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  Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms

Grosskopf, R., Stubner, S., & Liesack, W. (1998). Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 64(12), 4983-4989. doi:10.1128/AEM.64.12.4983-4989.1998.

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Grosskopf, R1, Autor
Stubner, S.2, Autor           
Liesack, W3, Autor                 
Affiliations:
1external, ou_persistent22              
2Department of Biogeochemistry, Alumni, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266312              
3Department-Independent Research Group Methanotrophic Bacteria, and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266274              

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 Zusammenfassung: Because excised, washed roots of rice (Oryza sativa) immediately produce CH(4) when they are incubated under anoxic conditions (P. Frenzel and U. Bosse, FEMS Microbiol. Ecol, 21:25-36, 1996), we employed a culture-independent molecular approach to identify the methanogenic microbial community present on roots of rice plants. Archaeal small-subunit rRNA-encoding genes were amplified directly from total root DNA by PCR and then cloned. Thirty-two archaeal rice root (ARR) gene clones were randomly selected, and the amplified primary structures of ca, 750 nucleotide sequence positions were compared. Only 10 of the environmental sequences were affiliated with known methanogens; 5 were affiliated with Methanosarcina spp., and 5 were affiliated with Methanobacterium spp. The remaining 22 ARR gene clones formed four distinct lineages (rice clusters I through IV) which were not closely related to any known cultured member of the Archaea, Rice clusters I and II formed distinct clades within the phylogenetic radiation of the orders "Methanosarcinales" and Methanomicrobiales. Rice cluster I was novel, and rice cluster II was closely affiliated with environmental sequences obtained from bog peat in northern England. Rice cluster III occurred on the same branch as Thermoplasma acidophilum and marine group II but was only distantly related to these taxa, Rice cluster IV was a deep-branching crenarchaeotal assemblage that was closely related to clone pGrfC26, an environmental sequence recovered from a temperate marsh environment. The use of a domain-specific oligonucleotide probe in a fluorescent in situ hybridization analysis revealed that viable members of the Archaea were present on the surfaces of rice roots. In addition, we describe a novel euryarchaeotal main line of descent, designated rice cluster V, which was detected in anoxic rice paddy soil. These results indicate that there is an astonishing richness of archaeal diversity present on rice roots and in the surrounding paddy soil.

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 Datum: 1998
 Publikationsstatus: Erschienen
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 Art der Begutachtung: Expertenbegutachtung
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Titel: APPLIED AND ENVIRONMENTAL MICROBIOLOGY
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 64 (12) Artikelnummer: - Start- / Endseite: 4983 - 4989 Identifikator: ISSN: 0099-2240