Lake Pavin History, geology, biogeochemistry, and sedimentology of a deep meromictic maar lake

© Springer International Publishing Switzerland 2016 245
T. Sime-Ngando et al. (eds.), Lake Pavin, DOI 10.1007/978-3-319-39961-4_15

Study of Prokaryotes and Viruses

in Aquatic Ecosystems by Metagenetic

and Metagenomic Approaches

Gisèle Bronner , Didier Debroas , François Enault ,

Mylène Hugoni , Isabelle Jouan-Dufournel , Isabelle Mary ,

Viviane Ravet , Simon Roux , and Najwa Taïb

Abstract

High-throughput sequencing methods have revolutionized the study of microbial communi-

ties in ecosytems. In this chapter, we present the use of metagenetics, targeted metagenom-

ics and viral metagenomics to depict the diversity and the role of Bacteria , Archaea and

viruses in the mixolimnion of the lake Pavin. Actinobacteria dominated the bacterial com-

munity and was represented by two typical clades: acI and acIV. Focusing on this phylum,

we describe its genomic properties characterized by a low GC content (42–52 %) and high

substitution rates. Phylogeny based on both SSU rRNA gene and concatenated proteins

showed that these clades represented different ecotypes. Archaea was a minor but active

component among prokaryotes. The Thaumarchaeota Marine Group I, already known to

play an important role in ammonia oxidation dominated the archaeal assemblage in surface

waters but surprisingly the Miscellaneous Euryarchaeotic Group (MEG) was the most

active in particular zones such as the oxycline. Finally, the analysis of viral particles by a

metagenomic approach in the lake Pavin was the fi rst study published about freshwater

temperate lakes. Among aquatic datasets, genetic richness of marine viromes was higher in

average than that of freshwater ones. The viral community was composed of viruses from

families of double-stranded ( Caudovirales ) and single-stranded ( Microviridae, Circoviridae,

Nanoviridae ) DNA viruses. The phylogeny of the complete Microviridae genomes from the

Lake Pavin virome led to the description of a new group, the Pichovirinae , and new “chi-

meric” genomes could be assembled, challenging the established view of ancient viral evo-

lutionary history.

Keywords

Bacteria • Archaea • Viruses • Metagenetics • Metagenomics • Viromes • High-throughput

sequencing

15.1 Introduction

Massive sequencing has provided fundamental insights into
the diversity of microbes and their function and roles in eco-
systems. Initially, this method was used largely as a way of

easily obtaining genomic information about organisms for

which culturing technique was unknown (Schloss and

Handelsman 2005 ). However, due to reduction of the cost

and decrease of the diffi culty of sequencing, « metagenom-

ics » has become a tool for studying any microbial or viral

community, regardless of cultivability. Metagenomics can

historically be defi ned as random shotgun sequencing of

DNA isolated from environmental samples. From sequence

data it is then possible to infer which organisms are present

in a sample ( i.e ., who is there?) as well as their functional

potential ( i.e. , what are they doing?). First metagenomics

G. Bronner • D. Debroas (*) • F. Enault • M. Hugoni
I. Jouan-Dufournel • I. Mary • V. Ravet • S. Roux • N. Taïb
LMGE, Laboratoire Microorganismes: Génome et Environnement,
UMR CNRS 6023 , Université Clermont-Auvergne, Université
Blaise Pascal , BP 80026 , 63177 Aubière Cedex , France
e-mail: [email protected]

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