Biomedical subjects

Jeffrey S Buyer

Publications and source records attributed to Jeffrey S Buyer.

9 recordsLinked to original sources

PubMed2006

Rapid and sensitive FAME analysis of bacteria by cold trap injection gas chromatography.

Whole cell fatty acid analysis is commonly used to identify bacteria. A cold trap, using a commercially available device that directs a stream of compressed air across a section of the GC column, is used to focus peaks at the head of the column. When combined with a rapid sample processing method that uses smaller volumes of solvents, it becomes possible to correctly identify bacteria from 1 to 2 mg of biomass.

Bacteria↗

PubMed2006

A mutation in an exbD gene reduces tagetitoxin production by Pseudomonas syringae pv. tagetis.

A mutant of Pseudomonas syringae pv. tagetis EB037 with limited ability to produce tagetitoxin was isolated after transposon mutagenesis and the mutation was characterized. The mutation occurred in a gene with a high degree of sequence identity to exbD. exbD is contiguous with tonB and exbB upstream and with a gene for a TonB-dependent receptor downstream. Using reverse transcription - polymerase chain reaction with RNA from the wild-type and exbD mutant strains, we demonstrated that the mutation in exbD did not have a polar affect on the expression of downstream genes. The exbD mutant was able to grow well in conditions where iron is not freely available. Siderophore production by the exbD mutant was similar to that of the wild-type strain. We conclude that the mutation in exbD disrupts tagetitoxin production without compromising iron metabolism. The results indicate that tagetitoxin export by P. syringae pv. tagetis involves an efflux pump that requires a functional TonB system that is not essential for normal iron metabolism.

Bacterial Proteins↗

PubMed2005

Endophytic bacteria in Coffea arabica L.

Eighty-seven culturable endophytic bacterial isolates in 19 genera were obtained from coffee plants collected in Colombia (n = 67), Hawaii (n = 17), and Mexico (n = 3). Both Gram positive and Gram negative bacteria were isolated, with a greater percentage (68%) being Gram negative. Tissues yielding bacterial endophytes included adult plant leaves, various parts of the berry (e.g., crown, pulp, peduncle and seed), and leaves, stems, and roots of seedlings. Some of the bacteria also occurred as epiphytes. The highest number of bacteria among the berry tissues sampled was isolated from the seed, and includes Bacillus , Burkholderia , Clavibacter , Curtobacterium , Escherichia , Micrococcus , Pantoea , Pseudomonas , Serratia , and Stenotrophomonas . This is the first survey of the endophytic bacteria diversity in various coffee tissues, and the first study reporting endophytic bacteria in coffee seeds. The possible role for these bacteria in the biology of the coffee plant remains unknown.

Coffea↗

PubMed2005

Phylum- and class-specific PCR primers for general microbial community analysis.

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening. The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups. Primers specific for the 16S ribosomal sequences of Alphaproteobacteria, Betaproteobacteria, Bacilli, Actinobacteria, and Planctomycetes and for parts of both the 18S ribosomal sequence and the internal transcribed spacer region of Basidiomycota were examined. Primers were tested by comparison to sequences in the ARB 2003 database, and chosen primers were further tested by cloning and sequencing from soil community DNA. Eighty-five to 100% of the sequences obtained from clone libraries were found to be placed with the groups intended as targets, demonstrating the specificity of the primers under field conditions. It will be important to reevaluate primers over time because of the continual growth of sequence databases and revision of microbial taxonomy.

Bacteria↗

PubMed2003

Improved fast gas chromatography for FAME analysis of bacteria.

Bacteria are frequently identified by fatty acid analysis. We previously reported on methods to speed up sample preparation and gas chromatography, resulting in greatly improved speed and throughput [J. Microbiol. Methods 51 (2002) 209]. In this paper, we demonstrate that further reductions in chromatographic retention times are readily achieved, leading to faster identification of bacteria.

Bacteria↗

PubMed2002

Identification of bacteria from single colonies by fatty acid analysis.

While a commercially available system for microbial identification by fatty acid analysis (Microbial Identification System, MIDI, Newark, DE, USA) is available, it requires approximately 40-mg wet weight of biomass. Various authors have published methods for fatty acid analysis of single colonies, but no database of organisms has been developed for those methods. A modification of the MIDI system to increase sensitivity while maintaining relative retention times and peak areas allows the standard peak naming tables and libraries of organisms to be used with single colonies. Samples are evaporated down before injection to concentrate the fatty acids, while splitless injection is used to allow more sample to enter the gas chromatograph. Several known bacteria were correctly identified by this method.

Bacteria↗

PubMed2002

Rapid sample processing and fast gas chromatography for identification of bacteria by fatty acid analysis.

A commercially available system for microbial identification by fatty acid analysis (Microbial Identification System (MIS), MIDI, Newark, DE, USA) requires a four-step sample derivatization procedure in screw-cap test tubes. By using glass tubes in a 96-well format with multichannel pipetting, the time required for sample preparation can be greatly reduced. The standard gas chromatography column, 25 m long by 0.20 mm ID, is replaced with a 10 m long by 0.10 mm ID column, reducing the gas chromatography run time to one third of the standard time. Either or both of these procedures can be easily implemented in any laboratory using the MIDI system, resulting in faster identifications and higher sample throughput.

Bacteria↗

PubMed2002

Soil and plant effects on microbial community structure.

We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.

Bacteria↗

PubMedDate not supplied

Soil microbial communities associated with Bt and non-Bt corn in three soils.

The effects of expression of Cry endotoxin by Bt corn (transgenic corn engineered to express Bacillus thuringiensis toxin) on soil microbial community structure were assessed in a growth chamber experiment. Two lines of transgenic corn expressing different Cry endotoxins were compared with their respective non-transgenic isolines in three soil types with differing textures. Phospholipid fatty acid (PLFA) profiles from bulk soil and community-level physiological profiles (CLPP) from the rhizosphere community were used to assess community structure. Differences in PLFA profiles due to soil type were significant, accounting for 73% of the total variability in the dataset. Differences in bacterial and fungal CLPP profiles due to soil type were statistically significant, but probably not biologically important, accounting for 6.3 and 3.8% of the total variability, respectively. Neither expression of Cry endotoxin nor corn line had a significant effect on microbial profiles, except in the high-clay soil where both factors significantly affected bacterial CLPP profiles (accounting for 6.6 and 6.1% of the variability in that soil, respectively). Expression of Cry endotoxin also significantly reduced the presence of eukaryotic PLFA biomarker in bulk soils, although it is unclear which groups of eukaryotes were affected. We conclude that the effects of transgenic Bt corn in this short-term experiment are small, and longer-term investigations are necessary.

Aluminum Silicates↗