Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems

Abstract

We used a partial 16S rRNA sequencing approach to compare the structure and composition of the bacterial communities in three large, deep subalpine lakes in France with those of communities in six shallow tropical reservoirs in Burkina Faso. Despite the very different characteristics of these ecosystems, we found that their bacterial communities share the same composition in regard to the relative proportions of the different phyla, suggesting that freshwater environmental conditions lead to convergence in this composition. In the same way, we found no significant difference in the richness and diversity of the bacterial communities in France and Burkina Faso. We defined core and satellite operational taxonomic units (OTUs) (sequences sharing at least 98% identity) on the basis of their abundance and their geographical distribution. The core OTUs were found either ubiquitously or only in temperate or tropical and subtropical areas, and they contained more than 70% of all the sequences retrieved in this study. In contrast, satellite OTUs were characterized by having a more restricted geographical distribution and by lower abundance. Finally, the bacterial community composition of these freshwater ecosystems in France and Burkina Faso was markedly different, showing that the history of these ecosystems and regional environmental parameters have a greater impact on the relative abundances of the different OTUs in each bacterial community than the local environmental conditions.

A Guide to the Natural History of Freshwater Lake Bacteria

“…The freshwater Actinobacteria are also present in the bottom waters (hypolimnion) of lakes (20), but their abundance often decreases with decreasing oxygen concentrations (3,205). This high level of abundance in the epilimnion has proven to be consistent across lake types, as the Actinobacteria are common among oligotrophic (101), mesotrophic (39,101,237), eutrophic (233), and dystrophic (141) lakes. Likewise, the dominance of the Actinobacteria is spread across the globe.…”

“…1 , manuscript in press at Environmental Microbiology (141a) (includes GenBank accession numbers FJ827781 to FJ828505); 2 , GenBank accession numbers for the sequenced clones are HQ386253 to HQ386631; 3 , GenBank accession numbers for the sequenced clones are FJ916807 to FJ916903 and HQ530565 to HQ532908, except HQ530583, HQ531638, and HQ532521. (Based on data from references 2, 3,4,11,20,22,24,27,35,38,41,42,44,45,46,48,49,52,61,63,69,73,74,82,83,84,85,89,93,95,101,105,106,108,116,124,126,127,134,135,139,140,141,147,148,149,15...…”

“…Likewise, the dominance of the Actinobacteria is spread across the globe. Studies have shown high actinobacterial abundances in lakes in North America (140), Europe (63), Africa (44,45,101), Asia (82,142,230), Australia (84), South America (35), and Antarctica (149,150).…”

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

“…Members of the acI lineage within the phylum Actinobacteria are an intriguing group of free-living ultramicrobacteria that dominate many freshwater ecosystems (Newton et al, 2011), including highnutrient eutrophic (Wu et al, 2007), low-nutrient oligotrophic (Humbert et al, 2009) and dystrophic lakes (Newton et al, 2006). They are also abundant in some marine estuaries (Glockner et al, 2000).…”

Biogeography of globally distributed bacteria in temperate and boreal Québec lakes as revealed by tag pyrosequencing of 16S rRNA genes

“…It is unclear if even deeper sequencing would have revealed the few common taxa seen in the global data set (Newton et al 2011) that were not detected in the Québec lakes. Much smaller data sets from temperate and tropical ecosystems also provided hints that freshwater lakes include a core set of common taxa (Humbert et al 2009). Other studies from circumpolar freshwaters indicated that the same common bacterial taxa can be identified throughout the pan-Arctic region (Crump et al 2009).…”