Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands


Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.

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We acknowledge the help of Victoria Ochoa and Beatriz Gozalo with laboratory analyses, and of all the colleagues that collected soil samples in global drylands. This research is supported by the Australian Research Council projects (DP170104634 and DP190103714), by the European Research Council (BIOCOM project, ERC Grant agreement n°242658) and by the Spanish Ministerio de Economía y Competitividad (BIOMOD project, ref. CGL2013-44661-R). M.D-B. acknowledges support from the Marie Sklodowska-Curie Actions of the Horizon 2020 Framework Programme H2020-MSCA-IF-2016 under REA grant agreement n°702057. FTM acknowledges support from the European Research Council (BIODESERT project, ERC Grant agreement n°647038).

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Statement of authorship: M.D.-B. conceived the idea of this study. F.T.M. designed and coordinated field surveys. Laboratory analyses were done by C.T. and F.T.M. in consultation with B.K.S. and M.D.B. Data analyses were done by C.T., B.K.S. and H.-W.H; interpretation was done by all authors. Statistical modeling was done by M.D.B. The manuscript was written by M.D.-B. and C.T., edited by P.B.R., B.K.S. and F.T.M., and all authors contributed to the final draft.

Correspondence to Brajesh K. Singh or Manuel Delgado-Baquerizo.

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Trivedi, C., Reich, P.B., Maestre, F.T. et al. Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands. ISME J 13, 2727–2736 (2019).

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