Abstract
Because excised, washed roots of rice (Oryza sativa) immediately produce CH4 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.
Abstract from the paper’s OpenAlex record, shown for indexing and research. Copyright remains with the authors or the publisher. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 8
Claim · model-written summary
Ten of 32 rice root archaeal sequences affiliated with known methanogens, split between Methanosarcina and Methanobacterium.
- Taxon
- Rice
Oryza sativat0 - Organ / stage
- Rootst0
- Interactor
- Methanosarcina spp.
Methanosarcinae0symbiont - Outcome
- 10 of the environmental sequences were affiliated with known methanogense0
- Value
- 10e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Only 10 of the environmental sequences were affiliated with known methanogens; 5 were affiliated with Methanosarcina spp., and 5 were affiliated with Methanobacterium spp.”
t0“Rice Roots”
Claim · model-written summary
Twenty-two rice root archaeal clones formed four lineages distant from known cultured Archaea.
- Taxon
- RiceOryza sativat0
- Outcome
- 22 ARR gene clones formed four distinct lineagese0
- Value
- 22e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
t0“Rice Roots”
Claim · model-written summary
Rice clusters I and II formed distinct clades within Methanosarcinales and Methanomicrobiales.
- Taxon
- RiceOryza sativat0
- Outcome
- Rice clusters I and II formed distinct cladese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rice clusters I and II formed distinct clades within the phylogenetic radiation of the orders "Methanosarcinales" and Methanomicrobiales”
t0“Rice Roots”
Claim · model-written summary
Rice cluster I was novel, whereas cluster II closely affiliated with bog peat sequences.
- Taxon
- RiceOryza sativat0
- Outcome
- Rice cluster I was novel, and rice cluster II was closely affiliated with environmental sequencese0
- Setting
- northern Englande0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rice cluster I was novel, and rice cluster II was closely affiliated with environmental sequences obtained from bog peat in northern England”
t0“Rice Roots”
Claim · model-written summary
Rice cluster III shared a branch with Thermoplasma acidophilum and marine group II but was distantly related.
- Taxon
- RiceOryza sativat0
- Interactor
- Thermoplasma acidophilumThermoplasma acidophilume0other
- Outcome
- Rice cluster III occurred on the same branch as Thermoplasma acidophilum and marine group II but was only distantly related to these taxae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rice cluster III occurred on the same branch as Thermoplasma acidophilum and marine group II but was only distantly related to these taxa”
t0“Rice Roots”
Claim · model-written summary
Rice cluster IV was a deep branching crenarchaeotal assemblage related to marsh clone pGrfC26.
- Taxon
- RiceOryza sativat0
- Outcome
- Rice cluster IV was a deep-branching crenarchaeotal assemblage that was closely related to clone pGrfC26e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
t0“Rice Roots”
Claim · model-written summary
Viable Archaea were detected on rice root surfaces by fluorescent in situ hybridization.
- Taxon
- riceOryza sativae0
- Organ / stage
- rootse0
- Outcome
- viable members of the Archaea were present on the surfaces of rice rootse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“viable members of the Archaea were present on the surfaces of rice roots”
Claim · model-written summary
A novel euryarchaeotal rice cluster V was detected in anoxic rice paddy soil.
- Taxon
- riceOryza sativae0
- Outcome
- rice cluster V, which was detected in anoxic rice paddy soile0
- Setting
- rice paddy soile0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a novel euryarchaeotal main line of descent, designated rice cluster V, which was detected in anoxic rice paddy soil”