Microarrays: Applications in Environmental Microbiology

Zhou, Jizhong; Thompson, Danielle

doi:10.1002/0471263397.env010

Cited by 5 publications

(5 citation statements)

References 77 publications

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“…On the basis of the types of probes arrayed, microarrays used in environmental studies can be divided into three major classes (7); namely, functional gene arrays, community genome arrays, and phylogenetic oligonucleotide arrays. Functional gene arrays contain genes encoding key enzymes involved in various ecological processes such as carbon fixation, nitrification, denitrification, and sulfate reduction.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples

et al. 2004

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Microarrays fabricated with oligonucleotides longer than 40 bp have been introduced for monitoring whole genome expression but have not been evaluated with environmental samples. To determine the potential of this type of microarray for environmental studies, a 50-mer oligonucleotide microarray was constructed using 763 genes involved in nitrogen cycling: nitrite reductase (nirS and nirK), ammonia monooxygenase (amoA), nitrogenase (nifH), methane monooxygenase (pmoA), and sulfite reductase (dsrAB) from public databases and our own sequence collections. The comparison of the sequences from pure cultures indicated that the developed microarrays could provide species-level resolution for analyzing microorganisms involved in nitrification, denitrification, nitrogen fixation, methane oxidation, and sulfite reduction. Sensitivity tests suggested that the 50-mer oligonucleotide arrays could detect dominant populations in the environments, although sensitivity still needs to be improved. A significant quantitative relationship was also obtained with a mixture of DNAs from eight different bacteria. These results suggest that the 50-mer oligonucleotide array can be used as a specific and quantitative parallel tool for the detection of microbial populations in environmental samples.

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Section: Introductionmentioning

confidence: 99%

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples

et al. 2004

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“…For example, when the pH value was 5, the degradation rate was 72%. With the consequent in the redox electric potential, the logarithmic growth phase of strain MG was shortened (Zhou and Wang, 2011). So the optimal pH value for strain MG growth ranged from 6 to 7.…”

Section: Resultsmentioning

confidence: 99%

“…Six different inoculation volumes (0, 10, 20, 30, 40 and 50 mL of strain MG incubation solution (biomass concentration: 1.5 3 10 9 cellsÁm/L) were examined with the other conditions as follows: nitrobenzene concentration, 600 lg/L; pH, 7.0 6 0.1. The optimum pH for most bacterial growth is 6.5 to 7.5 (Zhou and Wang, 2011); degradation time, 160 h.…”

Section: Methodsmentioning

confidence: 99%

Screening and Degradation Mechanism of a Cold‐Resistant Nitrobenzene‐Degrading Microorganism

Qiu

Wang

2017

Water Environment Research

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A cold-resistant nitrobenzene-degrading strain was screened from river sediment. The strain was identified as Methylobacillus glycogens, which has never been reported to be capable of degrading nitrobenzene. The degradation rates of 900 μg/L nitrobenzene reached respectively 99.3% and 88.6% in 144 h under both aerobic and anaerobic environments (30 mL inoculation volume at 12 ± 0.5 °C and pH7.0 ± 0.1). When aerobically degraded, nitrobenzene was firstly oxidized into o-nitrophenol, which was further oxidized into 1,2-benzenediol, meanwhile releasing NO2-. Then the 1,2-benzenediol was metabolized through either the ortho-cleavage into succinic acid and acetyl-CoA, or meta-cleavage into pyruvic acid and acetaldehyde, as well as other small molecule substances of non-toxicity or low-toxicity, which were finally decomposed into CO2 and H2O. When anaerobically degraded, nitrobenzene was firstly degraded into aniline (C6H5NH2), which was further degraded into 4-amino benzoic acid. The benzoic acid was degraded into benzoyl, which was finally metabolized and decomposed.

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“…Several sources are available that provide more information regarding image preprocessing and analysis (13,62,63).…”

Section: Notes On Hybridizationmentioning

confidence: 99%

Functional Gene Arrays for Analysis of Microbial Communities on Ocean Platform

McKindles

Tiquia-Arashiro

2012

Springer Protocols Handbooks

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Recently there has been an increased use of microarray technology as a tool to determine the presence of functional genes in a population of hard to culture communities (e.g., soil, extreme environments). A functional gene array (FGA), or GeoChip, uses probes to screen for specific functional genes vital in biological systems such as nitrogen and carbon cycling, and has even been expanded to include aquatic conditions. However, the time delay from when the sample is taken from the ocean to evaluating the test results back in the lab still posed a problem. The Environmental Sample Processor (ESP) minimizes this time difference by housing a robotic system placed in the ocean for a long period of time that can collect a small sample, concentrate the DNA, run a microarray, and take a picture of the array before sending the data ashore to be evaluated by a researcher. The included protocol and reagents list goes through both lab microarray procedures as well as the procedures list for the ESP, which briefly mentions deployment and data acquisition. The protocols described here should advance applications in microbial oceanography using robotic instrumentation.

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Microarrays: Applications in Environmental Microbiology

Abstract: Microarray Basics Using Microarrays to Monitor Gene Expression Applications of Microarrays for Microbial Detection in Natural Environments

Cited by 5 publications

References 77 publications

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples

Screening and Degradation Mechanism of a Cold‐Resistant Nitrobenzene‐Degrading Microorganism

Functional Gene Arrays for Analysis of Microbial Communities on Ocean Platform

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