Abstract
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.
Highlights
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms
To investigate the specificity of dependencies between free-living freshwater microorganisms, we focused on a group of cosmopolitan, yet streamlined, freshwater organisms from the actinobacterial lineage known as acI
Even when our cultures harbored reduced community-level diversity, they all contained more than one acI genotype and even multiple discrete populations as defined by 97% average nucleotide identity (ANI)
Summary
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. The fact that mixed cultures containing acI organisms do survive tests and propagations [14] serves as strong support that the free-living acI microorganisms are highly dependent on interactions with other microorganisms. Populations represented by these top 31 MAGs were assumed to be the dominant model community members in each of the cultures from which they were assembled (Table 1).
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