Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems. LNA_Study

Here we used flow cytometry (FCM) and filtration paired with amplicon sequencing to determine the abundance and composition of small, low nucleic acid (LNA)-content bacteria in a variety of freshwater ecosystems. We found that FCM clusters associated with LNA-content bacteria were ubiquitous across several ecosystems, varying from 50 to 90% of aquatic bacteria. Using filter size separation, we separated small LNA-content bacteria (passing 0.4 µm filter) from large bacteria (captured on 0.4 µm filter) and characterized communities with 16S amplicon sequencing. Small and large bacteria clearly represented different sub-communities within each ecosystems’ community. Moreover, we were able to identify individual operational taxonomical units (OTUs) that appeared exclusively with small bacteria or exclusively with large bacteria. Surprisingly, these exclusive OTUs clustered at the phylum level, with many of the OTUs appearing exclusively with small bacteria identified as candidate phyla (i.e. lacking cultured representatives) and symbionts. We propose that LNA-content bacteria observed with FCM represents an overarching group encompassing several previously characterized categories of bacteria (ultramicrobacteria, ultra-small bacteria, candidate phyla) that share many traits including small size and metabolic dependencies on other microorganisms.