Biodiversity and microbial activity in the epi-, meso- and bathypelagic realms of the ocean

Programa Oficial de Doutoramento en Bioloxía Celular e Molecular . 5004V01[Abstract] This research thesis examined the vertical variation in microbial abundance, activity, community composition and structure, together with optical properties of the dissolved organic matter (DOM), along a longitudinal transect off the Galician coast (NW Spain, from 43ºN, 9ºW to 43ºN, 15ºW). The decrease of microbial activity (heterotrophic and autotrophic) with depth coincided with a change in the microbial community composition. Thaumarchaeota was the dominant archaeal (on average 83% of the total Archaea) group throughout the water column and decreased with depth, whereas the bacterial community was dominated by Proteobacteria (79% of the total Bacteria) throughout the water column. However, Cyanobacteria and Bacteriodetes contributed ~ 15% to the bacterial community in the epipelagic, and SAR202 accounted for ~ 5% in the deep waters. The DOM quality and quantity exhibited pronounced vertical variations strongly connected to the depth patterns of archaeal and bacterial community composition, assessed by fingerprinting analysis. Moreover, different size fractions of DOM stimulated the growth of specific bacterial groups, which were linked to changes in the optical indexes of the DOM. Finally, we identified several microbial groups involved in dark inorganic carbon fixation rates in the deep ocean. Taken together, our results highlight the strong link between DOM quality and quantity and specific microbial groups, and the potential for autotrophic carbon fixation by different groups of deep ocean microbes, indicating that the distribution of microbial groups in the ocean is determined by the availability of their preferred substrates and suggest a large metabolic potential of deep ocean microbes.[Resumen] Esta investigación examinó la variación vertical de la abundancia, la actividad, la estructura y la composición de las comunidades microbianas en relación con las propiedades ópticas de la materia orgánica disuelta (MOD) a lo largo de una sección longitudinal de la costa gallega (NO España, de 43ºN, 9ºO a 43ºN, 15ºO). El descenso de la actividad microbiana (heterotrófica y autotrófica) con la profundidad coincidió con un cambio en la composición de la comunidad microbiana. Thaumarchaeota dominó la comunidad de Arquea en la columna de agua (en promedio, 83% del total de Archaea) y su abundancia descendió con la profundiad, mientras que la comunidad de Bacteria estuvo dominada por Proteobacteria (79% de bacterias totales) en la columna de agua. Sin embargo, Cianobacteria y Bacteroidetes representan ~ 10% de la comunidad bacteriana epipelágica, mientras que SAR202 representó ~ 5% de la comunidad bacteriana profunda. La calidad y cantidad de MOD exhibió variaciones verticales fuertemente correlacionadas con el patrón de distribución vertical de la comunidad de arqueas y bacterias, evaluada por técnicas de huella dactilar. Además, el fraccionamiento molecular de la MOD estimuló el crecimiento de grupos de bacterianos específicos que estuvieron correlacionados con cambios en las propiedades ópticas de la MOD. Finalmente, identificamos varios grupos microbianos implicados en la fijación oscura de carbono inorgánico en el océano profundo. Nuestros resultados destacan el fuerte vínculo entre la calidad y cantidad de MOD con grupos específicos microbianos y el potencial para la fijación oscura de carbono de diferentes grupos microbianos del océano profundo, lo que indica que el patrón de distribución de los grupos microbianos en el océano está determinado por el sustrato disponible y sugiere un gran potencial metabólico de los microbios en el océano profundo.[Resumo] A presente investigación examinou a variación vertical da abundancia, actividade, estructura e composición da comunidade microbiana en relación cás propiedades ópticas da materia orgánica (MOD) ó longo dunha sección lonxitudinal da costa galega (NO España, de 43ºN, 9ºO a 43ºN, 15ºO). O descenso da actividade microbiana (heterotrófica e autotrófica) coa profundidade coincidiu cun cambio na composición da comunidade microbiana. Thaumarchaeota dominou a comunidade de Arquea na columna de auga (en promedio, 83% do total de Archaea) e a súa abundancia descendeu coa profundidade, mentres a comunidade de Bacteria estivo dominada por Proteobacteria (79% de bacterias totais) na columna de auga. Cianobacteria e Bacteroidetes representaron ~ 10% da comunidade bacteriana epipeláxica, mentres SAR202 representou ~ 5% da comunidade bacteriana profunda. A calidade e cantidade da MOD exhibiu variacións verticais fortemente relacionadas co patrón de distribucion vertical das comunidades de arquea e bacteria, avaliadas por técnicas de pegada dactilar. O fraccionamento molecular da MOD estimulou o crecemento de grupos bacterianos específicos, que estiveron corelacionados con cambios nas propiedades ópticas da MOD. Finalmente, identificamos varios grupos microbianos implicados na fixación escura de carbono inorgánico no océano profundo. Os nosos resultados destacan o forte vínculo entre a cantidad e calidade da MOD con grupos microbianos específicos e o potencial para a fixación oscura de carbono dos diferentes grupos microbianos no océano profundo, indicando que a distribución dos grupos microbianos no océano oscuro está determinada pola preferencia do sustrato dipoñíbel e suxire un gran potencial metabólico dos microbios do océano profundo

