Abstract
Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.
Highlights
IntroductionTesting ecological and evolutionary theory in a highly controlled manner using simple laboratory setups with one or two microbial species (Fraser and Keddy, 1997; Buckling et al, 2009) has produced important insights into ecological interactions–e.g., competition, cooperation, and crossfeeding interactions (Helling et al, 1987; Treves et al, 1998; Rozen and Lenski, 2000; Shou et al, 2007; Harcombe, 2010); the role of cheaters (MacLean and Gudelj, 2006); predator–prey interactions (Shertzer et al, 2002); and host–parasite interactions (Morgan et al, 2005)–and evolutionary processes–e.g., the evolution of coexistence (Good et al, 2017), coevolution between species (Hall et al, 2011; Brockhurst and Koskella, 2013), and eco-evolutionary feedback dynamics (Yoshida et al, 2003; Hiltunen and Becks, 2014)
Strains from the University of Helsinki culture collection (HAMBI) representing diverse taxa were initially screened for the ability to grow individually at 28◦C in two complex liquid media: the nutrient-rich proteose peptone yeast extract (PPY: 20 g proteose peptone and 2.5 g yeast extract in 1 l deionized H2O) medium or a custom lower-nutrient-level medium containing M9 salt solution and King’s B (KB) nutrients at a 1% concentration compared with full-strength medium, and 0.2 g l−1 protozoan pellets (Carolina Biological Supply Co., Burlington, United States)
Genomic elements associated with horizontal gene transfer, including plasmids, genomic islands, prophages, integrons, and insertion sequences, occur frequently among the strains, as do clustered regularly interspaced short palindromic repeats (CRISPR) arrays that might be associated with CRISPR/Cas systems conferring adaptive immunity against mobile genetic elements
Summary
Testing ecological and evolutionary theory in a highly controlled manner using simple laboratory setups with one or two microbial species (Fraser and Keddy, 1997; Buckling et al, 2009) has produced important insights into ecological interactions–e.g., competition, cooperation, and crossfeeding interactions (Helling et al, 1987; Treves et al, 1998; Rozen and Lenski, 2000; Shou et al, 2007; Harcombe, 2010); the role of cheaters (MacLean and Gudelj, 2006); predator–prey interactions (Shertzer et al, 2002); and host–parasite interactions (Morgan et al, 2005)–and evolutionary processes–e.g., the evolution of coexistence (Good et al, 2017), coevolution between species (Hall et al, 2011; Brockhurst and Koskella, 2013), and eco-evolutionary feedback dynamics (Yoshida et al, 2003; Hiltunen and Becks, 2014). There is an increasing awareness that ecological and evolutionary processes can be fundamentally altered in more complex multispecies communities owing to several features such as altered competitive interactions and multiple selection pressures (Dunham, 2007). Even a basic understanding of certain characteristics of microbial life such as horizontal gene transfer (Smillie et al, 2011), metabolic interactions and spatial heterogeneity (Elias and Banin, 2012; van Gestel et al, 2014) requires investigation of multispecies settings integral to them. Several key ecological features are specific to multispecies communities, such as diversity, stability, succession and high-order (e.g., fourway) species interactions (Bairey et al, 2016). There is a profound need to expand the biotic complexity of study systems used in the fields of experimental microbial ecology and evolution
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
