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.