Diversity of Transcripts of Nitrite Reductase Genes (nirK and nirS) in Rhizospheres of Grain Legumes

• Published in: Applied and Environmental Microbiology Vol. 71; no. 4; pp. 2001 - 2007
• Main Authors: Sharma, Shilpi, Aneja, Manish Kumar, Mayer, Jochen, Munch, Jean Charles, Schloter, Michael
• Format: Journal Article
• Language: English
• Published: Washington, DC American Society for Microbiology 01.04.2005
• Subjects: Bacteria; Bacteria - classification; Bacteria - enzymology; Bacteria - genetics; Bacteriology; Biological and medical sciences; Cloning, Molecular; Comparative analysis; denitrifying bacteria; Electrophoresis - methods; faba beans; Fabaceae - enzymology; Fabaceae - genetics; Fundamental and applied biological sciences. Psychology; Gene expression; genes; Genetic Variation; Genetics; Legumes; Lupinus; Lupinus - enzymology; Lupinus - genetics; Lupinus albus; messenger RNA; Microbial Ecology; Microbiology; Molecular Sequence Data; nirK gene; nirS gene; nitrite reductase; Nitrite Reductases - genetics; Nitrite Reductases - metabolism; nucleotide sequences; peas; Pisum; Pisum sativum; Pisum sativum - enzymology; Pisum sativum - genetics; Plant Roots - microbiology; Quantitative genetics; restriction fragment length polymorphism; reverse transcriptase polymerase chain reaction; rhizosphere; Sequence Analysis, DNA; soil bacteria; Soil Microbiology; Transcription, Genetic; Vicia faba; Vicia faba - enzymology; Vicia faba - genetics; Transcription; Enzyme; Nitrite reductase; Genetic diversity; Vicia faba; Grain legume; Rhizosphere; Messenger RNA; Leguminosae; Gene; Dicotyledones; Pisum sativum; Angiospermae; Bacteria; Lupinus albus; Spermatophyta; Oxidoreductases
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.71.4.2001-2007.2005

Transcription of the nirK and nirS genes coding for dissimilatory bacterial nitrite reductases was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from rhizosphere samples of three economically important grain legumes at maturity: Vicia faba, Lupinus albus, and Pisum sativum. The nirK gene and transcripts could be detected in all the rhizosphere samples. In contrast, nirS could not be detected. Sampling variations were analyzed by comparing denaturing gradient gel electrophoresis profiles derived from nirK RT-PCR products. High similarity was observed between the replicates, and so one representative product per legume was cloned. Clones with the correct insert size were screened by restriction fragment length polymorphism by using the restriction enzyme MspI. The clones could be distributed into 12 different patterns. Patterns 1, 3, 4, 5, and 7 were common in clone libraries of the three rhizosphere types under study. Patterns 2, 9, 10, and 11 were absent from Pisum rhizospheres, while patterns 6, 8, and 12 were absent from the Vicia library. Pattern 1, which was the most dominant in the Vicia and Lupinus libraries, constituted about 25% of all clones. The Lupinus library had clones representing all 12 patterns, indicating it to be the most diverse among the three. Clones representative of each pattern were sequenced. All patterns grouped together forming a distinct cluster, which was divergent from previously described nirK sequences in the database. The study revealed a hitherto unknown diversity of denitrifiers in legume rhizospheres. A plant-dependent rhizosphere effect on the transcripts of a gene was evident.