Data from: Agricultural intensification and the functional capacity of soil microbes on smallholder African farms

1. Fertilization may impact ecosystem processes that sustain agriculture, such as nutrient cycling, by altering the composition of soil microbial communities that regulate such processes. These processes are crucial to low-input, smallholder tropical agriculture, which supports 900 million of the world's poorest people. Yet little is known about how efforts to increase crop yield on such farms will affect the capacity of soil microbial communities to carry out ecosystem processes. 2. We studied the diversity and functional capacity of microbial communities on smallholder farms in western Kenya. We measured functional capacity as the abundance of functional genes involved in several components of nutrient cycling as well as catabolism of multiple carbon substrates; taxonomic diversity was measured using metagenomic sequencing. Diversity and functional capacity were measured on short-term, experimental mineral fertilizer addition plots and on actively managed farms that have maintained for at least seven years a management strategy of low mineral fertilization, high mineral fertilization, or high fertilization combined with legume rotations. 3. Soil bacterial diversity decreased with mineral fertilizer addition, with a community shift towards taxa that thrive in high-resource conditions. This taxonomic response did not correspond with decreased microbial functional capacity. Instead, functional capacity was increased, along with yields, when fertilizers were combined with legume rotations that add organic matter to soil. 4. Policy implications. Mineral fertilizer use is associated with lower soil microbial diversity on smallholder farms, but not associated with changes in microbial functional capacity. Functional capacity is highest, along with yields, when mineral fertilizers are paired with legume rotations. Our findings suggest that this type of agroforestry can be an important strategy for maintaining the long-term functional capacity of soil microbes as well as increasing crop yields on smallholder farms. These observations support proposals to achieve long-term food production targets in sub-Saharan Africa by combining mineral fertilizers with organic inputs.

1. 施肥可通过改变调控此类过程的土壤微生物群落组成，影响维系农业的生态系统过程，例如养分循环。这类过程对支撑全球9亿最贫困人口的低投入热带小农农业至关重要。然而，目前对这类农场中提升作物产量的举措将如何影响土壤微生物群落执行生态系统过程的能力，仍知之甚少。
2. 本研究针对肯尼亚西部小农农场的微生物群落多样性与功能潜力展开探究。我们以参与养分循环多个环节的功能基因丰度以及多种碳底物的分解代谢能力作为功能潜力的衡量指标；分类多样性则通过宏基因组测序（metagenomic sequencing）进行测定。研究分别在短期施用矿质肥料的试验样地，以及至少7年来分别维持低矿质施肥、高矿质施肥，或高矿质施肥结合豆科作物轮作管理策略的常规经营农场中，测定了微生物的多样性与功能潜力。
3. 土壤细菌多样性随矿质肥料施用水平提升而降低，群落结构向适应高养分环境的类群偏移。这类分类学响应并未伴随微生物功能潜力的下降。相反，当肥料与向土壤输入有机质的豆科作物轮作配合施用时，功能潜力与作物产量均有所提升。
4. 政策启示：矿质肥料的施用与小农农场的土壤微生物多样性降低相关，但并未显著改变微生物功能潜力。当矿质肥料与豆科作物轮作配合时，功能潜力与作物产量均达到最高水平。本研究结果表明，此类农作模式可作为维持土壤微生物长期功能潜力，同时提升小农农场作物产量的重要策略。上述发现支持了通过将矿质肥料与有机投入物相结合，以实现撒哈拉以南非洲地区长期粮食生产目标的相关提案。