Analysis of Bacterial Community Composition by Oligonucleotide Fingerprinting of rRNA Genes

Valinsky, Lea; Vedova, Gianluca Della; Scupham, Alexandra J.; Alvey, S.; Figueroa, Andres; Yin, Bei; Hartin, R. Jack; Chrobák, Marek; Crowley, David E.; Jiang, Tao; Borneman, James

doi:10.1128/aem.68.7.3243-3250.2002

Cited by 120 publications

(77 citation statements)

References 34 publications

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“…Similar results were observed by other authors (e.g. Sessitsch et al, 2001;Valinsky et al, 2002;Sun et al, 2004;Toyota and Kuninaga, 2006) where variations in the composition of bacterial community also depended on the soil type, sample origin and plant growth stage. Smit et al (2001) suggested that the ratio between Proteobacteria and Acidobacteria frequency can be indicative of the soil nutrient status when calculated as % Proteobacteria/(sum of % Proteobacteria and % Acidobacteria).…”

Section: Introductionsupporting

confidence: 91%

Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

Ros

Knapp

Peintner

et al. 1970

Span. j. agric. res.

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Differences in the bacterial community composition of agricultural soils caused by a long-term (12 year) application of different composts were identified by cultivation-dependent and -independent methods (PCR-DGGE and 16S rRNA clone libraries). The number of colony forming units indicated that the successive incorporation of organic amendments increased the bacterial abundance (6.41-5.66 log 10 cfu g -1 dry soil) compared to control and mineral soils (5.54-3.74 log 10 cfu g -1 dry soil). Isolated bacteria were dominated by Actinobacteria, whereby compost-amended soils and green compost-amended soils showed, respectively, higher number of members of Actinobacteria (100% and 64%) than control and mineral soils (50% and 40%). The 16S rRNA clone libraries were dominated by Proteobacteria (43%), Acidobacteria (21%) and Actinobacteria (13%). Proteobacteria and Actinobacteria were most abundant in compost amended soils while Acidobacteria were more frequently found in mineral fertilizer and control soils. Partial 16S rRNA gene clone libraries revealed a higher bacterial diversity than cultivation. In conclusion, we found differences of bacterial community composition with a cultivation approach and clone libraries between compost amended soils and control and mineral soil.Additional key words: 16S rRNA clone libraries; fertilizer; isolated bacteria; organic amendments. ResumenComunicación corta. Respuesta de la composición bacteriana de un suelo agrícola a la incorporación a largo plazo de diferentes composts Se estudiaron las comunidades bacterianas de suelos agrícolas enmendados durante 12 años con diferentes tipos de compost, mediante el empleo de técnicas de cultivo en placa y técnicas moleculares (PCR-DGGE y genotecas de ARNr 16S). El cultivo en placa mostró un aumento del número de bacterias en los suelos enmendado con diferentes composts (6,41-5,66 log 10 cfu g -1 suelo), respecto a los suelos no enmendados o con fertilización mineral (5,54-3,74 log 10 cfu g -1 suelo). Esta técnica reveló que las Actinobacterias componen la mayoría de las bacterias identificadas en placa, encontrando un mayor número en los suelos enmendados con diferentes compost (100%-64%) frente a los no enmendados o con fertilización mineral (50%-40%). Las genotecas permitieron identificar además de Actinobacterias (13%), la presencia de Proteobacterias (43%) y Acidobacterias (21%). En los suelos enmendados con compost predominaron Proteobacterias y Actinobacterias, mientras que en los suelos sin enmendar y con fertilización mineral predominaron las Acidobacterias. Las genotecas mostraron mayor diversidad bacteriana que el método de cultivo en placa. En conclusión, los datos obtenidos mediante cultivo en placa y con genotecas mostraron diferencias en la composición de la comunidad microbiana entre suelos enmendados con compost y aquellos sin enmendar y con fertilización mineral. Palabras clave adicionales: bacterias aisladas; enmiendas orgánicas; fertilizantes; genotecas bacterianas.

