Niche differentiation is spatially and temporally regulated in the rhizosphere

Abstract

13 14 Running title: Decomposition gene expression in the rhizosphere 15 16 Corresponding authors: Erin Nuccio nuccio1@llnl.gov 925-423-9983, Jennifer Pett-Ridge 17 pettridge2@llnl.gov 925-424-2882, Lawrence Abstract 20 The rhizosphere is a hotspot for microbial C transformations, and the origin of root polysaccharides and 21 polymeric carbohydrates that are important precursors to soil organic matter. However, the ecological 22 109 110 Sample Collection 111 Rhizosphere soil <2 mm from the root was excised with a scalpel. Root sections and adhering soil were 112 placed immediately in ice cold Lifeguard Soil Preservation Reagent (MoBio), vortexed for 2 min on 113 medium speed, and pelleted according to the Lifeguard protocol. Roots were removed using flame-114

Sugars dominate the seagrass rhizosphere

“…Looking at substrate use patterns of GH families, our analyses revealed that MAGs occurring at the edge and outside sampling sites, in comparison to those inside the meadow, contained more genes for the degradation of common plant carbohydrates, including sucrose, cellulose, and pectin (Figure 7). Unlike reports from terrestrial systems 35 , our results indicate that fewer microorganisms living in the marine rhizosphere have genes to degrade organic carbon and the number of genes per organism are low. Alternatively, seagrass meadows support a specialized community of microbial taxa that can only use select substrates in their metabolism (e.g., sucrose).…”

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

“…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).…”

“…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.…”

Wheat domestication has dramatically affected the root-associated microbiome

“…In wild oat, the core microbiome showed strong phylogenetic clustering, indicating that selective processes were dominating the community assembly [37]. We observed strongest phylogenetic clustering in bacterial communities associated to the ancient accessions (higher values of NRI), suggesting that environmental filtering is strongest in the root environment of ancient lines, promoting the co-occurrence of OTUs phylogenetically closer to each other, and thus sharing traits essential for their survival in such environments.…”