Dark CO2 fixation by chemolithoautotrophic prokaryotes in the deep-water masses of the north-west coast of the Iberian Peninsule

Recent studies suggest that the prokaryotes inhabiting the dark ocean present higher chemolithoautotrophic activity than assumed previously. These chemolithoautotrophic microbes incorporate dissolved inorganic carbon (DIC) as carbon source for biomass production and use reduced inorganic compound as an energy source. We have quantified DIC fixation in the meso- and bathypelagic waters of the northwestern coast of the Iberian Peninsula, ranging from 1.04 to 46.83 mmol C m-2 d-1. Combining microautoradiography and fluorescence in situ hybridization (MICRO-CARD-FISH), we confirmed that both Thaumarchaeota and some bacterial groups such as SAR-11, SAR-202, SAR-406, Alteromonas take up bicarbonate uptake, particularly in the mesopelagic waters. Quantitative PCR analyses clearly showed a higher abundance of thaumarchaeal 16S and low ammonia concentration (LAC)- amoA genes in meso- and lower bathypelagic waters than in surface waters. In contrast, high ammonia concentration (HAC)- amoA genes dominated the subsurface samples. Taken together, both genomic and physiological evidences indicate that some archaeal and bacterial groups may be significant contributors to dark ocean chemoautolithotrophy

High dark CO2 fixation rates by active chemolithoautotrophic microbes along the water column (100-5000m) off Galicia (NW Iberian margin)

Poster communicationOur results provide evidence for the significant contribution to chemolithotrophy by specific archaeal and bacterial groups in the dark ocean

Bacterial activity and community composition response to the size-reactivity of dissolved organic matter

Heterotrophic bacteria respond dynamically to variations in organic matter availability in the dark ocean. However, our knowledge on how the differences in sized and/or reactivity of dissolved organic matter (DOM) affect the bacterial community dynamics is still scarce. Our study aims to investigate the response of bacterial activity and community composition to the degradability of filtered and of size-fractionated DOM. A natural bacterial community isolated from Mediterrean Water (MW; at 1000 m depth) was inoculated in seawater from the same location subjected to three different treatments: 0.2µm-filtered seawater (control), low molecular weight fraction (LMW) obtained by ultrafiltration, and the combination of low and high molecular weight fractions at the original ratio (H+L). Bacterial abundance and activity was monitored every 24h over 6 days, while bacterial community composition and DOM characterization were assessed at the beginning (day 0), middle (day 4) and at the end of the experiment (day 6). Low (LNA) and high nucleic acid content (HNA) bacterial abundance, as well as leucine incorporation rates, were consistently higher in the H+L incubations than in the LMW treatments, indicating different reactivity of the two organic matter size fractions. Moreover, actively respiring cells, estimated as CTC-positive cells, highly correlated to humic-like substances (FDOM-M; R=0.7, P<0.05, n=9, Spearman Rank Order), particularly in the H+L incubations. Interestingly, LNA cell abundance was highly correlated with the slope ratio (SR) values (R=-0.8, P<0.05, n=9, Spearman Rank Order), indicating that bacteria belonging to the LNA population are tightly linked to the molecular weight or aromaticity of the DOM. Taken together, our results indicate differences in the bio-reactivity of the low and high molecular weight size classes of DOM associated to the phylogenetic composition of the bacterial communities

