Category: Recent Publications

I was recently involved as an adviser in a report by the County Administrative Board in Västra Götaland (Länsstyrelsen) which has now been published [1]. [UPDATE: The PDF link at Länsstyrelsen’s page does not seem to work, but leads to another report in Swedish. I have reported this error to the web admin, we’ll see what happens. Once again, the PDF seems to work.] The report aims to identify gaps in the current monitoring system of hazardous substances in the Swedish environment. The report deals with effect based monitoring tools and their usefulness for predicting and/or observing effects of hazardous substances in the environment. The overall conclusion of the report is that there are several gaps in both knowledge and techniques, and a need for developing new resources. However, Sweden still has a good potential to adapt the monitoring system to fill the needs. I have been involved in one of the last chapters, describing the use of metagenomics if study ecosystem function (chapter 30.3). For people with an interest in environmental monitoring, the report is an interesting read in its entirety. For those more interested in applications for metagenomics I recommend turning to page 285 and continue to the end of the report (it’s only five pages on metagenomics, so you’ll manage).

1. Länsstyrelsen i Västra Götalands län. (2012). Swedish monitoring of hazardous substances in the aquatic environment (No. 2012:23). (A.-S. Wernersson, Ed.) Current vs required monitoring and potential developments (pp. 1–291). Länsstyrelsen i Västra Götalands län, vattenvårdsenheten.

It is a pleasure to annonce that the paper on Metaxa is now available as an Online early article in Antonie van Leeuwenhoek. In short, the paper describes a software tool that is able to extract small subunit (SSU) rRNA sequences from large data sets, such as metagenomes and environmental PCR libraries, and classify them according to bacterial, archaeal, eukaryote, chloroplast or mitochondrial origin. The program makes it easy to distinguish between e.g. the bacterial SSU sequences you like to analyze, and the SSU sequences you would like to remove prior to the analysis (e.g. mitochondrial and chloroplast sequences). This task is particularly important in metagenomics, where sequences can potentially derive from a variety of origins, but bacterial diversity often is the desired target for analysis. The software can be downloaded here, and the article can be read here. I would like to thank all the co-authors on this paper for a brilliant collaboration, and hope to be working with them again.

Reference:

• Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa: A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek Journal of Microbiology, 2011, doi:10.1007/s10482-011-9598-6.

If you did not already know, or at least suspected, that pesticides used in agriculture could have a negative impact on species diversity, there is now proof. In this article:

• Geiger et al. “Persistent negative effects of pesticides on biodiversity and biological control potential on European farmland“. Basic and Applied Ecology, Volume 11, Issue 2, March 2010.

the result of a joint study in eight European countries, we present that biodiversity indeed takes a strike by the use of pesticides, at several levels. Also, actions are needed for a change in the structure of the large-scale agriculture. And why do I say we? This isn’t exactly microbiology, is it? Well, this is the first publication related to the field assistant work I did during the Summers of 2007 and 2008. There is more in the pipeline, but this first publication at least shows that there are considerable risks with the way we use weed control.