Bacterial Communities: Interactions to Scale

Abstract

In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

Untangling the knots: Co‐infection and diversity of Bartonella from wild gerbils and their associated fleas

“…The proper identification of co‐infecting bacterial species and their potential interactions within natural hosts are essential for the understanding of their biodiversity and evolutionary potential (Stubbendieck et al., ). Vector‐borne bacteria represent an extraordinary example of organisms constantly exposed to different ecological niches within their reservoir hosts and arthropod vectors, in which intra‐ and inter‐specific interactions continuously take place.…”

“…These are two different ecological niches, where interactions between residential and recently acquired bacteria take place (Cirimotich, Ramirez, & Dimopoulos, ; Hawlena et al., ; Jones, Knight, & Martin, ). Bacterial interactions can significantly affect their evolution and biodiversity by providing opportunities for horizontal gene transfer (HGT) events and/or periodic selection through competition (Palys, Nakamura, & Cohan, ; Stubbendieck, Vargas‐Bautista, & Straight, ; Toft & Andersson, ). Such events and interactions are more frequent between closely related bacterial species, since recombination events increase directly with sequence similarities (Majewski & Cohan, ; Tham et al., ; Wiedenbeck & Cohan, ), and several direct competitive strategies are targeted exclusively to outcompete close relatives that occupy similar niches (Aoki, Poole, Hayes, & Low, ; Riley & Wertz, ; Stubbendieck & Straight, ).…”

“…HGT events may lead to novel pathogen emergence, influence host adaptability and complicate the taxonomic delineation of co‐existing species by blurring species boundaries as a consequence of recombination (Jensen, ). Additionally, non‐transitive competitive interactions have been suggested as a cause of the high biodiversity observed in nature (Czaran, Hoekstra, & Pagie, ; Stubbendieck et al., ). Thus, the proper delineation of bacterial diversity circulating among vertebrate hosts and arthropod vectors, and the identification of the associated co‐occurrence patterns are essential for the understanding of the evolutionary potential and ecology of vector‐borne bacteria.…”

Characterization of microbial mixtures by mass spectrometry

“…This allows for better time resolution (incl. real time analysis) and avoids artifacts that result from the MALDI matrix, features that will be increasingly exploited in the analysis of mixtures …”

“…Applications of electrospray ionization coupled with tandem MS for rapid characterization of microorganisms (including their proteomes and metabolomes) have been steadily increasing, for example, in mapping bacteria with unsequenced genomes, in bacterial metaproteomics, and proteogenomics . A number of platforms utilizing atmospheric pressure ionization (API) methods developed in the last decade or so have been employed for microbial characterization, including mixtures …”