basic program for reduction of data from community-level physiological profiling using Biolog microplates: rationale and critical interpretation of data

O'Connell, Sean P.; Lawson, Robert D.; Watwood, Mary E.; Lehman, R. Michael

doi:10.1016/s0167-7012(00)00128-7

Cited by 17 publications

(7 citation statements)

References 15 publications

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“…The first principal component contains the most variance present in the original data set, and each subsequent factor contains successively less of this original variance; the amount of variance associated with a factor is its eigenvalue. By using backgroundcorrected microplate readings at equivalent average well color development (14,15,42), PCA was performed on the correlation matrix of the variables (R matrix) with no factor rotation. Each sample possesses a score on each of the new factors (factor score) which can be plotted in factor space (factor score plot).…”

Section: Methodsmentioning

confidence: 99%

Attached and Unattached Microbial Communities in a Simulated Basalt Aquifer under Fracture- and Porous-Flow Conditions

Lehman

Colwell

Bala

2001

Appl Environ Microbiol

123

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Bench scale column studies were used to examine the partitioning of microorganisms between groundwater and a geologic medium and to examine the effect of hydrogeology (i.e., porous-versus fracture-flow) on organism partitioning. Replicated columns were constructed with intact basalt core segments that contained natural fractures and with the same basalt crushed into particles. The columns were perfused with groundwater, and upon reaching a steady state, the columns were sacrificed and the attached and unattached communities were analyzed by multiple approaches. The analyses included the total number of cells, the phylogenetic affiliation of the cells (i.e., the ␣, ␤, and ␥ subclasses of the class Proteobacteria and gram positives with high G؉C DNA content) by fluorescent in situ hybridization (FISH), number and taxonomic affiliation by fatty acid methyl ester profiles of culturable heterotrophs, most-probable-number estimates of methanotrophs and phenol oxidizers, and whole-community sole carbon source utilization patterns from Biolog GN microplates. In the packed columns, about 99% of the total biomass (per cubic centimeter of porous medium) was attached to the geologic medium. Lack of equitable units precluded a comparison of attached and unattached biomasses in the fractured columns where the attached biomass was expressed per unit of surface area. Compositional differences in the attached and unattached communities were evidenced by (i) the recovery of Pseudomonas stutzeri, an Enterococcus sp., and Bacillus psychrophilus from the groundwater and not from the basalt, (ii) differences between community carbon source utilization patterns, and (iii) the relative abundances of different phylogenetic groups estimated by FISH in both column types. In the packed columns, attached communities were depleted of members of the ␣-and ␤-Proteobacteria subclasses in comparison to those in the corresponding groundwater. In the fractured columns, attached communities were enriched in gram-positive Bacteria and ␥-Proteobacteria and depleted of ␤-Proteobacteria, in comparison to those in the corresponding groundwater. Segregation of populations and their activities, possibly modified by attachment to geologic media, may influence contaminant fate and transport in the subsurface and impact other in situ applications.Although the presence of microbes in both geologic media and groundwaters is undisputed (44), little work has described the partitioning of populations and activities between communities that colonize geologic media and those that exist planktonically in groundwaters. Clearly, the relative mobility of the microorganisms (i.e., attached or unattached) would have a great influence on processes related to subsurface contaminant fate and transport (29, 57), the stability of geologic radioactive waste repositories (45), microbially enhanced oil recovery, and solution mining. For example, consider the strategies required to deliver a substrate or nutrient to an attached organism versus a planktonic organism that might be ...

