Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes

12 páginas, 4 tablas, 3 figuras.Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism abundance, activity ,and diversity. Aquatic surface microlayers (SML) from a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP) populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE), total PPP abundance was higher at the SML .Heterotrophic nanoflagellates (HNF) were also more abundant in the SML. Bacteria in the SML had lower leucine incorporation rates, lower percentages of “live” cells, and higher numbers of highly-respiring cells ,likely resulting in a lower growth efficiency. No simple and direct linea rrelationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity ,microbial life in SML and underlyingwaters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton ,and that they are highly affected by potential stressful environmental factors, such as high UVR radiation.This work was supported by grants 2009SGR/1177 “Grup d’estructura i funcio de xarxes tròfiques microbianes planctòniques” and 2009SGR/361 “Grup d’Ecologia dels Canvis Ambientals, GECA” from Generalitat de Catalunya, AERBAC-2 178/2010 (to EOC) and EGALA 124/2010 (MF, LC) from the Ministerio de Medio Ambiente- Red de Parques Nacionales, and PIRENA CGL2009-13318 (EOC) and NITROPIR CGL2010-19373 (MF, LC) from MINECO. HS’s work was supported by CNPq and FAPESP (Process: 2014/ 14139-3).Peer reviewe

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes

Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism abundance, activity, and diversity. Aquatic surface microlayers (SML) form a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP) populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE), total PPP abundance was higher at the SML. Heterotrophic nanoflagellates (HNF) were also more abundant in the SML. Bacteria in the SML had lower leucine incorporation rates, lower percentages of "live" cells, and higher numbers of highly-respiring cells, likely resulting in a lower growth efficiency. No simple and direct linear relationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity, microbial life in SML and underlying waters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton, and that they are highly affected by potential stressful environmental factors, such as high UVR radiation

Les virus de l'estuaire de la Charente et du Bassin de Marennes-Oléron (dynamiques spatio-temporelles et interactions avec les communautés bactériennes)

Ce travail de thèse comprend dans un premier volet une étude in situ des communautés virales le long de l'estuaire de la Charente qui a permis de fixer un cadre temporel à la réalisation d'études in vitro réalisées dans un deuxième volet. La finalité de ces essais in vitro, basés sur des expériences d'enrichissement viral, était de déterminer l'influence des particules virales dulçaquicoles transportées par les eaux de la Charente sur la dynamique et la composition des communautés bactériennes du bassin de Marennes Oléron. Avec des abondances variant de 1.4 107 à 20.8 107 PAV ml-1, les virus constituent le compartiment planctonique le plus important en abondance. Ce compartiment présente une dynamique temporelle particulièrement marquée et influencée indirectement par la température via le contrôle du compartiment bactérien en terme d'évolution structurelle et fonctionnelle (abondance, diversité, activité). La forte similarité retrouvée dans les structures des communautés virales dulçaquicoles et côtières suggère l'existence d'un transfert de particules virales de la rivière vers le bassin. Les expériences in vitro ont permis de montrer qu'à l'instar des virus autochtones, les virus dulçaquicoles sont capables d'infecter, de lyser (71 % de la production bactérienne en 6 h) et de modifier la composition des communautés bactériennes côtières. La présence de 50 % des phylotypes dominants détectés dans la Charente au niveau des eaux du bassin permet d'expliquer un tel impact. De plus, les virus, comme le suggère la théorie du killing the winner , sont capables de maintenir la richesse spécifique à l'intérieur des communautés bactériennes côtières. Bien que de nombreux paramètres liés à l'infection virale restent à préciser (résistance, rôle des produits de lyses, importance de la lysogénie...), les résultats impliquent un effet potentiel des apports de particules virales dulçaquicoles sur la productivité des communautés bactériennes du bassin.LA ROCHELLE-BU (173002101) / SudocSudocFranceF

Partitioning of Thaumarchaeota populations along environmental gradients in alpine lakes.

