Ecological observations of pelagic bacterial and archaeal communities in the Atlantic-Arctic boundary zone

The global climate change has an unprecedented impact on the Arctic Ocean, resulting in warming of the Arctic surface air at much faster rates than the global average. The warming temperatures lead to constantly declining Arctic sea ice cover, which reached in September 2018 the sixth lowest summertime minimum extent in the satellite record (since the late 1970s). Shrinking sea ice has a strong impact on the entire Arctic marine ecosystem, through alterations of the primary production, grazers communities, and subsequently the biological carbon pump. Current predictions of entirely sea-ice free summers in the Arctic Ocean already in the second half of this century urges the need to understand the ongoing oceanographic and biological processes in order to predict how the Arctic ecosystem will respond to further environmental changes. The differentiation between natural temporal ecosystem variability and anthropogenically-induced impact of the climate change requires long-term observations. The Ocean Observing System FRAM (FRontiers in Arctic marine Monitoring), which was established in 2014, is an Arctic long-term observatory for investigating the impact of changing ocean properties and sea ice conditions of the Arctic Ocean on its marine ecosystem. The starting point for the FRAM project was the already existing long-term observatory HAUSGARTEN, situated in the main gateway between the Arctic and the Atlantic Oceans - the Fram Strait. To date, despite their importance for the biogeochemical cycling, very little is known regarding the diversity and function of microbial communities in the Arctic Ocean in general, and specifically in the Fram Strait. In the framework of FRAM, a Molecular Observatory was established, for conducting standardized molecular-based high-resolution observations of the Arctic microbial communities. This thesis was conducted as part of the FRAM Molecular Observatory, and as part of the establishment process of the observatory it contributes to the methodological and procedural standardization required for long-term microbial observations. This thesis provides a first comprehensive overview of currently existing long-term microbial observatories around the world, it provides guidelines for initial steps towards establishing a community network between them, and stresses the urgent need in community efforts towards methods standardization. Furthermore, as part of the methods standardization for long-term microbial observations, this thesis includes a performance comparison between two, broadly used in microbial oceanography, 16S rRNA gene primer sets. The main focus of the thesis is on the ecology of pelagic bacterial and archaeal communities in the Fram Strait. Its overall objective was to investigate the distribution of these communities in the Fram Strait, and to identify environmental drivers of their diversity. The observations of this thesis reveal that sea ice has a strong impact on the development of the seasonal phytoplankton bloom during the summer. As a result, sea ice conditions are affecting the bacterial diversity in surface water, and are leading to a distinct community in sea-ice free and sea-ice covered regions of the Fram Strait. However, the impact of the sea ice is not limited to the surface ocean, as it also heavily affects the vertical export of aggregated organic matter to the deep ocean. The results of this thesis also show that aggregates formed under the sea ice sink faster, and by that provide a stronger vector for transport of bacterial and archaeal taxa to the deep ocean, compared to ice-free waters. Altogether, this thesis contributes to the baseline knowledge needed for further long-term observations of pelagic microbial communities in the Arctic marine ecosystem. Furthermore, it provides an important insight into the strong impact of the sea ice on bacterial and archaeal communities throughout the entire water column, underlining the potential impact of further environmental changes on the Arctic Ocean in the light of prevalent global warming and climate change

Pelagic bacterial communities across the Arctic-Atlantic boundary zone

In recent decades, the Eurasian Basin of the Arctic Ocean has undergone remarkable variations as part of the large-scale environmental changes facing the planet. The Fram Strait connects the Arctic Ocean to the North Atlantic, and provides the main gateway for water exchange between the Arctic and the global oceans. Two major current systems are present in Fram Strait: the West Spitsbergen Current (WSC) carries Atlantic water northwards, and the East Greenland Current (EGC) brings cold Arctic waters and ice southwards (Fig 1 and 2). The proximity of these two distinct current systems creates a valuable opportunity for studying differences in microbial community composition across strong gradients of temperature and ice cover. Here we present a first preliminary investigation of both free-living and particle-associated pelagic bacterial communities in the upper water column across a longitudinal transect of the entire Fram Strait, conducted during RV Polarstern expedition PS85 (ARK-XXVIII/2) in June 2014

How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a “Candidatus Marithrix sp.” Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico

"Candidatus Marithrix" is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria). This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, "Candidatus Marithrix" was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the "Candidatus Marithrix" genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs) between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH) events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament

