Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle

Lake Kivu: Limnology and biogeochemistry of a tropical great lake

We review available data on archaea, bacteria and small eukaryotes in anattempt to provide a general picture of microbial diversity, abundances and microbedrivenprocesses in Lake Kivu surface and intermediate waters (ca. 0–100 m). Thevarious water layers present contrasting physical and chemical properties andharbour very different microbial communities supported by the vertical redoxstructure. For instance, we found a clear vertical segregation of archaeal and bacterialassemblages between the oxic and the anoxic zone of the surface waters. Thepresence of speci fi c bacterial (e.g. Green Sulfur Bacteria) and archaeal (e.g.ammonia-oxidising archaea) communities and the prevailing physico-chemicalconditions point towards the redoxcline as the most active and metabolically diversewater layer. The archaeal assemblage in the surface and intermediate water columnlayers was mainly composed by the phylum Crenarchaeota ,by the recently de fi nedphylum Thaumarchaeota and by the phylum Euryarchaeota .In turn, the bacterialassemblage comprised mainly ubiquitous members of planktonic assemblages offreshwater environments ( Actinobacteria ,Bacteroidetes and Betaproteobacteria among others) and other less commonly retrieved phyla (e.g. Chlorobi ,Clostridiumand Deltaproteobacteria ). The community of small eukaryotes (<5 m m) mainlycomprised Stramenopiles ,Alveolata ,Cryptophyta ,Chytridiomycota ,Kinetoplasteaand Choano fl agellida ,by decreasing order of richness. The total prokaryoticabundance ranged between 0.5 × 10 6 and 2.0 × 10 6 cells mL −1 ,with maxima locatedin the 0–20 m layer, while phycoerythrin-rich Synechococcus -like picocyanobacteriapopulations were comprised between 0.5 × 10 5 and 2.0 × 10 5 cells mL −1 in the samesurface layer. Brown-coloured species of Green Sulfur Bacteria permanentlydeveloped at 11m depth in Kabuno Bay and sporadically in the anoxic waters of thelower mixolimnion of the main basin. The mean bacterial production was estimatedto 336 mg C m −2 day −1 .First estimates of the re-assimilation by bacterioplankton ofdissolved organic matter excreted by phytoplankton showed high values of dissolvedprimary production (ca. 50% of total production). The bacterial carbon demand cantotally be fuelled by phytoplankton production. Overall, recent studies have revealeda high microbial diversity in Lake Kivu, and point towards a central role of microbesin the biogeochemical and ecological functioning of the surface layers, comprisingthe mixolimnion and the upper chemocline.info:eu-repo/semantics/publishe

Diversity and Processes in Lake Kivu (East Africa)

info:eu-repo/semantics/nonPublishe

Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave

Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using C-13-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the 'heavy' DNA and sequences related to nitriteoxidizing bacteria Nitrospira and Candidatus 'Nitrotoga' were also detected in the 'heavy' DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylovorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave. Other sequences detected in the bacterial 16S rRNA clone library included Verrucomicrobia, Firmicutes, Bacteroidetes, alphaproteobacterial Rhodobacterales and gammaproteobacterial Xanthomonadales. Archaeal 16S rRNA sequences retrieved were restricted within two groups, namely the Deep-sea Hydrothermal Vent Euryarchaeota group and the Miscellaneous Crenarchaeotic group. No sequences related to known sulfur-oxidizing archaea, ammonia-oxidizing archaea, methanogens or anaerobic methane-oxidizing archaea were detected in this clone library. The results provided molecular biological evidence to support the hypothesis that Movile Cave is driven by chemolithoautotrophy, mainly through sulfur oxidation by sulfur-oxidizing bacteria and reveal that ammonia-and nitrite-oxidizing bacteria may also be major primary producers in Movile Cave. The ISME Journal (2009) 3, 1093-1104; doi:10.1038/ismej.2009.57; published online 28 May 200

Iron-dependent nitrogen cycling in a ferruginous lake and the nutrient status of Proterozoic oceans

Nitrogen limitation during the Proterozoic has been inferred from the great expanse of ocean anoxia under low-O2 atmospheres, which could have promoted NO3− reduction to N2 and fixed N loss from the ocean. The deep oceans were Fe rich (ferruginous) during much of this time, yet the dynamics of N cycling under such conditions remain entirely conceptual, as analogue environments are rare today. Here we use incubation experiments to show that a modern ferruginous basin, Kabuno Bay in East Africa, supports high rates of NO3− reduction. Although 60% of this NO3− is reduced to N2 through canonical denitrification, a large fraction (40%) is reduced to NH4+, leading to N retention rather than loss. We also find that NO3− reduction is Fe dependent, demonstrating that such reactions occur in natural ferruginous water columns. Numerical modelling of ferruginous upwelling systems, informed by our results from Kabuno Bay, demonstrates that NO3− reduction to NH4+ could have enhanced biological production, fuelling sulfate reduction and the development of mid-water euxinia overlying ferruginous deep oceans. This NO3− reduction to NH4+ could also have partly offset a negative feedback on biological production that accompanies oxygenation of the surface ocean. Our results indicate that N loss in ferruginous upwelling systems may not have kept pace with global N fixation at marine phosphorous concentrations (0.04–0.13 μM) indicated by the rock record. We therefore suggest that global marine biological production under ferruginous ocean conditions in the Proterozoic eon may thus have been P not N limited.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage

Este artículo contiene 13 páginas, 7 figuras, 1 tabla.Members of the archaeal Miscellaneous Crenarchaeotic Group (MCG) are among the most successful microorganisms on the planet. During its evolutionary diversification, this very diverse group has managed to cross the saline–freshwater boundary, one of the most important evolutionary barriers structuring microbial communities. However, the current understanding on the ecological significance of MCG in freshwater habitats is scarce and the evolutionary relationships between freshwater and saline MCG remains poorly known. Here, we carried out molecular phylogenies using publicly available 16S rRNA gene sequences from various geographic locations to investigate the distribution of MCG in freshwater and saline sediments and to evaluate the implications of saline– freshwater transitions during the diversification events. Our approach provided a robust ecological framework in which MCG archaea appeared as a core generalist group in the sediment realm. However, the analysis of the complex intragroup phylogeny of the 21 subgroups currently forming the MCG lineage revealed that distinct evolutionary MCG subgroups have arisen in marine and freshwater sediments suggesting the occurrence of adaptive evolution specific to each habitat. The ancestral state reconstruction analysis indicated that this segregation was mainly due to the occurrence of a few saline–freshwater transition events during the MCG diversification. In addition, a network analysis showed that both saline and freshwater MCG recurrently co-occur with archaea of the class Thermoplasmata in sediment ecosystems, suggesting a potentially relevant trophic connection between the two clades.This research was funded by projects ARCANOX (ref. CGL2009-13318-C02-02) and ARCOS (ref. CGL2012-33033) to CMB, and DARKNESS CGL2012-32747 to EOC from the Spanish Ministry of Economy and Competitiveness (MINECO). J-CA was funded by project METMIC from the Pyrenean Work Community and the Aquitaine region.Peer reviewe