Some ecological trends that have already been observed for macroorganisms, such as taxa-area or distance-decay relationships [1], and especially the existence of biogeographical patterns, have been proposed to possibly exist also for microorganisms, thus pointing to the existence of common, global rules that govern the ecology of all living forms. Some analyses support the ubiquity of several prokaryotic species
[2, 3], but also the apparent existence of biogeographic patterns for AG-881 price some others [3–7]. The study of ecological trends in microorganisms has been traditionally hampered by different factors. First, the methods used to catalogue microbial diversity (mostly based on sequencing the 16S rDNA gene) are expensive, time-consuming, biased and inadequate for massive screening, although technologic advances in DNA sequencing technology can change this picture dramatically [8–10]. Another PRIMA-1MET clinical trial serious problem is the lack of a proper concept of prokaryote species. The current definition is mainly based on genotypic characteristics, such as the percentage of DNA-DNA hybridization or the percentage of identity between the 16S rDNA molecules [11]. However,
this 3-Methyladenine in vitro approach is known to group rather different strains together which should probably be considered as different species (as in Escherichia coli), or to separate organisms with an almost identical gene complement (as in the genus Bacillus). The ongoing debate on this topic includes the proposal that similarity in lifestyle, and not just in genes, is the best approach to classify microorganisms [12, 13]. Similar ecological and metabolic features are scattered through different clades among the prokaryotic world, conforming
Pregnenolone specific metabolic groups of prokaryotes, such as the different metabolic types of sulfur bacteria [14]. Polyphasic approaches [15], including an overview on genotypic, phenotypic, and ecological features, would be necessary to better understand the global distribution of prokaryotes. But in practice, most studies simply use the so-called Operational Taxonomic Units (OTUs) [16] obtained, for instance, by grouping 16rDNA genes at the 97-98% threshold of identity, as a way to circumvent the absence of an adequate definition of species [17]. Also the massive number of existing species makes cataloguing microbial diversity difficult [18]. Most sampling efforts miss present species, which, in some cases, can produce an inadequate picture of the patterns that underlie community structure [1]. Furthermore, knowledge about the most determining factors that shape the distribution of bacteria in the different environments is still limited. It is quite usual to ascribe whole bacterial clades to a single environment by identifying them as for instance, marine or terrestrial.
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