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Whole-cell hybridization with digoxigenin-labeled in vitro transcripts followed by an antibody-alkaline phosphatase detection of the digoxigenin reporter molecular helped trace the mRNA of the thiostrepton resistance gene (tsr) harbored by plasmid PIJ673 in streptomyces violacelatus. Before hybridization, the cells had to be permeabilized by lysozyme, the detergent Nonidet P-40 and toulene. Hybridization with digoxigenin-labeled, 16S rRNA-targeted oligonucleotides indicated the permeability of the Streptomyces violacelatus cells for probes and the antibody-alkaline phosphatase conjugate.

Frankia strains in pure cultures and in nodules is detected and identified by the use of whole-cell hybridization with non-radioactively labeled oligonucleotide probes. After the removal of the polysaccharide capsule surrounding the vesicles, identification of Frankia vesicles in nodule homogenates is possible. Specific hybridization is facilitated by incubation with H2O2 (15% in water for 1 h at room temperature) before lyzozyme and detergent treatments.

Oligonucleotide probes specific to complementary rRNA sequences of the domains Bacteria and Archaea were fused to horseradish peroxidase (HRP) in an attempt to evaluate the use of HRP-conjugated probes for the identification of single bacterial cells using light microscopy. The procedure also involved the use of lysozyme-EDTA to permeabilize gram-negative cells, although this was incorporated in the hybridization step for some archaebacterial cells. The procedure was effective for gram-negative and archaebacterial cells. However, the gram-positive cells are resistant to the penetration of the HRP-conjugated probe.

A dual staining technique using 4', 6-diamidino-2-phenylindole and fluoresent oligonucleotide probes specific for kingdom-level 16S rRNA sequence was developed. The method increased the sensitivity and visibility of natural bacterioplankton, thus allowing the microscopic characterization and quantification of specific phylogenetic group in dilute aquatic communities. The specific oligonucleotide probes could also be used at other taxonomic levels.

In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901(T)), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.