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Section: Methodsmentioning

confidence: 99%

Attached and Unattached Microbial Communities in a Simulated Basalt Aquifer under Fracture- and Porous-Flow Conditions

Lehman

Colwell

Bala

2001

Appl Environ Microbiol

123

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“…The Biolog R GN plates tend to select for copiotrophic, fast-growing bacteria that are not inhibited by tetrazolium salt (O'Connell et al, 2000). Thus, the metabolic signature is generated by a fraction of the original community (at best viable and cultivable).…”

Section: Plate Count Of Microbial Populations and Their Catabolic Promentioning

confidence: 99%

“…Thus, the metabolic signature is generated by a fraction of the original community (at best viable and cultivable). Since this fraction is considered to be reproducible (O'Connell et al, 2000), the Biolog R system was used in this study in a comparative manner to reveal distinct metabolic abilities between microbial communities harbored by the rhizosphere of the hyperaccumulator T. caerulescens and the bulk soil. Modification of microbial community structures as a consequence of modification of substrate availability has already been mentioned.…”

Section: Plate Count Of Microbial Populations and Their Catabolic Promentioning

confidence: 99%

Soil Microbial Diversity as Affected by the Rhizosphere of the Hyperaccumulator Thlaspi Caerulescens Under Natural Conditions

Aboudrar

Schwartz

Benizri³

et al. 2007

International Journal of Phytoremediation

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It is hypothesized that metal hyperaccumulator plants have specific rhizosphere conditions, potentially modifying the bioavailability of soil metals. This article aims to further the knowledge about the rhizosphere of the hyperaccumulator Thlaspi caerulescens, focusing on its microflora isolated from metalliferous soils collected in situ where the plants grow naturally. We characterized the cultivable microbial communities isolated from the rhizosphere of one population of this Ni hyperaccumulator species grown on a serpentine soil. The rhizosphere soil harbored a wide variety of microorganisms, predominantly bacteria, confirming the stimulatory effect of the T. caerulescens rhizosphere on microbial growth and proliferation. We tested the hypothesis that the rhizosphere of T. caerulescens influences (1) the metabolic diversity of the bacterial community and (2) the bacterial resistance to metals. The principal component analysis of the Biolog plate's data confirmed a structural effect of the rhizosphere of T. caerulescens on bacterial communities. The percentage of Ni-resistant bacteria was higher in the rhizosphere than in the bulk soil, suggesting a direct effect of the rhizosphere on Ni tolerance, reflecting a greater bacterial tolerance to Ni in the rhizosphere.

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“…The cultivation and taxonomic skills are not sufficient to identify such a great diversity of pathogens infecting the hosts. Thus the traditional phenotype systems are necessary to complement with multiple analytical techniques [1][2][3][4] for the rapid identification of pathogens. Nevertheless, the results of microbial genotyping should always be analyzed in the light of clinical and epidemiological data, especially when evaluating novel genotyping methods.…”

Section: Introductionmentioning

confidence: 99%

Electromigration techniques – a fast and economical tool for differentiation of similar strains of microorganisms

Horká

Horký

Kubešová

et al. 2010

Analyst

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The detection and identification of pathogens currently relies upon a very diverse range of techniques and skills, from traditional cultivation and taxonomic procedures to modern rapid and sensitive diagnostic methods. Real-time PCR is now exploited as a front line diagnostic screening tool in human, animal and plant health as well as bio-security. Nevertheless, new techniques for pathogen identification, particularly of unknown samples, are needed. In this study we propose the combination of electrophoresis-based procedures for the fast differentiation of microorganisms. The method feasibility is proved on the model of seven similar strains of Pseudomonas syringae pathovars from 37 sources, identified by gas chromatography of fatty acid methyl esters. The results from the routine laboratory were compared with results of the combination of the developed capillary and gel electrophoresis as well as mass spectrometry. According to our experiments appropriate combination of electromigration techniques appears to be useful for the fast and economical differentiation of unknown microorganisms.

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basic program for reduction of data from community-level physiological profiling using Biolog microplates: rationale and critical interpretation of data

Cited by 17 publications

References 15 publications

Attached and Unattached Microbial Communities in a Simulated Basalt Aquifer under Fracture- and Porous-Flow Conditions

Attached and Unattached Microbial Communities in a Simulated Basalt Aquifer under Fracture- and Porous-Flow Conditions

Soil Microbial Diversity as Affected by the Rhizosphere of the Hyperaccumulator Thlaspi Caerulescens Under Natural Conditions

Electromigration techniques – a fast and economical tool for differentiation of similar strains of microorganisms

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