Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. Desert farming and microbial diversity

BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.

背景：将沙漠转化为可耕种的绿色景观是一项全球性愿景，沙漠农业也是全球范围内发展迅猛的农业领域。然而，其对土壤微生物群落多样性的影响尚不明晰——而土壤微生物群落正是植物健康等重要生态系统服务功能的核心承担者。
研究方法与主要结果：本研究以埃及塞凯姆（Sekem）地区最具代表性的有机沙漠农业示范点之一为研究对象，探究长期农业活动对荒漠土壤的影响。采用多相研究方法，对土壤及栽培植物关联的微生物群落进行分析，发现30年的农业耕作已对土壤微生物群落造成了显著扰动。对细菌指纹图谱的分析结果显示，农业土壤与原生荒漠土壤的群落差异度约达60%，且该差异具有统计学显著性。基于焦磷酸测序（pyrosequencing）的16S rRNA基因区域分析表明，农业土壤的微生物多样性显著高于荒漠土壤（香农多样性指数分别为11.21与7.90），且群落结构存在明显差异。厚壁菌门（Firmicutes）在农田土壤中的相对丰度达37%，显著高于荒漠土壤的11%。芽孢杆菌属（Bacillus）与类芽孢杆菌属（Paenibacillus）发挥关键作用：它们占植物病原菌（phytopathogens）拮抗菌株总数的96%，且扩增子文库（amplicon library）与分离菌株的16S rRNA序列完全匹配。农田土壤中的拮抗菌株占比相较荒漠土壤提升了一倍（分别为21.6%与12.4%）；抑病细菌（disease-suppressive bacteria）在植物根际尤其富集。与之相反，多个嗜极细菌类群，如嗜酸微杆菌属（Acidimicrobium）、红微菌属（Rubellimicrobium）以及异常球菌-栖热菌门（Deinococcus-Thermus），在农业开垦后从土壤中完全消失。固氮的草螺菌属（Herbaspirillum）类群仅存在于荒漠土壤中。土壤细菌群落的组成主要受非生物因子（a-biotic factors）——水分供给与pH值——调控。
结论与意义：长期农业耕作后，荒漠土壤的细菌群落发生了显著转变。农业土壤的细菌群落多样性更高，对植物健康相关的生态系统服务功能更为优良，但同时也丧失了原有的嗜极细菌类群。有趣的是，本研究发现本土荒漠微生物能够促进荒漠农业生态系统中的植物健康。