7.3.2 Archaea
Archaea are commonly present in freshwater plankton, but most have remained
unseen to aquatic ecologists and limnologists. For many years, archaea strains
available in the laboratory were restricted to methanogens and microorganisms
adapted to extreme temperature, pH and salinity. Apparently, the archaeal metabolic
diversity and ecological distribution appeared more limited than their bacterial
counterparts. In the most recent years, the environmental ribosomal RNA surveys
unveiled Archaea as ubiquitous in freshwaters. Most of them but methanogens are
distantly related to any laboratory strain, and there is ample room for new discoveries related to archaea and cold water habitats in lakes (Auguet et al. 2010).
Curiously, freshwater archaeal richness and diversity appeared higher than in other
biomes such as the oceans and soils after a meta-analysis of globally distributed
clone libraries of the 16S rRNA gene (Auguet et al. 2010).
In the Pyrenean high mountain lakes, archaea are widespread and diverse. Archaea
could be detected in 90% of surface waters in a large dataset of lakes examined
(n = 313), with relative abundances generally up to 10% of the bacterioplankton
sequences (Ortiz-Alvarez and Casamayor 2016). Alpine archaea belong to 13 different lineages (Fig. 7.9), with Pacearchaeota and Woesearchaeota as the most
common groups, followed by Micrarchaeota–Diapherotrites (Euryarchaeota MEG
cluster), Methanogens, Thermoplasmata and planktonic AOA (ammonia-oxidising
Thaumarchaeota). Minor groups are related to the SM1K20 cluster, Aenigmarchaeota
(Euryarchaeota DSEG cluster), MCG (Miscellaneous Crenarchaeotic Group, currently Bathyarcheota) and soil AOA. In subsurface and bottom waters of deeper lakes,
accumulations of AOA and Aenigmarchaeota are however detected (Auguet et al.
2012; Restrepo-Ortiz and Casamayor 2013). This extensive study in the Pyrenean
lacustrine district unveiled the environmental preferences and habitat breadth for the
different lineages. The species with wide niche breadth, i.e. generalists, were related to
methanogens and Aenigmarchaeota, whereas the most specialists were
Thermoplasmata, Micrarchaeota and AOA. Pacearchaeota and Woesearchaeota, the
most abundant and widespread taxa, showed intermediate values (Ortiz-Alvarez and
Casamayor 2016).
The metabolic potential of most lacustrine archaea and the impact in freshwater
biogeochemical cycles are largely unknown. In some cases, the biogeochemical
activities of Archaea can be environmentally traced by the study of functional genes
coding for reactive enzymes such as the ammonia monooxygenase (Amo) present in
AOA (Fernàndez-Guerra and Casamayor 2012). The Amo plays a fundamental role
in the interconnection between N fixation and N losses, catalysing the oxidisation of
NH 4
+ to NO 2
− . Nitrification helps to remove excessive ammonium nitrogen and
prevent lakes from eutrophication. Thus, increasing evidence suggests that Archaea
may play a significant role in ammonia oxidation in freshwaters in general, and
specifically in alpine lakes with submerged vegetation (Vila-Costa et al. 2016). In
fact, the interaction between microbial ecology and macrophytes ecology determines
the ecosystem-level denitrification and the submerged vegetation landscape has a
170
E.O. Casamayor
Archaea are commonly present in freshwater plankton, but most have remained
unseen to aquatic ecologists and limnologists. For many years, archaea strains
available in the laboratory were restricted to methanogens and microorganisms
adapted to extreme temperature, pH and salinity. Apparently, the archaeal metabolic
diversity and ecological distribution appeared more limited than their bacterial
counterparts. In the most recent years, the environmental ribosomal RNA surveys
unveiled Archaea as ubiquitous in freshwaters. Most of them but methanogens are
distantly related to any laboratory strain, and there is ample room for new discoveries related to archaea and cold water habitats in lakes (Auguet et al. 2010).
Curiously, freshwater archaeal richness and diversity appeared higher than in other
biomes such as the oceans and soils after a meta-analysis of globally distributed
clone libraries of the 16S rRNA gene (Auguet et al. 2010).
In the Pyrenean high mountain lakes, archaea are widespread and diverse. Archaea
could be detected in 90% of surface waters in a large dataset of lakes examined
(n = 313), with relative abundances generally up to 10% of the bacterioplankton
sequences (Ortiz-Alvarez and Casamayor 2016). Alpine archaea belong to 13 different lineages (Fig. 7.9), with Pacearchaeota and Woesearchaeota as the most
common groups, followed by Micrarchaeota–Diapherotrites (Euryarchaeota MEG
cluster), Methanogens, Thermoplasmata and planktonic AOA (ammonia-oxidising
Thaumarchaeota). Minor groups are related to the SM1K20 cluster, Aenigmarchaeota
(Euryarchaeota DSEG cluster), MCG (Miscellaneous Crenarchaeotic Group, currently Bathyarcheota) and soil AOA. In subsurface and bottom waters of deeper lakes,
accumulations of AOA and Aenigmarchaeota are however detected (Auguet et al.
2012; Restrepo-Ortiz and Casamayor 2013). This extensive study in the Pyrenean
lacustrine district unveiled the environmental preferences and habitat breadth for the
different lineages. The species with wide niche breadth, i.e. generalists, were related to
methanogens and Aenigmarchaeota, whereas the most specialists were
Thermoplasmata, Micrarchaeota and AOA. Pacearchaeota and Woesearchaeota, the
most abundant and widespread taxa, showed intermediate values (Ortiz-Alvarez and
Casamayor 2016).
The metabolic potential of most lacustrine archaea and the impact in freshwater
biogeochemical cycles are largely unknown. In some cases, the biogeochemical
activities of Archaea can be environmentally traced by the study of functional genes
coding for reactive enzymes such as the ammonia monooxygenase (Amo) present in
AOA (Fernàndez-Guerra and Casamayor 2012). The Amo plays a fundamental role
in the interconnection between N fixation and N losses, catalysing the oxidisation of
NH 4
+ to NO 2
− . Nitrification helps to remove excessive ammonium nitrogen and
prevent lakes from eutrophication. Thus, increasing evidence suggests that Archaea
may play a significant role in ammonia oxidation in freshwaters in general, and
specifically in alpine lakes with submerged vegetation (Vila-Costa et al. 2016). In
fact, the interaction between microbial ecology and macrophytes ecology determines
the ecosystem-level denitrification and the submerged vegetation landscape has a
170
E.O. Casamayor