Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria

Lívia Kolesár Fecskeová,Martina Hanusová,Petr Znachor,Kasia Piwosz,Michal Koblížek,Jiří Nedoma

doi:10.1038/s41598-019-55210-x

Abstract

The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.

Highlights

PufM expression in freshwater communities of anoxygenic phototrophic bacteria Lívia Kolesár Fecskeová[1], Kasia Piwosz[1], Martina Hanusová[1], Jiří Nedoma[2], Petr Znachor2 & Michal Koblížek1*
We found that pufM expression underwent a strong diel cycle and was expressed only during the night in both lakes (Fig. 1)
One of the main results of this study is the inhibition of pufM expression during daylight hours in natural freshwater environments

Summary

Introduction

PufM expression in freshwater communities of anoxygenic phototrophic bacteria Lívia Kolesár Fecskeová[1], Kasia Piwosz[1], Martina Hanusová[1], Jiří Nedoma[2], Petr Znachor2 & Michal Koblížek1*. The first cultured APB species were anaerobic Proteobacteria (representatives of current genera Chromatium, Rhodospirillum and Rhodobacter), and Chlorobi[5] These organisms express their photosynthetic genes and conduct photosynthesis under anaerobic conditions, and their pigment synthesis is repressed by oxygen[6]. In contrast to classical anaerobic APB, these organisms grew, metabolized and synthesized BChl under fully oxic conditions[9] These species are called Aerobic Anoxygenic Phototrophic (AAP) bacteria, and are common in many natural habitats. They represent 1–10% of total bacteria in the euphotic zone of the ocean contributing significantly to the secondary carbon production[10], reviewed by Koblížek[11]. They are common in freshwaters, where they represent up to 37% of total bacteria[12,13,14]

Methods

Results

Conclusion