Hidden in plain sight\u2014highly abundant and diverse planktonic freshwater Chloroflexi

Maliheh Mehrshad,Shin-Ichi Nakano,Michaela M Salcher,Yusuke Okazaki,Karel Šimek,Adrian-Stefan Andrei,Rohit Ghai

doi:10.1186/s40168-018-0563-8

Abstract

BackgroundRepresentatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.ResultsHere, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.ConclusionsExtending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.

Highlights

The only genomic insights into their lifestyle come from a single metagenomic assembled genome (MAG) from Lake Michigan along with in situ expression patterns that revealed CL500-11 to be flagellated, aerobic, photoheterotrophic bacteria, playing a major role in demineralization of nitrogen-rich dissolved organic matter in the hypolimnion [16]
Another lineage is the CL500-9 cluster [12] that was described as a freshwater sister lineage of the marine SAR202 cluster [17], but since the original discovery, there have been no further reports of its presence in other freshwater environments
Using publicly available metagenomic data supplemented with additional sequencing from both epilimnion and hypolimnion at multiple sites, we describe three novel class-level groups of freshwater Chloroflexi, along with a diverse phylogenetic assortment of genomes dispersed virtually over the entire phylum

Summary

Introduction

Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. The only genomic insights into their lifestyle come from a single metagenomic assembled genome (MAG) from Lake Michigan (estimated completeness 90%) along with in situ expression patterns that revealed CL500-11 to be flagellated, aerobic, photoheterotrophic bacteria, playing a major role in demineralization of nitrogen-rich dissolved organic matter in the hypolimnion [16]. Another lineage is the CL500-9 cluster [12] that was described as a freshwater sister lineage of the marine SAR202 cluster ( class “Ca. Monstramaria”) [17], but since the original discovery, there have been no further reports of its presence in other freshwater environments. Apart from these, there are only sporadic reports (of 16S rRNA sequences) for pelagic Chloroflexi, with little accompanying ecological information (e.g., SL56 and TK10) [11, 15, 18,19,20]

Methods

Results

Conclusion