Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Environ Microbiol. 2016 Sep;18(9):2868-85. doi: 10.1111/1462-2920.13041. Epub 2015 Oct 14.
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.
水稻旱作轮种是一种常见的管理方式，可减少用水量和甲烷排放量。在稻田生态系统中引入旱地作物会导致田间条件（氧气可用性、氧化还原条件）发生剧烈变化。然而，这种做法对古菌和细菌群落的影响几乎没有研究过。在这里，我们进行了一项全面的研究，重点关注湿季淹水水稻与旱季旱地玉米（RM）的轮作，与两季淹水水稻（RR）进行了比较。通过对古菌和细菌 16S rRNA 基因和 16S rRNA 进行 454 焦磷酸测序，评估了驻留和活跃微生物群落的组成。结果表明，在轮作田中的古菌群落组成发生了剧烈变化，厌氧产甲烷菌减少，好氧 Thaumarchaeota 增加。在轮作田中，Methanomicrobiales、Methanosarcinaceae、Methanosaetaceae 和 Methanocellaceae 的成员同样受到抑制，这表明对乙酰辅酶 A 和氢营养型产甲烷菌都有影响。相反，土壤泉古菌组（主要是 Candidatus Nitrososphaera）的成员在轮作田中的丰度更高，可能表明在排水过程中氨氧化的重要性增加。相反，对细菌群落的影响较小。酸杆菌门和 Anaeromyxobacter spp. 在轮作田中富集，而厌氧 Chloroflexi 和硫酸盐还原菌 Delta 蛋白门的成员在稻田中丰度更高。定量聚合酶链反应和焦磷酸测序数据的结合表明，在作物轮作过程中，产甲烷菌的细胞内核糖体数量增加。然而，这种应激反应并不能使产甲烷菌在重新淹没和水稻种植期间在轮作田中恢复。总的来说，分析表明，与旱地玉米轮作导致古菌群落组成发生剧烈变化，而细菌群落仅受到轻微影响。