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Section: Introductionsupporting

confidence: 91%

Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

Ros

Knapp

Peintner

et al. 1970

Span. j. agric. res.

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“…DNA was purified and analyzed from all five initial isolates. As a result of this analysis, the sequence was assigned to the Enterobacter genus 16) , and specifically to sequence S000544285, which belongs to Enterobacter hormaechei 17) .…”

Section: Cultivation Of Clinical Isolates From Atheromatous Tissue Anmentioning

confidence: 99%

Cultivation of Enterobacter Hormaechei from Human Atherosclerotic Tissue

Rafferty

Dolgilevich

Kalachikov

et al. 2011

JAT

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Aim:To determine whether culturable bacterial strains are present in human atheromatous tissue and to investigate their properties using culture, quantitative PCR, metagenomic screening, genomic and biochemical methods. Methods: We analyzed femoral atherosclerotic plaque and five pairs of diseased and healthy arterial tissue for the presence of culturable bacteria using cell cultures and genomic analysis. Results: Gram negative aerobic bacilli were cultivated from the plaque tissue. Ribosomal 16S DNA amplification and sequencing identified the isolates as Enterobacter hormaechei. The isolate was resistant to ampicillin, cefazolin, and erythromycin. A circular 10kb plasmid was isolated from the strain. Antibiotic protection assays of the isolate demonstrated invasive ability in a human monocytic cell line. To extend the study, five matched pairs of diseased and healthy aortic tissue were analyzed via quantitative PCR. Eubacterial 16S rDNA was detected in all specimens, however, E. hormaechei DNA was detected in surprisingly high numbers in two of the diseased tissues only. Conclusions: While it is well documented that inflammation is an important risk factor for vascular pathophysiology, the association of bacteria with atherosclerosis has not been clearly established, in large part due to the inability to isolate live bacteria from atheromatous tissue. This is the first study providing direct evidence of Enterobacter spp. associated with atheromatous tissues. The data suggest that chronic infection with bacteria may be an under-reported etiologic factor in vascular pathogenesis. Importantly, characterization of the clinical isolate supports a model of atherogenesis where systemic dissemination of bacteria to atherosclerotic sites may occur via internalization in phagocytic cells. J Atheroscler Thromb, 2011; 18:72-81.

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“…While T-RFLP does often yield a higher number of OTUs when compared to DGGE, the disadvantage is that the PCR amplicons cannot be recovered and, hence, used to obtain taxonomic or phylogenetic information about the microbial community. While the above mentioned genetic fingerprinting techniques permit rapid analysis of numerous samples, they generate only superficial descriptions of microbial community compositions (Valinsky et al 2002).…”

Section: Terminal Restriction Fragment Length Polymorphismmentioning

confidence: 99%

Qualitative and quantitative methodologies for determination of airborne microorganisms at concentrated animal-feeding operations

Dungan

Leytem

2009

World J Microbiol Biotechnol

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The generation of airborne microorganisms from concentrated animal-feeding operations (CAFOs) is a concern from a human and animal health perspective. To better understand the airborne microorganisms found in these environments, a number of collection and analytical techniques have been utilized and will be discussed in this review. The most commonly used bioaerosol collection method is the liquid impingement format, which is suitable with a number of culture-based and non-culture molecularbased approaches, such as polymerase chain reaction. However, the vast majority of airborne microorganism studies conducted at CAFOs utilize culture-based analyses. Because of the limitations often associated with culturebased analyses, we focused our discussion on the application of molecular-based techniques to identify and/or quantify microorganisms, as they have promising application in bioaerosol research. The ability to rapidly characterize airborne microorganisms will help to ensure protection of public and environmental health.

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Analysis of Bacterial Community Composition by Oligonucleotide Fingerprinting of rRNA Genes

Cited by 120 publications

References 34 publications

Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

Cultivation of Enterobacter Hormaechei from Human Atherosclerotic Tissue

Qualitative and quantitative methodologies for determination of airborne microorganisms at concentrated animal-feeding operations

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