Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community

Abstract

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.

The effect of crop rotation between wetland rice and upland maize on the microbial communities associated with roots

“…Since crop rotation between rice and maize was also a rotation between flooded soil and upland soil conditions, it is likely the water content and the aeration of the soil that affected root colonization. Indeed, the soil bacterial community in rotational fields was significantly different of that vegetated with non-rotated rice confirming previous observations (Breidenbach et al 2016a).…”

“…The control fields (RR) fields were flooded and cropped with rice both in the dry and the wet season with drainage in between. A detailed overview of the crop rotation system and the sampling time points is given in Breidenbach et al (2016a). Fields were operated in triplicates (RR: fields No.…”

“…1). The field plots were adjacent on the same soil as described before (Breidenbach et al 2016a;Weller et al 2015). …”

“…However, extended crop rotation showed that the archaeal community composition was affected if flooded rice was rotated with non-flooded maize. The bacterial community, on the other hand, was comparatively little affected (Breidenbach et al 2016a).…”

“…In order to focus more definitely on the microbial community colonizing the plant roots, we used samples from the crop rotation experiment described by Breidenbach et al (2016a) and extracted the microbial community from the ecto-and endorhizosphere. The crop rotation system was on a soil at the International Rice Research Institute (IRRI) in the Philippines, and consisted of triplicate fields that were grown for two years with flooded rice during both the wet and the dry season, and of triplicate fields that were grown for two years with flooded rice during the wet season and nonflooded maize during the dry season.…”