Spatial Distribution of Arctic Bacterioplankton Abundance Is Linked to Distinct Water Masses and Summertime Phytoplankton Bloom Dynamics (Fram Strait, 79°N)

The Arctic is impacted by climate warming faster than any other oceanic region on Earth. Assessing the baseline of microbial communities in this rapidly changing ecosystem is vital for understanding the implications of ocean warming and sea ice retreat on ecosystem functioning. Using CARD-FISH and semi-automated counting, we quantified 14 ecologically relevant taxonomic groups of bacterioplankton (Bacteria and Archaea) from surface (0-30 m) down to deep waters (2,500 m) in summer ice-covered and ice-free regions of the Fram Strait, the main gateway for Atlantic inflow into the Arctic Ocean. Cell abundances of the bacterioplankton communities in surface waters varied from 10(5) cells mL(-1) in ice-covered regions to 10(6) cells mL(-1) in the ice-free regions. Observations suggest that these were overall driven by variations in phytoplankton bloom conditions across the Strait. The bacterial groups Bacteroidetes and Gammaproteobacteria showed several-fold higher cell abundances under late phytoplankton bloom conditions of the ice-free regions. Other taxonomic groups, such as the Rhodobacteraceae, revealed a distinct association of cell abundances with the surface Atlantic waters. With increasing depth (\u3e500 m), the total cell abundances of the bacterioplankton communities decreased by up to two orders of magnitude, while largely unknown taxonomic groups (e.g., SAR324 and SAR202 clades) maintained constant cell abundances throughout the entire water column (ca. 10(3) cells mL(-1)). This suggests that these enigmatic groups may occupy a specific ecological niche in the entire water column. Our results provide the first quantitative spatial variations assessment of bacterioplankton in the summer ice-covered and ice-free Arctic water column, and suggest that further shift toward ice-free Arctic summers with longer phytoplankton blooms can lead to major changes in the associated standing stock of the bacterioplankton communities

Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle

Bacterial membrane vesicles (MVs) are abundant in the oceans, but their potential functional roles remain unclear. In this study we characterized MV production and protein content of six strains of Alteromonas macleodii, a cosmopolitan marine bacterium. Alteromonas macleodii strains varied in their MV production rates, with some releasing up to 30 MVs per cell per generation. Microscopy imaging revealed heterogenous MV morphologies, including some MVs aggregated within larger membrane structures. Proteomic characterization revealed that A. macleodii MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs harbored ectoenzymes, such as aminopeptidases and alkaline phosphatases, which comprised up to 20% of the total extracellular enzymatic activity. Our results suggest that A. macleodii MVs may support its growth through generation of extracellular ‘hotspots’ that facilitate access to essential substrates. This study provides an important basis to decipher the ecological relevance of MVs in heterotrophic marine bacteria

Towards an integrated microbial observatory in the Arctic Ocean

The Fram Strait separates Northeast Greenland from the Svalbard Archipelago, and is the only deep connection to the Arctic Ocean. Therefore, this strait is the only gateway for direct exchange of intermediate and deep waters between the Arctic Ocean and the North Atlantic. Two main currents influence the exchanges: i) the West Spitsbergen Current, bringing Atlantic waters northwards, and ii) the East Greenland Current, which carries cold Arctic waters and ice southwards. These two currents consist of water masses with different origin, generate distinct physical and chemical conditions between the eastern and western parts of the strait, which effects the biological characteristics in this region. Oceanographic observations in the Fram Strait have been carried out for ~15 years with microbial research in the water column focusing mainly on eukaryotes, while very little exploratory work was conducted on pelagic Bacteria and Archaea. Here we present a preliminary report of the first extensive survey across the waters of the Fram Strait focused on Bacterial and Archaeal domains, conducted as part of the Arctic long-term observatory HAUSGARTEN annual expedition in summer 2016. Besides the investigation of “who is out there”, the observations gained in this survey will be integrated with other biological and physical data of the long-term observatory framework and will provide an essential step towards the understanding of the biochemical dynamics in the Fram Strait. In addition, on a long-term plan this project will contribute to the microbial observatory work as part of the FRAM Helmholtz research infrastructure and EU AtlantOS program

Microbial Communities in the East and West Fram Strait During Sea Ice Melting Season

