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  Succession of bacterial community structure and diversity in a paddy soil oxygen gradient

Noll, M., Matthies, D., Frenzel, P., Derakshani, M., & Liesack, W. (2005). Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environmental Microbiology, 7(3), 382-395. doi:10.1111/j.1462-2920.2005.00700.x.

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 Creators:
Noll, M.1, Author           
Matthies, D., Author
Frenzel, P.1, Author           
Derakshani, M.1, Author           
Liesack, W.2, Author           
Affiliations:
1Department of Biogeochemistry, Alumni, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266312              
2Department-Independent Research Group Methanotrophic Bacteria, and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266274              

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Free keywords: OXIDIZING BACTERIA; RICE PADDIES; GEN. NOV.; COMB-NOV; WATER; METHANE; HYBRIDIZATION; ENVIRONMENT; POPULATIONS; INTERFACE
 Abstract: Cultivation-independent techniques were applied to assess the succession and phylogenetic composition of bacterial communities in a vertical oxygen gradient in flooded, unplanted paddy soil microcosms. Microsensor measurements showed that within 6 h of flooding, oxygen was depleted from 200 microM at the floodwater-soil interface to undetectable amounts at a depth of approximately 2 mm and below. The gradient was quite stable over time, although the oxygen depletion was less pronounced 84 days than 6 h after flooding. Community fingerprint patterns were obtained by terminal restriction fragment length polymorphism (T-RFLP) analysis from the oxic, transition, and anoxic zones of triplicate soil microcosms at 0, 1 and 6 h, and 1, 2, 7, 21, 30, 42, 84, and 168 days after flooding. Correspondence analyses revealed that T-RFLP patterns obtained using either community DNA or RNA were affected by time and oxygen zone, and that there was a significant interaction between the effects of time and oxygen zone. The temporal dynamics of bacterial populations were resolved more clearly using RNA than using DNA. At the RNA level, successional community dynamics were most pronounced from 1 h to 2 days and less pronounced from 2 to 21 days after flooding, for both oxic and anoxic zones. No effect of time or oxygen zone on the community dynamics was observed from 21 to 168 days after flooding. Dominant early successional populations were identified by cloning and comparative sequence analysis of environmental 16S rRNA and 16S rRNA genes as members of the Betaproteobacteria (oxic zone) and the clostridial cluster I (anoxic zone). Dominant late successional populations belonged to the Verrucomicrobia and Nitrospira (detected mainly in the oxic zone), and to the Myxococcales (detected mainly in the anoxic zone). In conclusion, the bacterial community developed through successional stages, leading at the RNA level to almost stable community patterns within 21 days after flooding. This principal finding, in combination with the phylogenetic identity of early- and late-appearing populations, suggests that the community dynamics can be explained by the principles of r- and K-selection.

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Language(s): eng - English
 Dates: 2005-03
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: eDoc: 213698
DOI: 10.1111/j.1462-2920.2005.00700.x
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Title: Environmental Microbiology
Source Genre: Journal
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Pages: - Volume / Issue: 7 (3) Sequence Number: - Start / End Page: 382 - 395 Identifier: -