Supporting crop yields under climate change by engineering innate soil microbiomes

We test the idea that innate agricultural soil microbiomes can be engineered to help support crops under climate change conditions. Salinization is one of the key drivers of agricultural soil degradation globally, and rising sea levels combined with decreasing rainfall are exacerbating this threat to food production. Changes in soil microbial community structures measured from DNA and functions and fitness measured from RNA and labeled amino acid uptakes support the hypothesis that the deliberate use of part-saline irrigation adapts soil microbiomes to increased salinities. While saline irrigation suppressed crop establishment in some cases, this microbiome response combined with inferences of increased microbial nutrient cycling and energy management correlates with final crop yield data and supports the hypothesis that engineered soil communities have helped protect yields under increased salinity conditions. This work provides evidence of the efficacy of a novel pragmatic, cost-effective innate soil microbiome engineering intervention for optimizing and securing food systems for future climate change conditions.IMPORTANCEThe consequences of climate change comprise significant and increasing threats to sustainable global food security. The salinization of agricultural soils is one of the main threats to agricultural production globally: this currently affects around 30% and is predicted to affect 50% of agricultural land by 2050. We show innate agricultural soil microbial communities can be engineered by low levels of saline irrigation. The engineered soil communities are better able to tolerate saline conditions and are inferred to have better nutrient turnover, and this correlates with protecting crop yields of established plants under saline conditions. This shows that it is possible for growers and farmers to "teach" or "prepare" soil microbiomes to become more tolerant of elevated soil and irrigation salinities predicted due to climate change in a way that will also meet sustainable food security requirements.