Farm-scale differentiation of active microbial colonizers

William L King; Laura M Kaminsky; Sarah C Richards; Brosi A Bradley; Jason P Kaye; Terrence H Bell

doi:10.1038/s43705-022-00120-9

Farm-scale differentiation of active microbial colonizers

ISME Commun. 2022 Apr 20;2(1):39. doi: 10.1038/s43705-022-00120-9.

Authors

William L King¹, Laura M Kaminsky¹, Sarah C Richards^{1

2

3}, Brosi A Bradley⁴, Jason P Kaye^{2

4}, Terrence H Bell^{5

6

7}

Affiliations

¹ Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
² Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
³ Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
⁴ Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA.
⁵ Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA. thb15@psu.edu.
⁶ Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA. thb15@psu.edu.
⁷ Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA. thb15@psu.edu.

Abstract

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R² = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R² = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R² = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.