253Phylogenomic profi ling and genomic analyses of fresh-
water Actinobacteria highlighted both reduced, AT-rich
genomes and potential adaptation to peculiar nutrient niches.
Their capabilities to metabolise simple carbohydrate com-
pounds from degrading organisms, including amino sugar,
and potentially produce energy through actinorhodopsin can
explain their dominance in freshwater lakes. On the other
hand, some driving forces that are usually advanced for
genome reduction in free living microorganisms do not hold
for freshwater Actinobacteria. Considering Archaea, our
work revealed different patterns of active archaeal assem-
blages in the epilimnion and the oxycline of Lake Pavin and
suggested that Thaumarchaeota MGI were not obligate
ammonia-oxidizers. Moreover, this work highlighted the
importance of studying groups considered as “minor groups”
that could nevertheless be active. Those taxa, with no culti-
vated member and present in small proportions can be over-
represented in the active fraction and may thus play key
functional role in freshwater ecosystems. Finally, viruses
from freshwater viromes belong to families classically
observed in aquatic systems such as Caudovirales and differ-
ent families of small ssDNA viruses. Yet, genomic and phy-
logenetic analyses revealed that viruses are specifi c to these
ecosystems as they form distinct clades for all the cited fami-
lies. These studies are however hindered by the lack of culti-
vated references and additional metagenomic datasets will
be required to better understand the extent of freshwater
virus diversity and their dynamics.
Acknowledgement We are indebted to Dr Steven M. SHORT,
University of Toronto (Canada), for a critical review of the
manuscript.
References
Allgaier M, Brückner S, Jaspers E, Grossart H-P (2007) Intra- and
inter-lake variability of free-living and particle-associated
Actinobacteria communities. Environ Microbiol 9:2728–2741
Auguet J-C, Nomokonova N, Camarero L, Casamayor EO (2011)
Seasonal changes of freshwater ammonia-oxidizing archaeal assem-
blages and nitrogen species in oligotrophic alpine lakes. Appl Env
Microbiol 77:1937–1945
Barberán A, Fernández-Guerra A, Auguet J-C, Galand PE, Casamayor
EO (2011) Phylogenetic ecology of widespread uncultured clades
of the Kingdom Euryarchaeota. Mol Ecol 20:1988–1996
Batut B, Knibbe C, Marais G, Daubin V (2014) Reductive genome evo-
lution at both ends of the bacterial population size spectrum. Nat
Rev Microbiol Dec 12(12):841–850
Beier S, Bertilsson S (2011) Uncoupling of chitinase activity and
uptake of hydrolysis products in freshwater bacterioplankton.
Limnol Oceanogr 56:1179–1188
Blazewicz SJ, Barnard RL, Daly RA, Firestone MK (2013) Evaluating
rRNA as an indicator of microbial activity in environmental com-
munities: limitations and uses. ISME J 7:2061–2068
Boucher D, Jardillier L, Debroas D (2006) Succession of bacterial com-
munity composition over two consecutive years in two aquatic sys-
tems: a natural lake and a lake-reservoir. FEMS Microbiol Ecol
55:79–97
Buck U, Grossart H-P, Amann R, Pernthaler J (2009) Substrate
incorporation patterns of bacterioplankton populations in strati-
fi ed and mixed waters of a humic lake. Environ Microbiol
11:1854–1865
Casamayor EO, Massana R, Benlloch S, Ovreas L, Diez B, Goddard VJ
et al (2002) Changes in archaeal, bacterial and eukaryal assem-
blages along a salinity gradient by comparison of genetic fi nger-
printing methods in a multipond solar saltern. Environ Microbiol
4:338–348
Debroas D, Humbert JF, Enault F, Bronner G, Faubladier M, Cornillot
E (2009) Metagenomic approach studying the taxonomic and func-
tional diversity of the bacterial community in a mesotrophic lake
(Lac du Bourget–France). Environ Microbiol 11:2412–2424
DeLong EF (1992) Archaea in coastal marine environments. Proc Natl
Acad Sci U S A 89:5685–5689
DeLong EF (1998) Everything in moderation: archaea as “non-
extremophiles.”. Curr Opin Genet Dev 8:649–654
Diemer GS, Stedman KM (2012) A novel virus genome discovered in
an extreme environment suggests recombination between unrelated
groups of RNA and DNA viruses. Biol Direct 7:13
Dunlap DS, Ng TFF, Rosario K, Barbosa JG, Greco AM, Breitbart M,
Hewson I (2013) Molecular and microscopic evidence of viruses in
marine copepods. Proc Natl Acad Sci U S A 110:1375–1380
Fancello L, Trape S, Robert C, Boyer M, Popgeorgiev N, Raoult D,
Desnues C (2013) Viruses in the desert: a metagenomic survey of
viral communities in four perennial ponds of the Mauritanian
Sahara. ISME J 7:359–369
Galand PE, Lovejoy C, Vincent WF (2006) Remarkably diverse and
contrasting archaeal communities in a large arctic river and the
coastal Arctic Ocean. Aquat Microb Ecol 44:115–126
Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba
A, Stepanauskas R, Grossart H-P, Woyke T, Warnecke F (2012)
Metabolic potential of a single cell belonging to one of the most
abundant lineages in freshwater bacterioplankton. ISME
J 7:137–147
Garcia SL, Salka I, Grossart H-P, Warnecke F (2013) Depth-discrete
profi les of bacterial communities reveal pronounced spatio- temporal
dynamics related to lake stratifi cation. Environ Microbiol Rep
5:549–555
Ghai R, McMahon KD, Rodriguez-Valera F (2012) Breaking a para-
digm: cosmopolitan and abundant freshwater actinobacteria are low
GC. Environ Microbiol Rep 4:29–35
Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F (2014)
Key roles for freshwater Actinobacteria revealed by deep metage-
nomic sequencing. Mol Ecol 23:6073–6090
Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest
KT, ... McMahon KD (2014) Comparative single-cell genomics
reveals potential ecological niches for the freshwater acI
Actinobacteria lineage. ISME J 8(12):1–14
Giovannoni SJ, Thrash CJ, Temperton B (2014) Implications of stream-
lining theory for microbial ecology. ISME J 8(8):1553–1565
Grossart H-P, Frindte K, Dziallas C, Eckert W, Tang KW (2011)
Microbial methane production in oxygenated water column of an
oligotrophic lake. Proc Natl Acad Sci 108:19657–19661
Hahn MW, Pöckl M (2005) Ecotypes of planktonic actinobacteria with
identical 16S rRNA genes adapted to thermal niches in temperate,
subtropical, and tropical freshwater habitats. Appl Environ
Microbiol 71:766–773
Hahn MW, Lünsdorf H, Wu Q, Schauer M, Höfl e MG, Boenigk J,
Stadler P (2003) Isolation of novel ultramicrobacteria classifi ed as
actinobacteria from fi ve freshwater habitats in Europe and Asia.
Appl Environ Microbiol 69:1442–1451
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims
H, Wagner M (2008) A moderately thermophilic ammonia-15 Omic Approaches for Studying Microorganisms and Viruses