Deciphering Interactions Within a 4-Strain Riverine Bacterial Community.

The dynamics of a community of four planktonic bacterial strains isolated from river water was followed in R2 broth for 72 h in batch experiments. These strains were identified as Janthinobacterium sp., Brevundimonas sp., Flavobacterium sp. and Variovorax sp. 16S rRNA gene sequencing and flow cytometry analyses were combined to monitor the change in abundance of each individual strain in bi-cultures and quadri-culture. Two interaction networks were constructed that summarize the impact of the strains on each other's growth rate in exponential phase and carrying capacity in stationary phase. The networks agree on the absence of positive interactions but also show differences, implying that ecological interactions can be specific to particular growth phases. Janthinobacterium sp. was the fastest growing strain and dominated the co-cultures. However, its growth rate was negatively affected by the presence of other strains 10 to 100 times less abundant than Janthinobacterium sp. In general, we saw a positive correlation between growth rate and carrying capacity in this system. In addition, growth rate in monoculture was predictive of carrying capacity in co-culture. Taken together, our results highlight the necessity to take growth phases into account when measuring interactions within a microbial community. In addition, evidence that a minor strain can greatly influence the dynamics of a dominant one underlines the necessity to choose population models that do not assume a linear dependency of interaction strength to abundance of other species for accurate parameterization from such empirical data.

Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains.

BACKGROUND: Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome. RESULTS: We sequenced and assembled de novo the complete genome sequences of five V. fluvialis isolates recovered from marine sponges. Pangenome analysis of the V. fluvialis species (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered all V. fluvialis species together and separated them from other sequenced Vagococcus species. V. fluvialis strains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequenced V. fluvialis strains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes. CONCLUSIONS: Our findings highlight the dynamics and plasticity of the V. fluvialis genome. The abundance of mobile genetic elements in the genomes of sponge-isolated V. fluvialis strains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.

The Dynamic of a River Model Bacterial Community in Two Different Media Reveals a Divergent Succession and an Enhanced Growth of Most Strains Compared to Monocultures.

The dynamic of a community of 20 bacterial strains isolated from river water was followed in R2 broth and in autoclaved river water medium for 27 days in batch experiments. At an early stage of incubation, a fast-growing specialist strain, Acinetobater sp., dominated the community in both media. Later on, the community composition in both media diverged but was highly reproducible across replicates. In R2, several strains previously reported to degrade multiple simple carbon sources prevailed. In autoclaved river water, the community was more even and became dominated by several strains growing faster or exclusively in that medium. Those strains have been reported in the literature to degrade complex compounds. Their growth rate in the community was 1.5- to 7-fold greater than that observed in monoculture. Furthermore, those strains developed simultaneously in the community. Together, our results suggest the existence of cooperative interactions within the community incubated in autoclaved river water.

Carbon utilization profiles of river bacterial strains facing sole carbon sources suggest metabolic interactions.

Microbial communities play a key role in water self-purification. They are primary drivers of biogenic element cycles and ecosystem processes. However, these communities remain largely uncharacterized. In order to understand the diversity-heterotrophic activity relationship facing sole carbon sources, we assembled a synthetic community composed of 20 'typical' freshwater bacterial species mainly isolated from the Zenne River (Belgium). The carbon source utilization profiles of each individual strain and of the mixed community were measured in Biolog Phenotype MicroArrays PM1 and PM2A microplates that allowed testing 190 different carbon sources. Our results strongly suggest interactions occurring between our planktonic strains as our synthetic community showed metabolic properties that were not displayed by its single components. Finally, the catabolic performances of the synthetic community and a natural community from the same sampling site were compared. The synthetic community behaved like the natural one and was therefore representative of the latter in regard to carbon source consumption.