Molecular processes underlying synergistic linuron mineralization in a triple‐species bacterial consortium biofilm revealed by differential transcriptomics

Abstract

The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple‐species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis. Differentially expressed pathways and cellular systems were inferred using the network‐based algorithm PheNetic. Coculturing affected mainly metabolism in WDL1. Significantly enhanced expression of hylA encoding linuron hydrolase was observed. Moreover, differential expression of several pathways involved in carbohydrate, amino acid, nitrogen, and sulfur metabolism was observed indicating that WDL1 gains carbon and energy from linuron indirectly by consuming excretion products from WDL7 and/or WDL6. Moreover, in consortium conditions, WDL1 showed a pronounced stress response and overexpression of cell to cell interaction systems such as quorum sensing, contact‐dependent inhibition, and Type VI secretion. Since the latter two systems can mediate interference competition, it prompts the question if synergistic linuron degradation is the result of true adaptive cooperation or rather a facultative interaction between bacteria that coincidentally occupy complementary metabolic niches.

Herbicide bioremediation: from strains to bacterial communities

“…The Variovorax strain also had an elevated stress response and overexpressed genes involved in cell-to-cell interaction systems, such as quorum molecule signaling and type VI secretions. The latter two systems could be used by Variovorax in interference competition with C. testosteroni and H. sulfonivorans ( Albers et al., 2018 ).…”

“…Next-generation Illumina transcript-sequencing technology (RNAseq) that allows analysis of global gene expression between strains, has been used to identify potential genes related to interspecies interactions. This technique has proven to be especially useful in examining microbial consortia present in biofilms that have the ability to transform (mineralize) xenobiotic compounds such as the phenylurea herbicide linuron ( Albers et al., 2018 ). Nevertheless, it is important to keep in mind that there are novel methods beyond omics-based techniques that have been used to study bioremediation and biodegradation.…”

“…This ultimately can provide needed information on possible ecological impacts. Such was the case when RNAseq-based differential transcriptomics were used to examine consortia gene expression occurring during linuron degradation ( Albers et al., 2018 ). This approach led to discovery of previously uncharacterized proteins with functions relevant to cellular performance.…”

Community-intrinsic properties enhance keratin degradation from bacterial consortia

“…Such community synergies have been shown in several cases e.g. with increased biofilm formation from mixed species communities [5][6][7] and also for degradation of complex recalcitrant organic molecules such as lignocellulose [8]. A variety of different factors can contribute to the emergence of intrinsic community properties, including substrate complexity that may lead to positive interactions among community members, enabling degradation of recalcitrant substrates [9] or yield complementary by-products [10].…”

Transcriptional analysis reveals the metabolic state ofBurkholderia zhejiangensisCEIB S4-3 during methyl parathion degradation

“…RNA-Seq data are commonly used to define the genome-wide transcript expression profiling and the identification of differentially expressed genes (DEGs) among different biological or experimental conditions (Han et al, 2015; Pereira, Imada & Guedes, 2017). RNA-Seq has emerged as a powerful tool for transcriptomic analysis in the field of environmental microbiology, which has especially been applied in the assessment of the microbial diversity in polluted sites (Yan et al, 2017), as well as in the discovery and characterization of genes implicated in the tolerance, biodegradation, and bioremediation of xenobiotics by different microorganisms (Zhang et al, 2015; Yang et al, 2016; Albers et al, 2018).…”