Niche differentiation is spatially and temporally regulated in the rhizosphere

Abstract

The rhizosphere is a hotspot for microbial C transformations, and the origin of root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter. However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial function in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Population transcripts were binned with a unique reference database generated from soil isolate and single amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition gene expression, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were high in the combined rhizosphere-detritusphere-suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling. .

The generalizability of water‐deficit on bacterial community composition; Site‐specific water‐availability predicts the bacterial community associated with coast redwood roots

“…The term "rhizosphere soil" typically refers to the soil that is tightly adhered to roots and "bulk soil" refers to soil sampled some distance away from the root zone and it is understood that these two habitats represent unique niches, particularly for bacteria (Nuccio et al, 2020). Due to the abundance and density of shallow fine roots in our soil cores, we herein refer to all soil collected from these soil cores as "rhizosphere soil," even though the soil was not necessarily tightly adhered to the roots, as it was clearly in close proximity to root influences.…”

“…This compares to the bacterial community in the soil which is probably more representative of the larger pool of bacterial taxa, including those that were not necessarily actively growing and seeking out root resources and/or formed endospores (Goodfellow & Williams, 1983;Nuccio et al, 2016). Thus, root bacterial communities are more likely to be representative of the active bacterial community using a 16s rRNA amplicon approach (Nuccio et al, 2020).…”

Colonization of naïve roots fromPopulus tremula x albainvolves successive waves of fungi and bacteria with different trophic abilities

“…Similarly, fungal community detected after two and four days of growth in natural soil were dominated by saprotrophs. These observations suggest that saprotrophs, even rare in soil, are the fastest colonizers of tree roots, certainly due to newly available carbon source from the plant and root exsudates (13).…”

Nutrient Source and Mycorrhizal Association jointly alters Soil Microbial Communities that shape Plant-Rhizosphere-Soil Carbon-Nutrient Flows

“…Similarly, nutrient content and type of decomposing organic matter can significantly alter associated decomposer communities and their activity (Güsewell and Gessner, 2009; Meier et al, 2015; Strickland et al, 2009) to influence rates of nutrient cycling in soil. Recent findings based on functional analysis of rhizosphere microbial communities strongly indicate that a functionally diverse microbial community is maintained for exudate utilization in the rhizosphere compared to the bulk soil (Nuccio et al, 2020). Though exudate and litter associated shifts in the microbial community of the rhizosphere are well known, understanding the underlying carbon-nutrient flux between plant-AMF association and these decomposer communities across various nutrient sources can offer further insights into mechanisms of plant nutrient uptake.…”

“…Moreover, the porous nature of soil matrix and presence of complex surfaces ensures that nutrient rich microbial residues are bound within nutrient poor exopolysaccharides as part of soil biofilms (Kallenbach et al, 2016). Though exchange of nutrients between the microbial pool and plants are commonplace, however, unlike plant root litter, little is known about how their turnover impacts carbon-nutrient flux during litter decomposition in the rhizosphere (Nuccio et al, 2020), thus underscoring the need for further investigation through labelled nutrient amendments.…”