Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

Abstract

Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a ␥-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G؉C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH 4 ؉ was lower and the level of extractable SO 4 2؊ was higher without protists, indicating that nitrogen mineralization and SO 4 2؊ reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O 2 was a major control, and O 2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.

Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana

“…A. castellanii most strongly affected the diversity of Betaproteobacteria (DGGE) whereas decreasing their relative abundance (FISH). Betaproteobacteria in particular seem less grazing tolerant to protozoa than other soil bacterial groups as corresponding findings by Kreuzer et al (2006) and Murase et al (2006) indicate. For example, Variovorax sp., a member of the Comamonadaceae (Betaproteobacteria) had virtually disappeared 2 days after the addition of the protozoan grazers, demonstrating that not all Comamonadaceae are as grazing resistant as reported from aquatic systems (Hahn and Hö fle, 1998;Matz and Kjelleberg, 2005).…”

“…FISH analyses further showed a relative decrease of Alphaproteobacteria and Firmicutes, but an increase of Actinobacteria. The results for Firmicutes are surprising because Gram-positive bacteria are believed to be less preferred by protozoa due to their protective cell wall and have been shown to benefit from protozoan grazing (Griffiths et al, 1999;Rønn et al, 2002;Murase et al, 2006).…”

“…Protozoa and bacteria form one of the oldest predator-prey systems on earth, but apart from reports on phenotypic changes (Jü rgens and Matz, 2002;Pernthaler, 2005) surprisingly little is known on the factors driving grazing resistance (Matz and Kjelleberg, 2005) and on the identity of bacterial groups that are consumed and those that survive protozoan grazing in the rhizosphere and soils (Griffiths et al, 1999;Rønn et al, 2002;Kreuzer et al, 2006;Murase et al, 2006). Roughly estimated, 1 g of grassland soil may contain up to 10 9 bacteria and 100 000 protozoa (Finlay et al, 2000).…”

Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

“…Since that time, additional nonculture-based studies describing eukaryotic diversity in a variety of ecological settings have emerged. Among these habitats are: a multipond saltern (Casamayor et al, 2002), rice soil (Murase et al, 2006), an anoxic Norwegian fjord (Behnke et al, 2006), Mediterranean sea water (Diez et al, 2001), a sulfide-rich freshwater spring (Luo et al, 2005), a seafloor hydrothermal vent field (Ló pez- García et al, 2007) and an anaerobic aquifer polluted with landfill leachate (Brad et al, 2008). The latter study, most relevant to data presented here, used Eukarya-specific PCR primers (Diez et al, 2001) to amplify 18S rRNA genes and analyze them through denaturing gradient gel electrophoresis profiling and sequence analysis.…”

One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic–anoxic interface in a flooded paddy soil

“…When methane was supplied from below and air was supplied from above, a functioning methanotrophic community developed within a few days, oxidizing virtually all the methane that otherwise would have passed through this soil layer. We used cryosectioning (Murase et al, 2006) to subsample the soil from top to bottom in 100-mm steps. Focusing on pmoA as a functional and phylogenetic marker, we analyzed genes and transcripts along this depth profile, using pmoA transcripts as a proxy for species-specific activity.…”