Farm-scale differentiation of active microbial colonizers

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.

Leveraging microbiome rediversification for the ecological rescue of soil function

“…These observations could be due to inadvertent fungal selection imparted in agricultural settings [ 68 ]. Recently, we observed that active fungal colonizer composition was strongly shaped across environments relative to bacterial colonizers [ 28 ] and agricultural settings often select for copiotrophic microorganisms [ 75 ]. It could be possible that a greater proportion of the farm soil fungal composition is copiotrophic in nature, explaining differences between the farm and forest soils.…”

“…Our study used a dilution-to-extinction approach to recolonize thrice autoclaved soils, similar to a previous study by Wagg et al [ 67 ] albeit with only a single autoclave step. Autoclaving can break down soil nutrients and may impact other soil physicochemical properties [ 76 ] but allows for large-scale processing of soil for performing experiments at scale [ 28 , 33 , 74 , 77 , 78 ] and more closely resembles agricultural management practices such as soil steaming. We have previously observed greater unintended microbial regrowth in gamma irradiated soils relative to autoclaved soils (unpublished data).…”

“…enhanced P mineralization), but microbial establishment and functional performance in novel recipient environments is often unreliable due to various abiotic and biotic constraints [25][26][27]. Passive management can include increasing crop diversity and/or retaining natural lands that may provide reservoirs for diverse microbial influx [28]. Since many soil functions are provided by the combined contributions of many microbial taxa rather than the outsized impacts of a few, there may be value in the rediversification of whole microbial assemblages that have experienced biodiversity loss.…”