I know there is so much more so I encourage you to leave a comment and let us know what paper or papers came out recently that you think will have a big impact on your field and why. Let us know what are your picks for hot papers in microbiology.

This entry was posted on Monday, March 1st, 2010 at 5:03 pm and is filed under New papers in microbiology. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.