Unravelling interspecies interactions across heterogeneities in complex biofilm communities

Abstract

The importance of microbial biofilms has been wellrecognized for several decades, and focus is now shifting towards investigating multispecies biofilm communities rather than mono-or dual-species biofilms. Therefore, the demand for techniques that provide a sufficient amount of information at adequate resolution is increasing. One major challenge for multispecies studies is that diversity and spatial organization often lead to a high degree of spatial and chemical heterogeneity. Many current approaches do not account for such heterogeneity and therefore only provide average information (−omics techniques in particular), which could obscure important information about the community. Here, we bring attention to the issues of heterogeneity when analysing synthetic multi-species biofilms, in vitro, and the importance of multi-scale approaches. We provide an overview of current and newer approaches that can be applied to biofilm communities, in order to elucidate interactions at the appropriate scale.

Spatial alanine metabolism determines local growth dynamics ofEscherichia colicolonies

“…Several cross-feeding interactions have been described in detail for multi-species communities (Henson et al, 2019;Kim et al, 2017;Moree et al, 2012;Pande et al, 2016;Røder et al, 2020;Smith et al, 2019;Watrous et al, 2013;Yang et al, 2009). Even though cross-feeding interactions are likely a ubiquitous process in single-species bacterial multicellular structures (San Roman & Wagner, 2018), only a few metabolic interactions between subpopulations have been documented for single-species biofilms (Arjes et al, 2021;Cole et al, 2015;Evans et al, 2020;Lin et al, 2018;Liu et al, 2015).…”

“…The physiological responses to these microenvironmental conditions result in spatially segregated subpopulations of cells with different metabolism (Barroso-Batista et al, 2020;D'Souza et al, 2018;Stewart & Franklin, 2008). Bacterial growth into densely-packed spatially structured communities, and metabolic activity of the constituent cells, therefore naturally lead to physiological differentiation (Evans et al, 2020;Røder et al, 2020;Serra, Richter, Klauck, et al, 2013;Stewart & Franklin, 2008).…”

More than words: the chemistry behind the interactions in the plant holobiont

“…The presence of certain bacterial species can modulate the plant microbiome composition, and their effects on their host via antagonistic, competitive, and cooperative interactions can determine plant microbiota interactions under specific conditions (Rodriguez et al ., 2019). For this reason, recent efforts have focused on studying bacterial interactions, from simple interactions to those occurring in complex consortia, in an attempt to decipher how bacteria communicate and influence their local environment (Granato et al ., 2019; Molina‐Santiago et al ., 2019; Roder et al ., 2019; Roder et al ., 2020).…”

Bacterial chatter in chronic wound infections

“…While human samples are the ultimate test, care should be taken to standardize sample collection, to take consistent follow‐up samples from the same patients, and to obtain proper control samples (ideally, a swab from an uninfected chronic wound of the same patient). In fact, since microbes in a biofilm are spatially organized, proper sampling at a macro scale, and combining it with shotgun metagenomics that can differentiate between various strains of the same bacterial species, becomes important to maximize the identification of different bacterial species present in the wound and to uncover their interactions 111 . Recently, a four‐zone model has been described to study bacterial behavior with respect to its micro‐ and macro‐environment in the wound.…”