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Applied and Environmental Microbiology, July 2000, p. 2732-2742, Vol. 66, No. 7
Max-Planck-Institut für terrestrische
Mikrobiologie, D-35043 Marburg, Germany
Received 1 February 2000/Accepted 11 April 2000
The population dynamics of Archaea after flooding of an
Italian rice field soil were studied over 17 days. Anoxically incubated rice field soil slurries exhibited a typical sequence of reduction processes characterized by reduction of nitrate, Fe3+, and
sulfate prior to the initiation of methane production. Archaeal population dynamics were followed using a dual approach involving molecular sequence retrieval and fingerprinting of small-subunit (SSU)
rRNA genes. We retrieved archaeal sequences from four clone libraries
(30 each) constructed for different time points (days 0, 1, 8, and 17)
after flooding of the soil. The clones could be assigned to known
methanogens (i.e., Methanosarcinaceae,
Methanosaetaceae, Methanomicrobiaceae, and
Methanobacteriaceae) and to novel euryarchaeotal (rice
clusters I, II, and III) and crenarchaeotal (rice clusters IV and VI)
lineages previously detected in anoxic rice field soil and on rice
roots (R. Grosskopf, S. Stubner, and W. Liesack, Appl. Environ.
Microbiol. 64:4983-4989, 1998). During the initiation of
methanogenesis (days 0 to 17), we detected significant changes in the
frequency of individual clones, especially of those affiliated with the
Methanosaetaceae and Methanobacteriaceae.
However, these findings could not be confirmed by terminal restriction
fragment length polymorphism (T-RFLP) analysis of SSU rDNA amplicons.
Most likely, the fluctuations in sequence composition of clone
libraries resulted from cloning bias. Clonal SSU rRNA gene sequences
were used to define operational taxonomic units (OTUs) for T-RFLP
analysis, which were distinguished by group-specific TaqI
restriction sites. Sequence analysis showed a high degree of
conservation of TaqI restriction sites within the different
archaeal lineages present in Italian rice field soil. Direct T-RFLP
analysis of archaeal populations in rice field soil slurries revealed
the presence of all archaeal lineages detected by cloning with a
predominance of terminal restriction fragments characteristic of rice
cluster I (389 bp), Methanosaetaceae (280 bp), and
Methanosarcinaceae/rice cluster VI (182 bp). In general,
the relative gene frequency of most detected OTUs remained rather
constant over time during the first 17 days after flooding of the soil.
Most minor OTUs (e.g., Methanomicrobiaceae and rice cluster
III) and Methanosaetaceae did not change in relative
frequency. Rice cluster I (37 to 30%) and to a lesser extent rice
cluster IV as well as Methanobacteriaceae decreased over
time. Only the relative abundance of Methanosarcinaceae (182 bp) increased, roughly doubling from 15 to 29% of total archaeal gene frequency within the first 11 days, which was positively correlated to the dynamics of acetate and formate concentrations. Our
results indicate that a functionally dynamic ecosystem, a rice field
soil after flooding, was linked to a relatively stable archaeal
community structure.
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Archaeal Population Dynamics during Sequential
Reduction Processes in Rice Field Soil
*
Corresponding author. Mailing address:
Max-Planck-Institut für terrestrische Mikrobiologie,
Karl-von-Frisch Strasse, D-35043 Marburg, Germany. Phone: 49-6421-178 830. Fax: 49-6421-178 809. E-mail:
friedric{at}mailer.uni-marburg.de.
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