Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

Abstract

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivationdependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrientpoor forest ecosystems.KEYWORDS mineral chemistry, bacterial communities, forest soil, mesh bags, mineral weatherability

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).…”

“…As initially hypothesized, the bacterial community which assembled on the minerals were at each time point substantially different from both the adjacent and control soils, which indicates a selective process of community assembly. Primary minerals such as apatite, biotite, oligoclase, obsidian and calcite are colonized by different microbial communities (Ahmed et al, 2017;Colin et al, 2017). 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.…”

“…The latter demonstrated that microbial communities changed over relatively short time spans of 6 to 18 months (Heckman et al, 2012;Hemkemeyer et al, 2014;Ditterich et al, 2016). 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, 2018) and, vice versa, whether differences in colonization patterns observed after several years represent the initial colonizers (Ahmed et al, 2017;Colin et al, 2017). 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, 2017;Colin et al, 2017).…”

“…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, 2018) and, vice versa, whether differences in colonization patterns observed after several years represent the initial colonizers (Ahmed et al, 2017;Colin et al, 2017). 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, 2017;Colin et al, 2017). However, the minerals tested are characteristic of larger soil particles (Churchman and Lowe, 2012).…”

Microbial community assembly differs across minerals in a rhizosphere microcosm

“…Using high‐throughput sequencing to analyse samples from the same trial, they confirmed that Burkholderia was a key genus responsible for apatite weathering in soils (Lepleux et al ., ). At the same site, Colin and colleagues () found strong differences in bacterial communities on buried minerals of varying weatherability (apatite, obsidian and calcite) compared to the bulk soil after two and a half years. Additionally, they found that bacterial taxa associated with mineral‐weathering capabilities (from the Betaproteobacteria class and Burkholderia and Collimonas genera) were more abundant on the less easily‐weathered mineral types (obsidian and apatite).…”