Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils

<div><p>Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the <i>in silico</i> evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.</p></div

Schematic representation of compartmentalization.

<p><b>A.</b> Compartmentalized metabolic network representation with four compartments evaluated. <b>B.</b> Non-compartmentalized metabolic network representation.</p

Metabolic characterization of the consensus metabolic networks.

<p>Metabolic characterization of the consensus metabolic networks.</p

Comparison between the relative abundance of the metabolic processes performed in the non-intervened ecosystem (S1) and in the ecosystem intervened by agricultural processes (S2).

<p>Comparison between the relative abundance of the metabolic processes performed in the non-intervened ecosystem (S1) and in the ecosystem intervened by agricultural processes (S2).</p

Number of metabolites associated to each one of the compartments in the initial reconstructions.

<p>Importantly, a metabolite may be present in more than one compartment. This information excludes generic metabolites (metabolites that do not have specific stoichiometric coefficient: RNA, DNA, generic lipids and glycan).</p

Global topological properties.

<p>S1_C: non-intervened soil sample, compartmentalized.</p

Pipeline used for the compartmentalized metabolic network analysis and functional reconstruction of the microbial community in agriculturally intervened and non-intervened soils.

<p>Pipeline used for the compartmentalized metabolic network analysis and functional reconstruction of the microbial community in agriculturally intervened and non-intervened soils.</p

Number of common problem metabolites between the cytoplasm and the inner compartments.

<p>Number of common problem metabolites between the cytoplasm and the inner compartments.</p

Objective functions for the carbon, sulfur, and nitrogen cycles.

<p>Objective functions for the carbon, sulfur, and nitrogen cycles.</p

Results of the compartmentalized metabolic network curation.

<p><b>A.</b> Total metabolite problems found in each one of the compartments evaluated. <b>B.</b> Percentage of reconnection before and after the Gapfilling process. S1_C: compartmentalized, non-intervened soil sample. S2_C: compartmentalized, intervened soil sample. S1_NC: non-compartmentalized, non-intervened sample. S2_NC: non-compartmentalized, intervened sample. S1_CC: compartmentalized and curated, non-intervened sample. S2_CC: compartmentalized and curated, intervened sample. S1_NCC: non-compartmentalized and curated non-intervened soil sample. S2_NCC: non-compartmentalized and curated intervened soil sample.</p