Molecular ecology of microbes: A review of promises, pitfalls and true progress

Abstract

Ecosystems, including engineered ones, are complex systems in which microorganisms occur in heterogenous communities. Their behaviour in the environment is often unknown due to the lack of proper detection and identification techniques. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA/RNA level without unreliable steps of cultivation of microbes. During the last few years genetically modified microbes have been constructed by recombinant DNA techniques for putative use in the environment. The slow progress in this field is due to the lack of integration of microbial ecology and molecular biology. In the present review, examples will be given of the use of DNA probes and marker genes in our study on the ecology of genetically modified microbes and wild‐type recalcitrant microorganisms that are difficult to cultivate or even 'non‐culturable'. Emphasis is given to the development and use of oligonucleotide probes directed towards 16S rRNA, to detect microbes in various engineered ecosystems: (i) Frankia in root nodules, and (li) propionate‐oxidizing sulfate‐reducing bacteria in anaerobic granular sludge. Expression of genes is demonstrated by studies on the localization of nifH transcripts in root nodules of Coriaria and Alnus. In addition we will describe examples of the use of marker genes (gusA gene and aphV gene) to study competition and genetic stability of released engineered Rhizobium and Streptomyces strains.

Recovery of total microbial RNA from lactic acid fermented foods with a high starch content

“…However, it is well established that such a strategy leads to bias in the estimation of the biodiversity and quantification of the microbial groups (Amann et al 1995). An alternative approach is the use of molecular tools for the characterization of microbial ecosystems (Akkermans et al 1994). Since the pioneering work of Stahl et al (1988) on the ecology of rumen microflora, molecular tools have successfully been used to quantify the microbial groups in different ecosystems but, as far as is known, never in fermented foods.…”

“…1995 ). An alternative approach is the use of molecular tools for the characterization of microbial ecosystems ( Akkermans et al . 1994 ).…”

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

“…In order to overcome this fundamental difficulty, culture-independent approaches, including DNA hybridization ( e.g. , microarray and fluorescent in situ hybridization), DNA cloning, and PCR have been used to detect specific members and/or functional genes in microbial communities (3, 8, 9, 32, 34, 47, 56, 61, 74, 157, 174, 185). High-throughput sequencing technologies have recently popularized shotgun metagenomic and (typically 16S ribosomal RNA [rRNA] gene) amplicon sequencing methods, which identify members and/or functional genes at a greater scale and in more detail.…”

Molecular analysis of actinorhizal symbiotic systems: Progress to date

“…Recent advances in molecular detection and identification methods at the DNA/RNA level (for reviews see Akkermans et al, 1991Akkermans et al, , 1994 have allowed nodulation and/or isolation and cultivation steps to be circumvented and have provided more reliable means to estimate Frankia populations in the environment both quantitatively and qualitatively. Many of the techniques described above for identification and taxonomic analysis of Frankia strains have been developed with the primary purpose of studying Frankia directly in root nodules and in soil.…”