Rice plants, drainage and crop rotation influence the methanogenic community in rice field soil
The continuous flooding of rice fields results in anoxic conditions in the soil, creating an optimal habitat for anaerobic bacteria and methanogenic archaea. Furthermore, rice plants supply important nutrients for soil microbes by significantly contributing to the carbon pool by excreting carbon com...
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|Summary:||The continuous flooding of rice fields results in anoxic conditions in the soil, creating an optimal habitat for anaerobic bacteria and methanogenic archaea. Furthermore, rice plants supply important nutrients for soil microbes by significantly contributing to the carbon pool by excreting carbon compounds through their root system. It is assumed that this supply of nutrients from the rice plants influences the microbial community structure and diversity, but this influence is poorly understood.
The first part of this thesis investigates the impact of the rice plant and its growth stages on the microbial community inhabiting flooded rice field soil. In a greenhouse experiment we showed that the presence of the rice plant leads to increased growth of both Archaea and Bacteria by detecting a doubling of the 16S rRNA gene copies. The overall microbial community composition was mainly similar in planted and unplanted soil. However, specific bacterial lineages were more abundant in the presence of the rice plant (e.g Geobacter). In the planted soil major OTUs increased in relative abundance with plant growth stage, indicating that the rice growth stages and dynamics in root exudation influenced the microbial community. Together, these results suggest that the microbial community in the rice field soil is highly adapted to the presence of rice plants, possibly because of the plant-supplied carbon compounds in the soil.
The traditional method for rice cultivation is the flooding of the field. However, with the anticipated increase in the human population the demand on resources such as water will increase. Therefore, rice farmers will probably face periods of restricted water availability. A method decreasing the water demand of rice cultivation is the rotation with plants cultivated under upland conditions such as maize, which require less water. Therefore, the second part of this thesis deals with the influence of the rice plant growth stages, field conditions and maize cultivation on the microbial community in rice field soil. During the plant growth stages we detected only minor changes in abundance, composition and activity of both archaeal and bacterial communities. In contrast, changes in field management such as drainage and the cultivation of maize resulted in comparatively stronger changes in the bacterial community. Bacterial lineages that increased in relative abundance under non-flooded conditions were either aerobes such as Spartobacteria and Sphingobacteria or were characterized by their ability to grow under low substrate conditions such as Bacteroidetes and Acidobacteria. Besides archaeal lineages commonly found in rice fields (Methanosarcinaceae, Methanosaetaceae, Methanobacteriaceae and Methanocellaceae) we found notably high numbers of GOM Arc I species within the order of Methanosarcinales, which may be anaerobic methane oxidizers. The archaeal community remained mainly unchanged throughout the monitored season. Interestingly, we observed increased ribosomal RNA levels per cell under the drained conditions. As these conditions were unfavorable for anaerobic bacteria and methanogenic archaea we interpreted this behavior as preparedness for becoming active when conditions improve.
In the third part of the thesis we followed the introduction of maize cultivation and concomitant non-flooded conditions on fields that had previously been managed as flooded rice fields. The crop rotation was monitored for two additional years. Thereby we found only minor differences in the bacterial community abundance and activity in the rotational fields in comparison to flooded rice fields. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields while members of anaerobic Chloroflexi and sulfite reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. In contrast, we showed that rotation of flooded rice and upland maize lead to dramatic changes in the archaeal community, indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. This was especially apparent in the strong enrichment of Thaumarchaeota of the Soil Crenarchaeotic Group, mainly Candidatus Nitrososphaera, indicating the increasing importance of ammonia oxidation during drainage. Combining qPCR and pyrosequencing data again 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 the season of re-flooding and rice cultivation.
This thesis provides evidence that the rice plants influence the microbial community in the soil (first part), and that alterations in field management such as drainage or maize cultivation under upland conditions have minor immediate effects on the overall microbial community (second part) but more strongly pronounced long term effects mainly on the archaeal community (third part).|