Plants predictably select growth boosting microbes regardless of soil type

A new study shows crop species, and not soil type, primarily determines the beneficial functions provided by root-associated microbes.

In the study, soil obtained from across nine UK locations was used to cultivate six key arable crops (wheat, barley, oats, fava beans, oilseed rape, and sugar beet). Researchers found that although the local soil environment selected which kinds of bacteria were present, the crop species determined the beneficial microbial functions of those bacteria.  The findings have significant implications for the design of microbial inoculants and microbiome-assisted breeding strategies for sustainable agriculture.

The research team from Rothamsted Research, CABI, The John Innes Centre, The James Hutton Institute and The Scottish Rural Agricultural College used the UK Crop Microbiome Cryobank (UKCMCB, https://agmicrobiomebase.org/), the world’s first open crop and soil microbiome resource, to characterise more than 24,000 bacterial cultures and 315 soil microbiome libraries.

“What really stood out was that the soil environment dictates which bacteria are present, but the crop selects bacteria based on what beneficial functions they provide,” said lead author Dr Rodrigo Taketani of Rothamsted Research. “This tells us that plants are actively selecting microbes for their functional properties — for example, to help with nutrient acquisition or stress tolerance — drawing on locally available bacteria to provide these services.”

Microbes with skillsets

 Different crops seemed to “choose” microbes with different skills:

• Sugar beet and oilseed rape rhizospheres attracted microbes that help plants survive dry conditions, likely because their large tap roots create a drier root environment.
• Barley attracted microbes that help unlock zinc from the soil, which plants need to grow.
• Fava bean rhizospheres attracted fewer microbes capable of breaking down organic sources of nitrogen in the soil, potentially because the legume–Rhizobium partnership already provides a sufficient nitrogen supply.

“These functional differences between crops are remarkably consistent across very different soils and locations,” said co-author Ian Clark of Rothamsted Research. “The fact that we see the same crop-specific patterns whether the soil came from Scotland or Hertfordshire tells us this is a genuine biological selection driven by the plant, not a quirk of any particular soil type.”

“Due to the high microbial diversity and competition in soil a ‘one size fits all’ approach to microbial inoculation is unlikely to be optimal,” said senior author Dr Tim Mauchline, also of Rothamsted Research. “A more effective long-term approach may be to breed crops that are better at selecting beneficial native soil microbes, rather than relying on introduced strains that often fail to establish.”