Joke Geets

Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys

ABSTRACT We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. The technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. SP-GSTs are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the anchoring enzyme recognition sequence, and (iii) the type IIS restriction enzyme which defines the tag length. We evaluated the SP-GST method in silico for bacterial identification using the genes rpoC, uvrB, and recA and the 16S rRNA gene. The best distinguishing tags were obtained with the restriction enzyme Csp6I upstream of the 16S rRNA gene, which discriminated all organisms in our data set to at least the genus level and most organisms to the species level. The method was successfully used to generate Csp6I-based tags upstream of the 16S rRNA gene and allowed us to discriminate between closely related strains of Bacillus cereus and Bacillus anthracis. This concept was further used successfully to identify the individual members of a defined microbial community.

Chapter 21 Microbial activities, monitoring and application as part of a management strategy for heavy metal-contaminated soil and ground water

Publisher Summary This chapter focuses on monitoring for heavy metal-contaminated soil and ground water. Because of the threat they pose to human health and the extent of the problem of both natural and anthropogenic contamination by heavy metals, major efforts are being made to develop remediation technologies for the treatment of metal-contaminated soils, sediments and groundwater. Heavy metal pollution in soils and waters is conventionally treated using methods based on physical or chemical processes. Pump and treat, using precipitation or flocculation techniques, followed by sedimentation and disposal of the resulting contaminated sludge, is frequently used for treating heavy metal contamination in water. Other methods for heavy metal removal from water involve ion exchange, reverse osmosis, and microfiltration. For in situ treatment of groundwater, a reactive barrier may be installed that removes the heavy metals either by chemical means—that is, reduction by ferrous iron—or by biological means. This chapter describes concepts related to biological treatment of heavy metals. Heavy metal resistance in bacteria is discussed and The methods for studying microbial community composition and activity are described in the chapter Bioremediation processes based on microbial heavy metal detoxification mechanisms are elaborated. Treatment of heavy metal-contaminated soil is also analyzed.