The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.
Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison with flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae and Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. On the contrary, members of soil crenarchaeotic group, mainly Candidatus Nitrososphaera, were higher in the rotational fields, possibly indicating increasing importance of ammonia oxidation during drainage. In contrast, minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields, whereas members of anaerobic Chloroflexi and sulfate-reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative polymerase chain reaction and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.
Background and aims Microorganisms colonize plant roots for mutual benefits. Colonization is initiated by the soil microbial community but is also affected by soil conditions and plant type. Rice typically grows under wetland conditions that are anoxic, thus being supportive for an anaerobic methanogenic microbial community. Maize, however, grows under upland conditions that are oxic, thus being supportive for an aerobic microbial community. Crop rotation between wetland rice and upland maize is not uncommon, but the effect of this management on microbial colonization of plant roots is largely unknown and was the aim of our study. Methods We used the roots of rice and maize from a two-year study in the Philippines, where on the same soil wetland rice was cultivated either in both wet and dry season or was rotated with upland maize in the dry season. The microbial colonization of the root ecto-and endorhizosphere was assessed by using quantitative PCR and illumina sequencing of the bacterial and archaeal 16S rRNA genes. Results The data showed that maize roots had completely different microbial community structures than the rice roots from continuous wetland cultivation, while rice roots from crop rotation were in-between. These effects of management were seen for each of the different bacterial phyla. For example, among the most abundant operational taxonomic units (OTUs) Firmicutes, Deltaproteobacteria and the methanogenic Methanocella spp. were less abundant while Alphaproteobacteria and the methanogenic Methanobacterium spp. were more abundant on maize than on rice roots. Conclusions Our study showed that root colonization by Archaea and Bacteria was strongly affected by crop rotation between wetland rice and upland maize.
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