11 páginas, 6 figuras, 4 tablas.We investigated the spatial distribution and diversity of ammonia-oxidizing Archaea (AOA) across gradients of pH, trophic status and altitude in a set of high mountain lakes (Limnological Observatory of the Pyrenees, north-east Spain). Both phylogeny- and taxonomy-based approaches revealed well-defined AOA community patterns with pH as the main potential driving environmental factor. The I.1a and SAGMGC-1 Thaumarchaeota clusters, and their potentially associated amoA gene variants (clusters Fresh 5 and Soil/Fresh 1, respectively) showed highest relative abundances in the most oligotrophic lakes. Euryarchaeota (i.e. HV-Fresh cluster, Methanomicrobiales and Thermoplasmatales) dominated in lakes with higher trophic status. Phylogenetic diversity (PD) in Pyrenean lakes was 1.5- to 2.3-fold higher than the PD from an equivalent number of globally distributed marine and soil sites. We observed segregated distributions for SAGMGC-1, preferentially distributed in the lakes with the lowest pH ( 0.12 μm), and I.1a in lakes with lower nitrite and dissolved organic carbon concentrations below 0.5 mg L−1. Overall, these results showed strong selection by local environmental conditions, unveiled new ecological niches for freshwater SAGMGC-1 in low pH oligotrophic lakes, and suggested specific and successful adaptations of planktonic archaea to the high mountain lakes landscape.This research was supported by the projects PIRENA CGL2009-13318 and CONSOLIDER GRACCIE CSD2007-00067 from the Spanish Office of Science and Innovation (MICINN). J.C.A. was supported by the Juan de la Cierva postdoctoral fellowship program (MICINN).Peer reviewe

Winter to spring changes in the slush bacterial community composition of a high mountain lake (Lake Redon, Pyrenees)

7 páginas, 4 figuras, 1 tabla.Bacterial community composition was analysed in the slush layers of snow-covered Lake Redon (2240 m altitude, Limnological Observatory of the Pyrenees, LOOP, NE Spain) in winter and spring and compared with bacteria from the lake water column, using 16S rRNA gene clone libraries and CARD-FISH counts. The set of biological data was related to changes in bacterial production and to other relevant environmental variables measured in situ. In winter, up to 70% of the 16S rRNA sequences found in the slush were closely related to planktonic bacteria from the water column beneath the ice. Conversely, during spring ablation, 50% of the sequences had > 97% identity with bacteria from the cryosphere (i.e. globally distributed glaciers, snow and ice) and may have originated from remote aerosol deposition. The transition winter to spring was characterized by consistent community changes switching from assemblages dominated by Betaproteobacteria, Verrucomicrobia and Bacteroidetes during snowpack growth to communities essentially dominated by the Bacteroidetes of classes Cytophagia and Sphingobacteria. This strong bacterial composition switch was associated with consistent increases in bacterial abundance and production, and decreasing bacterial diversity.This research was supported by grants PIRENA CGL2009-13318 and GOS-LAKES CGL2009-08523-E to E.O.C., and CONSOLIDER grant GRACCIE CSD2007-00067 from the Spanish Office of Science and Innovation (MICINN). J.C.A. benefits from a Juan de la Cierva postdoctoral fellow (MICINN).Peer reviewe

Seasonal changes in the freshwater ammonia-oxidizing archaeal assemblages and nitrogen species of an oligotrophic alpine area

10 páginas, 5 figuras, 3 tablas.The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.This research was supported by grants CRENYC CGL2006-12058 and PIRENA CGL2009-13318 to E.O.C. and CONSOLIDER grant GRACCIE CSD2007-00067 from the Spanish Office of Science and Innovation (MICINN). J.-C.A. benefits from a Juan de la Cierva postdoctoral fellow (MICINN).Peer reviewe

Rojo en medio del verde

Peer Reviewe

Biofilm recovery in a wastewater treatment plant-influenced stream and spatial segregation of ammonia-oxidizing microbial populations

