247on the functional potential of freshwater bacterioplankton
(Debroas et al. 2009 ) Actinobacteria were mainly associated
with pathways for replication and repair, nucleotide, cofac-
tors, vitamin and energy metabolism. This was confi rmed by
the genome sequencing of a single cell acI-B1 isolate from
lake Mendota (Garcia et al. 2012 ). These functions seemed
indeed prevalent in this latter genome together with protein
metabolism, while stress response, motility and chemotaxis
were under-represented. Thus, it has been proposed that
freshwater Actinobacteria (at least clade acI-B) have a « pas-
sive » lifestyle, persisting on constant background concentra-
tion of resources (Livermore et al. 2014 ).
Freshwater Actinobacteria were suggested to have a lim-
ited carbohydrate substrate range of preferentially small
simple compounds, being primary polysaccharide degraders
or commensalists of polysaccahride degradation products by
other heterotrophic microorganisms (Garcia et al. 2012 ).
While amino sugars are a major component of bacteria and
algae cells, the amino sugars metabolism was the most repre-
sented in the metagenome (Debroas et al. 2009 ). The impli-
cation of members of clade acI in the mineralization of
N-acetylglucosamine, a breakdown product of chitin and
bacterial cell walls was also reported (Beier and Bertilsson
2011 ). Genes encoding for transporters of xylose, the most
abundant monosaccharide in terrestrial plants, arabinose or
ribose, and enzymes for their incorporation into the glycoly-
sis pathway have been detected in the genome of a acI-B1
member (Garcia et al. 2012 ). The nutrient uptake pattern of
acI Actinobacteria suggests adaptation to phytoplankton
exudates (Salcher et al. 2012 ), and cyanobacterial blooms
could affect the actinobacterial community composition
(Parveen et al. 2011 ). On the other hand, it has been sug-
gested that the comparatively minor fl uctuations in the abun-
dance of acI taxa point to a consistent source of energy
generated through actinorhodopsin, including the acI and
Luna lineages (Sharma et al. 2008 ). Although, various sub-
strate and incorporation rates observed for the freshwater
Actinobacteria may refl ect preferences of individual tribes
for different substrate sources (Buck et al. 2009 ), it is not
known whether genomes from different tribes refl ect differ-
ent adaptation patterns to peculiar conditions.
15.2.2 Phylogenomics of the Main Tribes
Phylogenetic analyses of both 16S rRNA gene and eight pro-
teins coding genes common to eleven actinobacterial
genomic fragments sampled from six different lakes
(Philosof et al. 2009 ; Ghylin et al. 2014 ) confi rmed the close-
ness of clade acIV to Acidimicrobium , while the sister group
of the AcI clade was less clearcut. In the 16S rRNA phylog-
eny, clade acI branch as a sister group to all Actinomycetales
orders except Frankiale , which emerges as a paraphyletic
group at the root of the Actinobacteria class. In the eight
protein concatenated phylogeny, the AcI clade is a sister
group to Acidothermus cellulolyticus , although moderately
supported, and shares a common ancestor with all
Actinomycetale orders except Micromonosporales ,
Glycomycetales ( Stackenbrandtia ) and Frankiales , which
emerge at the root of the Actinomycetales (Fig. 15.1a ).
Interestingly, freshwater Actinobacteria clades previously
defi ned from 16S rRNA sequences analysis were recovered
in the protein phylogeny. At the genomic level, clade acI-B
has the lowest G + C content (37–43 %) observed in the
Actinobacteria phylum, while the acI-A and acIV lineages
are moderately low G + C (41–50 % and 49–53 %) (Ghai
et al. 2012 ). Whatever the lineage, this low GC is associated
with a fast evolutionary rate, an excess of mutations from
A/T to G/C in clade acI-B, suggesting a G + C genome
enrichment for this clade, and different evolutionary con-
straints among clades. For all lineages, functional character-
ization of these genomic fragments was found to be mostly
related to nucleic and amino-acid transport and metabolism,
translation and ribosomal structure and biogenesis. Among
others, an arginine operon upstream the rRNA operon shows
a divergent organization depending on freshwater tribes (Fig.
15.1b ). While the arginine operon is almost complete except
for gene argG in acIV tribes, it is shuffl ed in the acI clade.
Indeed, arginine operons lack genes argG and argF in tribes
acI-A1 and acI-A7. ArgJ is also absent from the operon in
acI-A6 and the operon in acI-B1 is reduced to genes
argHRBC. We can speculate that the arginine genes were
scattered along the genome through rearrangements, as argG
and argF have been found elsewhere in single-cell genome
contigs. However, there is no evidence of the presence of
argJ or argD in the acI-B1 or argJ in acI-A6 genomes (but
only 97 % genome acI-B1 is assembled – Garcia et al. 2013 ).
It has been postulated that the turnover of operon structure of
genes with a close functional relationship can lead to adap-
tive changes in gene expression (Price et al. 2006 ). Thus, the
regulation of arginine metabolism, which is related to numer-
ous metabolic pathways, might refl ect tribes adaptations to
the nutrients present in particular niches.15.2.3 Genomic Features of ActinobacteriaThe independent 16S based selection for acI and acIV acti-
nobacterial genomic fragments from the six lakes revealed a
similar genomic organization around the rRNA operon, with
conserved synteny suggesting that both acI and acIV actino-
bacterial clades may have a unique rRNA operon. This fi nd-
ing is in agreement with the estimation of a low number of
rRNA operon in the genome of freshwater Actinobacteria
compared to that of their marine counterparts (Roux et al.
2011 ). Since a relation between rDNA operon number and15 Omic Approaches for Studying Microorganisms and Viruses