Development of molecular methods for the detection of specific bacteria in the environment

Pickup, Roger W.

doi:10.1099/00221287-137-5-1009

Cited by 116 publications

(43 citation statements)

References 55 publications

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“…Recent developments in molecular detection techniques have greatly increased the ability to track microorganisms and engineered genetic markers in natural environments (Pickup 1991). Molecular biology techniques that allow the detection of microorganisms in soil include the use of DNA probes (Holben et al 1988), polymerase chain reaction (Steffan and Atlas 1988;Ruppel et al 2006), use of selective markers such as antibiotic resistance genes, and the use of chromogenic markers such as b-galactosidase (Drahos et al 1986) and b-glucuronidase (Jefferson 1989).…”

Section: Molecular Monitoring Methodsmentioning

confidence: 99%

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Ahmad

Husain²,

Ahmad³

2011

Microbes and Microbial Technology

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Roots serve a multitude of functions in plants including anchorage, acquisition of nutrients and water, and production of exudates with growth regulatory properties. The root-soil interface, or rhizosphere, is the site of greatest biological and chemical activity within the soil matrix. Plant growth-promoting rhizobacteria (PGPR) are known to influence plant health by controlling plant pathogens or via direct enhancement of plant development in the laboratory and in greenhouse experiments. Unfortunately, however, results in the field have been less consistent. The colonization of roots by inoculated bacteria is an important step in the interaction between beneficial bacteria and the host plant. However, colonization is a complex phenomenon influenced by many biotic and abiotic parameters, some of which are only now apparent. Monitoring fate and metabolic activity of microbial inoculants as well as their impact on rhizosphere and soil microbial communities are needed to guarantee safe and reliable application, independent of whether they are genetically modified or not. The first and most crucial prerequisite for effective use of PGPRs is that strain identity and activity are continuously confirmed. A combination of both classical and molecular techniques must be perfected for more effective monitoring of inoculants strain (both genetically modified and unmodified) after release into the soil. Recent developments in techniques for studying rhizobacterial communities and detection and tracking systems of inoculated bacteria are important in future application and assessment of effectiveness and consistent performance of microbial inoculants in crop production and protection.

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Section: Molecular Monitoring Methodsmentioning

confidence: 99%

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Ahmad

Husain²,

Ahmad³

2011

Microbes and Microbial Technology

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“…This classical approach, however, is hampered by the lack of information on appropriate culture conditions for many of the micro-organisms. Earlier studies indicate that only about 10% of a population is cultivable (Jones, 1977;Hoppe, 1978;Ferguson e t al., 1984;Atlas, 1983;Pickup, 1991). Recently, comparative sequence analysis of ribosomal RNA has been widely accepted as a tool for the identification and phylogenetic classification of bacteria (Woese e t al., 1985;Olsen e t al., 1986;Woese, 1987;Winker & Woese, 1991;Fox e t al., 1992 Comparative 16s rRNA sequence analysis has been applied to studies of natural microbial communities and has resulted in the discovery of unexpectedly high levels of biodiversity Weller & Ward, 1989;Giovannoni e t al., 1990;Amann e t al., 1991 ;Schmidt et al, 1991 ;Fuhrman e t al., 1992).…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis

et al. 1995

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The analysis of complex microbiota present in activated sludge is important for the understanding and possible control of severe separation problems in sewage treatment such as sludge bulking or sludge foaming. Previous studies have shown that nocardioform actinomycetes are responsible for these conditions, which not only affect the efficiency of sewage treatment but also represent a threat to public health due to spread of pathogens. However, isolation and identification of these filamentous, nocardioform actinomycetes is hampered by their fastidious nature. Most species are still uncultivable and their taxonomy is unresolved. To study the ecology of these micro-organisms at the molecular level, w e have established a clone library of 165 rRNA gene fragments amplified from bulk sludge DNA. A rough indication of the predominant flora in the sludge was given by sequencing randomly chosen clones, which revealed a great diversity of bacteria from different taxa. Colony hybridization with oligonucleotide probe MNPI detected 27 clones with 165 rDNA inserts from nocardioform actinomycetes and mycobacteria. The sequence data from these clones together with those from randomly chosen clones were used for comparative 165 rRNA analysis and construction of dendrograms. All sequences differed from those of previously sequenced species in the databases. Phenotypic characterization of isolates of nocardioform actinomycetes and mycobacteria cultivated in parallel from the same activated-sludge sample revealed a large discrepancy between the two approaches. Only one 165 rDNA sequence of a cultured isolate was represented in the clone library, indicating that culture conditions could select species which represent only a small fraction of the organisms in the activated sludge.

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“…The mostsuitable rapid detection systems are based on detection of marker genes using nucleic acid probes or on immunological detection (Pickup, 1991). More and more nucleic acid probes are being described for the detection of L. monocytogenes but they are not always suited to large-scale use.…”

Section: Introductionmentioning

confidence: 99%

Analysis of surface proteins of Listeria in relation to species, serovar and pathogenicity

Tabouret¹,

Rycke²,

Dubray³

1992

Journal of General Microbiology

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SDS extracts of whole bacteria, representing five species and 15 serovars of Lisferk, were andysed by SDS-PAGE and by immunoblotthg with serum directed against whole formalin-treated L. mowyfogenes. Profiles of L. mnocytqgenes were very different from those of other species of Lisferia (i.e. L. innacua, L. welshimeri, L. seeliigeri and L. ioavrodi. This low degree of similarity between species was found even in the case of common serovam. Within the species L. mnocyfogenes, protein patterns were characterized, 011 the one hand, by a higb degree of homogeneity between all strains of the same serovar and, 011 the other hand, by large differences between serovam, especially between sv. 1/2 and 4b. Thus we have identified mqjor, surface-located protein antigens, specific for L. monocytogenes, either cornmoll to all serovars (64 and 68 kDa) or characteristic of certain serovars: 98 kDa for sv. 112 and 3; 76 and 78 kDa for sv. 4b, 4d and 4e; and 80 and 100 kDa for sv. 4a and 4c. Moreover, some of these bands (68 and 98 kDa) might be related to virulence, since differences were noticed between the profiles of haemolytic L. monocytogenes sv. 1/2a differing only in their virulence for immunocompromised mice. All these results confirmed, for the first time, the classif~cation of Lisferh obtained previously by genomic studies.They should help in the identification of new virulence factors and the development of easier and more specific methods of detection and identification.

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Development of molecular methods for the detection of specific bacteria in the environment

Cited by 116 publications

References 55 publications

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis

Analysis of surface proteins of Listeria in relation to species, serovar and pathogenicity

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