communication among microbial ecologists, a high-quality census needs full-length
16S rRNA gene sequences and the short sequence lengths provided by current NGS
methodologies need to be substantially improved (Amann and Rosselló-Mora
2016). Genomes and metagenomes currently available are growing exponentially
(Fig. 7.1), and single cell genomics permits to reach the genetic potential of a
microorganism without culturing. For the microbial world, the inadequacy of
methods and conceptual separation of microbiology from natural sciences with
strong ecological and evolutionary background such as zoology and botany should
not be an unaffordable challenge anymore. In fact, microbial systems may push
classical natural sciences disciplines and theoretical ecology forward to new
unexplored frontiers. An integrative approach prevails today in the environmental
sciences with an inclusive view on biological interactions networks (Faust and Raes
2012; Fuhrman et al. 2015), and on the integration of molecular biology at the
community and ecosystem levels (Raes and Bork 2008). Merging community
ecology and phylogenetics among co-occurring species can provide a new view for
the study of microbial assemblages in situ (Barberán and Casamayor 2014). The use
of phylogenetic approaches as a measure of biodiversity based on the phylogenetic
difference between species (i.e. phylogenetic diversity, PD), offers new perspectives
without previously fixing an operational taxonomic unit definition, and reduces to a
single value the whole community complexity (see below). This approach may help
to find patterns and to develop hypotheses based on the coexistence and adaptation
of closely related species and to try to unveil the processes that shape community
structure and composition.
7.3 A Natural History Perspective for Microorganisms
in High Mountain Lakes
High-altitude mountain lakes hold a larger microbial biodiversity than could be
initially expected in such very diluted waters. Typically, several hundred million
prokaryotic cells and around a million of microscopic eukaryotes are present per
litre of alpine lake water (Felip et al. 1999). In general, freshwater archaea in high
mountain lakes show one to two orders of magnitude lower abundances than
bacterial cells, and the richness within the Bacteria domain is substantially higher
than within the Archaea. For instance, the analysis of the plankton in three connected shallow Pyrenean lakes within the Aiguestortes i Estany de Sant Maurici
National Park estimated a bacterial richness of c. 2500 OTUs and an archaeal
richness of c. 900 OTUs (Fig. 7.2, upper panel). These estimations required a
sampling effort of c. 250,000 bacterial and c. 20,000 archaeal 16S rRNA gene
sequences (Fig. 7.2, lower panel), only accessible through recent NGS
technologies.
7 Towards a Microbial Conservation Perspective …
163
16S rRNA gene sequences and the short sequence lengths provided by current NGS
methodologies need to be substantially improved (Amann and Rosselló-Mora
2016). Genomes and metagenomes currently available are growing exponentially
(Fig. 7.1), and single cell genomics permits to reach the genetic potential of a
microorganism without culturing. For the microbial world, the inadequacy of
methods and conceptual separation of microbiology from natural sciences with
strong ecological and evolutionary background such as zoology and botany should
not be an unaffordable challenge anymore. In fact, microbial systems may push
classical natural sciences disciplines and theoretical ecology forward to new
unexplored frontiers. An integrative approach prevails today in the environmental
sciences with an inclusive view on biological interactions networks (Faust and Raes
2012; Fuhrman et al. 2015), and on the integration of molecular biology at the
community and ecosystem levels (Raes and Bork 2008). Merging community
ecology and phylogenetics among co-occurring species can provide a new view for
the study of microbial assemblages in situ (Barberán and Casamayor 2014). The use
of phylogenetic approaches as a measure of biodiversity based on the phylogenetic
difference between species (i.e. phylogenetic diversity, PD), offers new perspectives
without previously fixing an operational taxonomic unit definition, and reduces to a
single value the whole community complexity (see below). This approach may help
to find patterns and to develop hypotheses based on the coexistence and adaptation
of closely related species and to try to unveil the processes that shape community
structure and composition.
7.3 A Natural History Perspective for Microorganisms
in High Mountain Lakes
High-altitude mountain lakes hold a larger microbial biodiversity than could be
initially expected in such very diluted waters. Typically, several hundred million
prokaryotic cells and around a million of microscopic eukaryotes are present per
litre of alpine lake water (Felip et al. 1999). In general, freshwater archaea in high
mountain lakes show one to two orders of magnitude lower abundances than
bacterial cells, and the richness within the Bacteria domain is substantially higher
than within the Archaea. For instance, the analysis of the plankton in three connected shallow Pyrenean lakes within the Aiguestortes i Estany de Sant Maurici
National Park estimated a bacterial richness of c. 2500 OTUs and an archaeal
richness of c. 900 OTUs (Fig. 7.2, upper panel). These estimations required a
sampling effort of c. 250,000 bacterial and c. 20,000 archaeal 16S rRNA gene
sequences (Fig. 7.2, lower panel), only accessible through recent NGS
technologies.
7 Towards a Microbial Conservation Perspective …
163