Biomarker panels for characterizing microbial community biofilm formation as composite molecular process

<div><p>Microbial consortia execute collaborative molecular processes with contributions from individual species, on such basis enabling optimized molecular function. Such collaboration and synergies benefit metabolic flux specifically in extreme environmental conditions as seen in acid mine drainage, with biofilms as relevant microenvironment. However, knowledge about community species composition is not sufficient for deducing presence and efficiency of composite molecular function. For this task molecular resolution of the consortium interactome is to be retrieved, with molecular biomarkers particularly suited for characterizing composite molecular processes involved in biofilm formation and maintenance. A microbial species set identified in 18 copper environmental sites provides a data matrix for deriving a cross-species molecular process model of biofilm formation composed of 191 protein coding genes contributed from 25 microbial species. Computing degree and stress centrality of biofilm molecular process nodes allows selection of network hubs and central connectors, with the top ranking molecular features proposed as biomarker candidates for characterizing biofilm homeostasis. Functional classes represented in the biomarker panel include quorum sensing, chemotaxis, motility and extracellular polysaccharide biosynthesis, complemented by chaperones. Abundance of biomarker candidates identified in experimental data sets monitoring different biofilm conditions provides evidence for the selected biomarkers as sensitive and specific molecular process proxies for capturing biofilm microenvironments. Topological criteria of process networks covering an aggregate function of interest support the selection of biomarker candidates independent of specific community species composition. Such panels promise efficient screening of environmental samples for presence of microbial community composite molecular function.</p></div

Node details of the biofilm process network in relation to experimental data.

<p>Violin plots for (<b>A</b>) degree and (<b>B</b>) stress centrality of network nodes comparing the wild type microbial community situation with laboratory conditions on fold change significance, complemented by correlation of species coverage with (<b>C</b>) degree and (<b>D</b>) stress centrality for nodes holding a significant fold change.</p

Listing of copper sites.

<p>Listing of copper sites.</p

Biofilm ortholog graph.

<p>Nodes represent protein coding genes and edges resemble aggregate interaction information. The layout reflects node degree, the node diameter scales with stress centrality. Node color-coding indicates microbial species coverage scaling from one to 25 (upper semicircle, scaling from light to dark blue), and selected COG term assignment in the context of biofilm formation (lower semicircle, orange: cell wall/membrane/envelop biogenesis; green: cell motility; magenta: extracellular structures). Node annotation refers to biomarker candidates according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0202032#pone.0202032.t004" target="_blank">Table 4</a>.</p

Molecular function terms and COG term assignment.

<p>Molecular function terms and COG term assignment.</p

Workflow for candidate biomarker selection.

<p>Microbial species and molecular feature details: step 1—data stocktaking at the microbial species and biological function level; step 2—assignment of genes to biological function terms. Interaction data and networks: step 3—all-against-all ortholog mapping; step 4—aggregation of protein interaction data; step 5—deriving a molecular process model. Biomarker candidates and experimental evaluation: step 6—selection of biomarker candidates utilizing network topology characteristics; step 7—experimental evaluation of biomarker candidates.</p

Microbial species annotation details.

<p>Microbial species annotation details.</p

Biomarker candidate panel for capturing the biofilm molecular process.

<p>Biomarker candidate panel for capturing the biofilm molecular process.</p