Microbial community assembly differs across minerals in a rhizosphere microcosm

Abstract

Mineral-associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral-sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months - the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.

Bacterial colonization of minerals in grassland soils is selective and highly dynamic

“…From the abundant sequence variants, 134 could be classified at genus level and fell into 55 different genera. Comparing these 55 genera to the results of existing studies on mineral colonization (Supporting Information Table S1), 30 had been reported previously to colonize different minerals or mineral mixtures (Ding et al ., ; Colin et al ., ; Whitman et al ., ). Representatives of the genera Streptomyces , Pedobacter and Paenibacillus were identified as mineral associated on the majority of the minerals or mineral mixtures tested (Table S1).…”

“…Also, the presence of the clay minerals illite, montmorillionite and the iron oxyhydroxide goethite in (mostly artificial) soils has previously been shown to change the relative abundances of different bacterial phyla or classes. These were attributed to specific physicochemical properties of the mineral surfaces and differences in nutrient availability (Heckman et al, 2012;Ding et al, 2013;Ditterich et al, 2016;Whitman et al, 2018). Different bacterial taxa show different capabilities of binding to minerals (Frey et al, 2010), which are due to distinct mineral surface charge (Roberts, 2004), roughness (Huang et al, 2015) and chemical composition (Gleeson et al, 2006).…”

“…Only limited information on mineral colonization patterns of distinct bacterial genera and species is available to date (Ding et al, 2013;Colin et al, 2017;Whitman et al, 2018). We were able to discern specific temporal colonization patterns of individual sequence variants and compared them to results from literature, to gain more insights into their potential preferences and adaptations.…”

“…The latter demonstrated that microbial communities changed over relatively short time spans of 6 to 18 months (Heckman et al ., ; Hemkemeyer et al ., ; Ditterich et al ., ). It is not known whether differences in associated bacterial communities between different minerals observed over a few months persist over longer time periods (Whitman et al ., ) and, vice versa , whether differences in colonization patterns observed after several years represent the initial colonizers (Ahmed et al ., ; Colin et al ., ). In situ studies so far determined the bacterial communities colonizing fresh surfaces of primary minerals after a fixed incubation time of 2 or 2.5 years (Ahmed et al ., ; Colin et al ., ).…”

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures

“…As the novelty of our method lies in the recovery of proteins from the phenol phase, typically discarded in the protocol of Griffiths et al (), we further demonstrate that our biomolecule co‐extraction is suitable for metaproteomics analysis of other soil types with varying clay contents. Indeed, the DNA and RNA co‐extraction protocol from Griffiths et al () has been cited to date by over 1,250 papers including many reporting on downstream high‐throughput sequencing, including 16SrRNA and ITS amplicon analysis (Haas et al, ; Morawe et al, ; Sayer et al, ; Whitman et al, ), metagenomics (Malik, Thomson, Whiteley, Bailey, & Griffiths, ; Soares et al, ; Wilhelm, Hanson, Chandra, & Madsen, ) and metatranscriptomics (Alessi et al, ; de Menezes, Clipson, & Doyle, ; Hesse et al, ). Here, 16S rRNA profiling from DNA and cDNA was performed on three samples corresponding to three biological replicates from one soil type (with a clay content of 11.1%) while metaproteomics was conducted for nine samples corresponding to three biological replicates from three soil types (with clay content of 11.1%, 19.4% and 35.1%).…”