Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi

Abstract

21Background: Representatives of the phylum Chloroflexi, though reportedly highly abundant (up to 22

Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences

“…nov.) within the ‘Patescibacteria’ group, and ‘ Candidatus Aquadulcis frankliniae’ gen. nov. sp. nov., represented by WB4_1_0576 (GenBank: RFPZ00000000), from a novel genus within the recently described class ‘ Candidatus Limnocylindria’ (Mehrshad et al ., 2018) (‘Chloroflexi’). Additional description of these taxa including protologues is available as Supplementary Material (Text S3 and Fig.…”

“…BQH has been used to explain the genome reduction of taxa with large population size (small effective population sizes are typically used to explain genome reductions such as those observed in endosymbionts), as observed in the marine members of the genera ‘ Ca . Pelagibacter’ and Prochlorococcus (Morris et al ., 2012; Giovannoni et al ., 2014) as well as in freshwater microorganisms including members of ‘Actinobacteria’ and ‘Chloroflexi’ (Mehrshad et al ., 2018; Neuenschwander et al ., 2018). Here, we show that the effects predicted by BQH may be observed across Bacteria .…”

“…In fact, only a 10th of freshwater microbial cells belong to cultivated species or genera, one of the smallest cultivated fractions among all major environments on Earth [i.e., environments with over 10 25 microbial cells estimated worldwide (Lloyd et al ., 2018); but see also (Martiny, 2019)]. Recent efforts to recover metagenome‐assembled genomes (MAGs) from freshwater environments have largely targeted specific taxa (Cabello‐Yeves et al ., 2017; He et al ., 2017; Mehrshad et al ., 2018; Neuenschwander et al ., 2018; Tsementzi et al ., 2019).…”

“…This species phylogeny obtained by coalescent‐based reconstruction based on the trees of 67 genes. In both panels the genomes derived from metagenomes (MAGs) are prefixed with a label in squared brackets indicating the study from where they were derived, including: A13 (Albertsen et al ., 2013), B15 (Brown et al ., 2015), M18 (Mehrshad et al ., 2018), P18 (Parks et al ., 2018), and Z18 (Zhao et al ., 2018), as well as the current study (This study) or publicly available data currently missing a published manuscript (Unpub). Genomes including a 16S rRNA gene sequence are marked with an asterisk.…”

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

“…Genomeresolved studies focusing on other ubiquitous lineages, such as LD12 (Alphaproteobacteria) and acI (Actinobacteria), have also shown that geographically isolated lakes are generally inhabited by distinct species (i.e., ANI < 95%) [39,40]. Meanwhile, genomes sharing ANI > 95% were isolated from lakes located up to hundreds of kilometers apart and separated by the Alps [41,42] and even between lakes on different continents [40,43,44]. No global phylogeographic patterns at the phylogenetic resolutions of ITS [45] and ANI [46] were observed for Microcystis, ubiquitous bloom-forming freshwater cyanobacteria.…”