We monitored the effects of wastewater treatment plant (WWTP) inputs on the recovery of stream biofilms after a large flood event that eroded most of the former biofilm communities. We monitored biomass recovery, chlorophyll a, nitrogen content, and stable isotope natural abundance (15N) over 8 weeks in light- and dark-exposed biofilms upstream and downstream from WWTP inputs, respectively, as well as the abundance of ammonia oxidizers by quantitative polymerase chain reaction. Biomass and chlorophyll a recovered quickly (< 2 weeks), and were significantly higher for light- than for dark-exposed biofilms. There was no consistent effect of WWTP inputs on these parameters, except for the biomass on dark-exposed biofilm that was higher at the WWTP-influenced sites. The influence of the WWTP inputs on stream-water ammonium concentration and its isotopic 15N signature increased as the flood receded. Biofilm 15N downstream of WWTP increased over time, tracking the increase in 15N-ammonium from the WWTP waters. Bacterial and archaeal ammonia oxidizers were present within the biofilm assemblages from early stages of postflood recovery. However, spatial distribution of these two clades was clearly segregated among sites and between light- and dark-exposed biofilms, probably related to ammonium availability and the development of photoautotrophic organisms.Peer reviewe

Targeting spatiotemporal dynamics of planktonic SAGMGC-1 and segregation of ammonia-oxidizing thaumarchaeota ecotypes by newly designed primers and quantitative polymerase chain reaction

12 páginas, 5 figuras, 1 tablaThe annual dynamics of three different ammoniaoxidizing archaea (AOA) ecotypes (amoA gene) and of the SAGMGC-1 (Nitrosotalea-like aquatic Thaumarchaeota) group (16S rRNA gene) were studied by newly designed specific primers and quantitative polymerase chain reaction analysis in a deep oligotrophic high mountain lake (Lake Redon, Limnological Observatory of the Pyrenees, Spain). We observed segregated distributions of the main AOA populations, peaking separately in time and space, and under different ammonia concentrations and irradiance conditions. Strong positive correlation in gene abundances was found along the annual survey between 16S rRNA SAGMAGC-1 and one of the amoA ecotypes suggesting the potential for ammonia oxidation in the freshwater SAGMAGC-1 clade. We also observed dominance of Nitrosotalea-like ecotypes over Nitrosopumilus-like (Marine Group 1.1a) and not the same annual dynamics for the two thaumarchaeotal clades. The fine scale segregation in space and time of the different AOA ecotypes indicated the presence of phylogenetically close but ecologically segregated AOA species specifically adapted to specific environmental conditions. It remains to be elucidated what would be such environmental drivers.This research was supported by grants PIRENA CGL2009-13318 and DARKNESS CGL2012-32747 from the Spanish Office of Science (MINECO) to EOC. JCA was hired by the Spanish Juan de la Cierva postdoctoral program and CRO by a Spanish FPI predoctoral scholarship (MINECO).Peer reviewe

Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios

11 páginas,6 figuras, 1 tabla.Bacteria and Archaea of the air–water surface microlayer (neuston) and plankton from three high mountain lakes (Limnological Observatory of the Pyrenees, Spain) were analysed by 16S rRNA gene 454 pyrosequencing (V6 region) in two dates with different atmospheric aerosol loading conditions: (1) under a Saharan dust plume driven by southern winds; and (2) under northern winds with oceanic influence. In general, bacterial communities were richer than archaea, with estimated total richness of c. 2500 OTUs for Bacteria and c. 900 OTUs for Archaea equivalent to a sequencing effort of c. 250 000 and c. 20 000 sequences, respectively. The dominant bacterial OTU was affiliated to Actinobacteria. Archaea were one to two orders of magnitude less abundant than bacteria but were more evenly distributed. Apparently, Bacteroidetes and Thaumarchaeota sequences were preferentially found at the neuston, but no consistent pattern in either total microbial abundance or richness was found in any sample. However, we observed more marked changes in microbial relative abundances between neuston and plankton in the dust-influenced scenario. Higher community dissimilarities between neuston and plankton were also found during the Saharan dust episode, and such differences were higher for Bacteria than for Archaea. Nonetheless, relatively few (< 0.05%) of the neuston sequences matched previously identified airborne microorganisms, and none became important in the dates analysed.This study was co-funded by the 7th Framework Programme (FP7) Marie Curie Fellowship (GenS FP7-MC-IOF- 219811) and a fellowship ‘Juan de la Cierva’ from the Ministry of Spanish Office of Science and Innovation (MICINN) to M.V.-C. and supported by grants PIRENA CGL2009-13318 and CONSOLIDER GRACCIE CSD2007-00067 from the MICINN, AERBAC-2 178/2010 from the Ministerio de Medio Ambiente-Red de Parques Nacionales to EOC and the Gordon and Betty Moore Foundation.Peer reviewe