Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide‐producing bacteria during soil formation

Abstract

Summary Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post‐mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide‐producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide‐producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.

Importance of microbial communities at the root-soil interface for extracellular polymeric substances and soil aggregation in semiarid grasslands

“…For instance, a relative large cluster with ASV 84 (Inquilinus limosus), ASV 114 (Burkholderiaceae), ASVs 116 and 117 (Pseudomonadaceae), ASV 33 (Pseudonocardiaceae), and ASVs 70/72/73 (Rhizobiaceae) were mainly found in Anthyllis rhizoplane, independent of parent material, but correlated well to both EPS-saccharide contents and aggregation in the other compartments. As discussed in the previous section, Rhizobiaceae contain many N-fixing taxa that are often capable of producing EPS (Rodriguez-Navarro et al, 2007;Vuko et al, 2020). Moreover, Inquilinus limosus and species belonging to Pseudomonadaceae have been studied for their cooperation in sturdy biofilm formation in patients with cystic fibrosis (Herasimenka et al, 2007;Lopes et al, 2012Lopes et al, , 2014, indicating that taxonomically related strains adapted to the soil environment have likely the capability to produce EPS as well (Lennon et al, 2012;Vuko et al, 2020).…”

“…As discussed in the previous section, Rhizobiaceae contain many N-fixing taxa that are often capable of producing EPS (Rodriguez-Navarro et al, 2007;Vuko et al, 2020). Moreover, Inquilinus limosus and species belonging to Pseudomonadaceae have been studied for their cooperation in sturdy biofilm formation in patients with cystic fibrosis (Herasimenka et al, 2007;Lopes et al, 2012Lopes et al, , 2014, indicating that taxonomically related strains adapted to the soil environment have likely the capability to produce EPS as well (Lennon et al, 2012;Vuko et al, 2020).…”

Correlation of the abundance of bacteria catalyzing phosphorus and nitrogen turnover in biological soil crusts of temperate forests of Germany

“…Biocrusts are mostly dominated by organisms like phototrophic cyanobacteria, microalgae, lichens, or mosses, which drive the input of nutrients into the system. Together with associated heterotrophic microorganisms such as archaea, bacteria, or fungi, they create stable microhabitats, for example, by the excretion of polysaccharides (Cania et al 2020;Mugnai et al 2018, Vuko et al 2020. Biocrusts have been mostly studied in arid and nutrient-poor habitats (Belnap et al 2001), where they are the predominant vegetation form and their growth is limited by water and nutrient availability.…”

Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition

“…PCR reaction mixtures (25 μL) contained 12.5 μL of Sybr Green PCR Master Mix (Thermo Fisher Scientific, Darmstadt, Germany), 10 pmol of each primer, 8.5 μL of DEPC treated water, and 2 μg of DNA template. Amplification program of 16S rRNA gene was initiated by a denaturation step at 95 °C for 10 min, followed by 35 For the assessment of bacterial communities and diversity, the "16S Metagenomic Sequencing Library Preparation" protocol (Illumina, San Diego, USA) and quality guidelines recommended by Schöler et al [50] were used. DNA extracts were amplified in triplicate using the primer S-D-Bact-0008-a-S-16 and the primer S-D-Bact-0343-a-A-15 [51] (Table S2).…”

“…The impacts of microbial diversity and community shifts on ecosystem function have been studied in natural settings. For example, chronosequences of soil from the same parental material with different developmental stages (e.g., retreating glaciers) have been used as a model to assess correlations between microbial community composition and its function [ 34 , 35 ]. Furthermore, some authors focused on soils with different agricultural management history (e.g., monoculture vs. crop rotation) and investigated differences in functional patterns of soil microbial communities [ 36 , 37 ].…”