Vertical Distribution of Ammonia-Oxidizing Crenarchaeota and Methanogens in the Epipelagic Waters of Lake Kivu (Rwanda-Democratic Republic of the Congo)

Abstract

over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0-to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake. Lake Kivu is a meromictic lake located in the volcanic region between Rwanda and the Democratic Republic of the Congo and is the smallest of the African Great Rift Lakes. The monimolimnion of the lake contains a large amount of dissolved CO 2 and methane (300 km 3 and 60 km 3 , respectively) as a result of geological and biological activity (24,73,85). This massive accumulation converts Lake Kivu into one of the largest methane reservoirs in the world and into a unique ecosystem for geomicrobiologists interested in the methane cycle and in risk assessment and management (34,71,72,85). Comprehensive studies on the diversity and activity of planktonic populations of both large and small eukaryotes and their trophic interplay operating in the epilimnetic waters of the lake are available (33,39,49). Recent surveys have also provided a deeper insight into the seasonal variations of photosynthetic and heterotrophic picoplankton (67, 68), although very few data exist on the composition, diversity, and spatial distribution of bacterial and archaeal communities. In this regard, the studies conducted so far of the bacterial/archaeal ecology in Lake Kivu have been mostly focused on the implications on the methane cycle (34, 73), but none have addressed the presence and distribution of additional archaeal populations in the lake.During the last few years, microbial ecology studies carried out in a wide variety of habitats have provided compelling evidence of the ubiquity and abundance of mesophilic archaea (4,10,13,19). Moreover, the discovery of genes encoding enzymes related to nitrification and denitrification in archaeal metagenomes from soil and marine waters (29,86,88) and the isolation of the first autotrophic archaeal nitrifier (40) demonstrated that some archaeal groups actively participate in the carbon and nitrogen cycles (56,64,69). In relation to aquatic environments, genetic markers of ammonia-oxidizing archaea (AOA) of the marine Crenarchaeota group 1.1a (MCG1) have consistently been found in water masses of several oceanic regions (...

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

“…Eluents were then passed through 0.22-μm pore size filters (ISOPORE, Millipore, MA) to retain free-living prokaryotes. Filters for DNA extraction were preserved in Lysis Buffer as previously described [21], whereas filters for RNA extraction were preserved in 300 μL of RNAlater (Ambion) and all stored frozen until further analyses.…”

“…In spite of the presence of high amounts of CH 4 at the bottom of Lake Kivu, the CH 4 concentration in the oxic zone is surprisingly low compared to other lakes globally, due to intense microbial methane oxidation [18,19]. The vertical stratification of microbial taxa and their potential role in biogeochemical cycles in Lake Kivu were recently studied for both archaeal and bacterial counterparts using DNA-based analysis, and important key players of carbon, nitrogen, and sulfur cycles were identified [20,21]. Furthermore, evaluation of the effect of temporal variations on abundant versus rare taxa in different layers revealed that abundant taxa were more stable between two sampling times than rare ones, indicating a potentially higher contribution of rare taxa to biogeochemical processes [20].…”

Microbial Ecology of Lake Kivu

“…Furthermore, the detection of archaeal ammonia monooxygenase subunit A ( amoA ) genes at the depths where maxima of nitrate and nitrite were observed in two basins of the lake (Fig. 6.1 ) points to the involvement of planktonic archaea in nitri fi cation processes in the oxycline (Llirós et al 2010 ) . Although con fi rmation by in situ activity measurements is still needed, available data suggest an active contribution of ammonia-oxidizing archaea (AOA) in the N cycle of Lake Kivu.…”

“…The sharp oxycline and the oligotrophic nature of the lake's mixolimnion offer an optimal niche for the development of autotrophic nitrifying archaeal populations (Martens-Habbena et al 2009 ) . Llirós et al ( 2010 ) reported the recovery in Lake Kivu of a large set of sequences af fi liated to Marine Crenarchaeota Group 1.1a and assigned to a unique OTU (operational taxonomic unit) related to Nitrosopumilus maritimus , indicating the presence of active archaeal nitri fi ers in the lake water column. Furthermore, the detection of archaeal ammonia monooxygenase subunit A ( amoA ) genes at the depths where maxima of nitrate and nitrite were observed in two basins of the lake (Fig.…”

“…6.1 ). It results from nitri fi cation of ammonium released by decaying organic matter (Wimba 2008 ;Llirós et al 2010 ) . Consequently nitri fi cation may substantially contribute to oxygen depletion in the (Schubert et al 2006 ) .…”