BactoTraits – A functional trait database to evaluate how natural and man-induced changes influence the assembly of bacterial communities

Abstract

In the environment, abiotic (climatic conditions, physico-chemical parameters), biotic (interactions between microorganisms, vegetation and fauna), and anthropogenic (stress, pollution) filters are driving the microbial diversity observed locally. A key question in microbial ecology is to understand the impact of these filters on bacterial diversity and ecosystem functioning. To highlight the responses of bacterial assemblages to these ecological filters, a new approach based on bacterial functional traits has been developed. This approach provides a functional picture of bacterial assemblages using morphological, physiological, and genomic traits as proxies of functions, and leads to a generalizable approach over a larger range of ecosystems with different bacterial diversities.We have created a user-friendly database of bacterial functional traits, thanks to the properties of 19,455 bacterial strains. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and temperature, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations.As an example of application, BactoTraits was used to characterize the traits and functional diversity of bacterial assemblages in soil samples from 10 sites with different physico-chemical properties and various levels of metal and polycyclic aromatic hydrocarbon (PAH) contaminations. Inference of functional traits was based on taxonomic diversity information obtained by high-throughput sequencing of 16S rDNA. This trait-based approach has allowed to discriminate soils according to their physico-chemical properties and levels of contamination and to go further into the description of the bacterial assemblages. Several bacterial traits were identified as indicators of specific contaminants such as metals (e.g. filament shape, microaerophile and temperature optimum/range higher than 40 °C) or PAHs (e.g. spherical shape, facultative anaerobe/aerobe, no spore production, pH optimum ≥ 8, low temperature optimum but high temperature variation tolerance).Inferring trait values from a taxonomy-based approach can be extended readily to other microbial systems and contexts such as (i) studies on soils and aquatic ecosystems, (ii) microbial ecology along various environmental gradients, (iii) human, plant and animal microbiotes, as well as (iv) trophic interactions between bacterial communities and their predators.