Microbial Diversity and Processes in Lake Kivu (East Africa)

Lake Kivu is a deep meromictic and oligotrophic tropical African lake with a permanent
thermal- and haline stratification with huge accumulations of dissolved
CO2 and CH4 (ca. 300 km3 and 60 km3, respectively) in the deep anoxic monimolimnion
(from 60 o 480 m depth). Although there are a wealth of information
on the ecology of small eukaryotes and their trophic role on Kivu, available information
on prokaryotic planktonic assemblages is scarce. Molecular analysis of
archaeal and bacterial communities showed a vertical segregation imposed by the
permanent redoxcline. In relation to Bacteria, Actinobacteria, Betaproteobacteria,
Green Sulfur Bacteria and Bacteroidetes were the most commonly retrieved groups.
For Archaea, a marked dominance of Thaumarchaeota and Crenarchaeota (75% of
all archaeal OTUs) over Euryarchaeota was observed. In the anoxic hypolimnion,
Euryarchaoeta (Methanosarcinales and Methanocellales) lineages together with
Miscellaneous Crenarchaeotic Group phylotypes were mainly recovered. In turn,
Thaumarchaeota phylotypes were recovered in oxic and suboxic waters. CARDFISH
analyses over the first 100 m revealed the dominance of Bacteria (51.4% –
95.7% of DAPI-stained cells), especially Actinobacteria (epilimnion), Betaproteobacteria
(oxic-anoxic interface) and Bacteroidetes (upper hypolimnion), over
Archaea (1.0% – 4.5%; maximum abundances at the oxic-anoxic interface). In
turn, flow cytometry evidenced the dominance of HNA cells in the euphotic layer,
whereas the proportion of LNA cells increased with depth. HNA and LNA populations
were still observed in the anoxic hypolimnion suggesting facultative or
strict anaerobic metabolisms. The detection of distinct depth maxima of nitrate,
nitrite, archaeal amoA and Marine Thaumarchaeota 16S gene copy numbers
together with regularly detection of deep maxima of 3H-Thymidine uptake, and the
presence of low-light adapted GSB species point towards a strong link of N, C,
and S cycles in the redoxcline of Lake Kivu.