Changes in activity and community composition shape bacterial responses to size-fraccionated marine DOM

To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-µm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.Versión del edito

Vertical Niche Partitioning of Archaea and Bacteria Linked to Shifts in Dissolved Organic Matter Quality and Hydrography in North Atlantic Waters

Understanding the factors that modulate prokaryotic assemblages and their niche partitioning in marine environments is a longstanding challenge in marine microbial ecology. This study analyzes amplicon sequence variant (ASV) diversity and co-occurrence of prokaryotic (Archaea and Bacteria) communities through coastal-oceanic gradients in the NW Iberian upwelling system and adjacent open-ocean (Atlantic Ocean). Biogeographic patterns were investigated in relation with environmental conditions, mainly focusing on the optical signature of the dissolved organic matter (DOM). Alpha- and beta-diversity were horizontally homogeneous [with the only exception of Archaea (∼1700 m depth), attributed to the influence of Mediterranean water, MW], while beta-diversity was significantly vertically stratified. Prokaryotic communities were structured in four clusters (upper subsurface, lower subsurface, intermediate, and deep clusters). Deep (>2000 m) archaeal and bacterial assemblages, and intermediate (500-2000 m) Bacteria (mainly SAR202 and SAR406), were significantly related to humic-like DOM (FDOM-M), while intermediate Archaea were additionally related to biogeochemical attributes of the high-salinity signature of MW. Lower subsurface (100-500 m) Archaea (particularly one ASV belonging to the genus Candidatus Nitrosopelagicus) were mainly related to the imprint of high-salinity MW, while upper subsurface (≤100 m) archaeal assemblages (particularly some ASVs belonging to Marine Group II) were linked to protein-like DOM (aCDOM254). Conversely, both upper and lower subsurface bacterial assemblages were mainly linked to aCDOM254 (particularly ASVs belonging to Rhodobacteraceae, Cyanobacteria, and Flavobacteriaceae) and nitrite concentration (mainly members of Planctomycetes). Most importantly, our analysis unveiled depth-ecotypes, such as the ASVs MarG.II_1 belonging to the archaeal deep cluster (linked to FDOM-M) and MarG.II_2 belonging to the upper subsurface cluster (related to FDOM-T and aCDOM254). This result strongly suggests DOM-mediated vertical niche differentiation, with further implications for ecosystem functioning. Similarly, positive and negative co-occurrence relationships also suggested niche partitioning (e.g., between the closely related ASVs Thaum._Nit._Nit._Nit._1 and _2) and competitive exclusion (e.g., between Thaum._Nit._Nit._Nit._4 and _5), supporting the finding of non-randomly, vertically structured prokaryotic communities. Overall, differences between Archaea and Bacteria and among closely related ASVs were revealed in their preferential relationship with compositional changes in the DOM pool and environmental forcing. Our results provide new insights on the ecological processes shaping prokaryotic assembly and biogeography.Versión del edito

Changes in bacterial activity and community composition in response to water mass mixing

PosterMixing zones and boundaries between different water masses are "hot spots" of marine biodiversity and activity. We aimed to investigate the effects of water mass mixing in the dark-ocean microbial communities by collecting and incubating natural bacterial communities from the Mediterranean Water (MW; at 1000 m depth), the Subpolar Modal Water (SPMW, 500m) and the Labrador Sea Water (LSW, 1800 m), and comparing them with artificially mixed communities. Mixing experiment 1 consisted of incubating at in sity conditions the original LSW and MW communities, plus a mixture of both (MIX1, dilution 1:1), whereas the Mixing experiment 2 included the original prokaryotic communities from SPMW and MW and a mixture of both (MIX2, dilution 1:1). Bacterial abundance and activity was monitored every 24 h over 8 days, while bacterial community composition and DOM characterization were assessed at the beginning (day 0), middle (day 4) and at the end of the experiment (day 8). Live prokaryotic cell abundance was higher in the MIX1 and MIX2 treatments as compared to the original communities. Moreover, MIX bacteria showed slightly higher leucine incorporation rates than MW or LSW. These metabolic responses were accompanied by changes in the optical properties of DOM, suggesting a change in the dynamics of the organic matter. Taken together, our results indicate differences in the bio-reactvity of the organic matter after mixing as compared to the original water masses that could influence the composition and activity of the bacterial community

Vertical zonation of bacterial assemblages attributed to physical stratification during the summer relaxation of the coastal upwelling off Galicia (NW Spain)

Research articleWe combined flow cytometry, CARD-FISH, and 16S rRNA gene tag pyrosequencing to investigate bacterioplankton dynamics along a transect in shelf waters off A Coruña (Galicia, NW Spain). Over five days (16-20th July 2012) we sampled during the relaxation of a summer upwelling pulse, providing an opportunity to examine the impact of pulses of cold nutrient-rich water into coastal microbial communities. The hydrographic conditions, characterized by intense density stratification of surface waters and the presence of a deep chlorophyll maximum (DCM) at 20–30 m, were relatively maintained over the sampling period. Indeed, bacterial abundance and composition displayed low day to day variation. Alpha diversity analysis suggested that species richness and diversity increased from coastal to shelf stations and from the surface down to the coastal DCM, which could be caused by the mixing of upwelled bacteria with the coastal surface waters. SAR11, SAR86, and Roseobacter were the most abundant bacteria detected in the samples by using CARD-FISH. The assemblages observed by pyrosequencing displayed a strong vertical zonation along the transect. Rhodobacteraceae (under class Alphaproteobacteria) and Bacteriodetes dominated the surface waters and decreased during the upwelling pulse, while SAR 86 (under class Gammaproteobacteria), Actinobacteria and SAR11 clade increased their relative abundance at the coastal DCM with upwelling relaxation, particularly at the shelf stations. Bacterial assemblages from surface waters were associated with higher temperature and light conditions, while coastal DCM assemblages were rather associated to salinity, inorganic nutrients and a diatom-bloom leading to high chlorophyll-a. Our findings suggest that the vertical variability in environmental conditions induced by the intense density stratification, the exportation of warmer and less saline surface water from the rias to the adjacent shelf, and the fertilizing effect of recently upwelled water at the deeper layer, determined the composition of distinct bacterial assemblages at the subsurface and DCM layers.XUNTA DE GALICIA (O9MMA 027604PR, 10MMA604024PR), IEO (PROYECTO RADIALES) y PLAN NACIONAL (MODUPLAN CTM2011-24008)Versión del editor2,24

Bacterial community composition and optical signature of DOM shape empirical leucine-to-carbon conversion factors in north-eastern Atlantic waters (0-4000 m)

Oral communicationMicrobial heterotrophic activity is a major process regulating the flux of dissolved organic matter (DOM) in the ocean. DOM quantity and quality strongly influence its microbial utilization and fate in the ocean. In order to broaden the vertical resolution of leucine-to-carbon conversion factors (CFs), needed for converting substrate incorporation into biomass production by heterotrophic bacteria, nine dilution experiments were performed in the north Atlantic. We found a very consistent depth-stratification in empirical CFs values from epipelagic to bathypelagic waters (3.95 &#177; 0.05 to 0.90 &#177; 0.51 kg C mol Leu-1). Our results demonstrated that the customarily used CF of 1.55 kg C mol Leu-1 in oceanic waters leads to an underestimation of prokaryotic heterotrophic production in epi- and mesopelagic waters, while it causes a severe overestimation in bathypelagic waters. Pearson correlations showed that CFs were related not only to hydrographic variables but also to specific phylogenetic groups and DOM quality and quantity indicators. Furthermore, a multiple linear regression model predicting CFs from relatively simple hydrographic and optical spectroscopic measurements is provided. Taken together, our results suggest that differences in CFs throughout the water column might be mostly associated to the quality of DOM affecting the response of particular phylogenetic groups.ASL

Short term variability of bacterial communities in the shelf waters off Galicia (NW Iberian Peninsula): Patterns and drivers shaping the diversity

PósterEcological and biogeochemical processesEcological and biogeochemical processes in the ocean are dependent on a diverse assemblage of microbes, including members of Bacteria (Glöckner et al, 2012). These bacterial assemblages occurs in vast numbers and represent a huge genetic diversity, fulfilling a wide of ecological roles in the marine system such as carbon geochemical cycle and energy transfer into higher trophic levels.We combined flow cytometry, CARD-FISH and 16S rRNA gene tag pyrosequencing to investigate the short-term variability of the bacterial communities in samples collected along a transect in the shelf off NW Iberian Peninsula over one week