Climate models project that the Arctic Ocean may experience ice-free summers by the second half of this century. This may have severe repercussions on phytoplankton bloom dynamics and the associated cycling of carbon in surface waters. We currently lack baseline knowledge of the seasonal dynamics of Arctic microbial communities, which is needed in order to better estimate the effects of such changes on ecosystem functioning. Here we present a comparative study of polar summer microbial communities in the ice-free (eastern) and ice-covered (western) hydrographic regimes at the LTER HAUSGARTEN in Fram Strait, the main gateway between the Arctic and North Atlantic Oceans. Based on measured and modeled biogeochemical parameters, we tentatively identified two different ecosystem states (i.e., different phytoplankton bloom stages) in the distinct regions. Using Illumina tag-sequencing, we determined the community composition of both free-living and particle-associated bacteria as well as microbial eukaryotes in the photic layer. Despite substantial horizontal mixing by eddies in Fram Strait, pelagic microbial communities showed distinct differences between the two regimes, with a proposed early spring (pre-bloom) community in the ice-covered western regime (with higher representation of SAR11, SAR202, SAR406 and eukaryotic MALVs) and a community indicative of late summer conditions (post-bloom) in the ice-free eastern regime (with higher representation of Flavobacteria, Gammaproteobacteria and eukaryotic heterotrophs). Co-occurrence networks revealed specific taxon-taxon associations between bacterial and eukaryotic taxa in the two regions. Our results suggest that the predicted changes in sea ice cover and phytoplankton bloom dynamics will have a strong impact on bacterial community dynamics and potentially on biogeochemical cycles in this region

Microbial Communities in the East and West Fram Strait During Sea Ice Melting Season

Climate models project that the Arctic Ocean may experience ice-free summers by the second half of this century. This may have severe repercussions on phytoplankton bloom dynamics and the associated cycling of carbon in surface waters. We currently lack baseline knowledge of the seasonal dynamics of Arctic microbial communities, which is needed in order to better estimate the effects of such changes on ecosystem functioning. Here we present a comparative study of polar summer microbial communities in the ice-free (eastern) and ice-covered (western) hydrographic regimes at the LTER HAUSGARTEN in Fram Strait, the main gateway between the Arctic and North Atlantic Oceans. Based on measured and modeled biogeochemical parameters, we tentatively identified two different ecosystem states (i.e., different phytoplankton bloom stages) in the distinct regions. Using Illumina tag-sequencing, we determined the community composition of both free-living and particle-associated bacteria as well as microbial eukaryotes in the photic layer. Despite substantial horizontal mixing by eddies in Fram Strait, pelagic microbial communities showed distinct differences between the two regimes, with a proposed early spring (pre-bloom) community in the ice-covered western regime (with higher representation of SAR11, SAR202, SAR406 and eukaryotic MALVs) and a community indicative of late summer conditions (post-bloom) in the ice-free eastern regime (with higher representation of Flavobacteria, Gammaproteobacteria and eukaryotic heterotrophs). Co-occurrence networks revealed specific taxon-taxon associations between bacterial and eukaryotic taxa in the two regions. Our results suggest that the predicted changes in sea ice cover and phytoplankton bloom dynamics will have a strong impact on bacterial community dynamics and potentially on biogeochemical cycles in this region

Long-Term Summertime Investigations of Pelagic and Benthic Realms with Continuous Observations of Vertical Particle Flux in the Fram Strait and the Central Arctic Ocean

Sea ice volume and extent currently experience massive reduction in the Arctic Ocean due to climate change. Our long-term study aims at tracing effects of environmental changes in pelagic and benthic systems and investigate accompanying impacts on the fate of organic matter produced in the upper water column on its way down to the seafloor. Since the start of our observations in 1999, we have already seen some effects and will present selected data sets from the upper water column and benthic data during summer expeditions as well as results from vertical particle flux measurements that were obtained from annually deployed sediment traps at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN in the eastern Fram Strait (79°/4°E) and on fewer occasions in the central Arctic Ocean (CAO). Highest biomass was found in the eastern Fram Strait and lowest in the heavily ice-covered regions in the CAO. Flux rates of POC where at least one order of magnitude lower in the CAO than in the eastern Fram Strait. While in the CAO ice algae dominate the recognizable flux fraction, faecal material prevailed in eastern Fram Strait traps. This points towards different systems of organic matter production and modification and, thus, different mechanisms determine the efficiency of the biological carbon pump. These differences are also reflected in the benthic communities in the CAO and in the eastern Fram Strait. These first results have shown the importance of long-term observations and encouraged the continuation of the Arctic Ocean Observing System FRAM (FRontiers in Arctic marine Monitoring) to record environmental and biological data at high temporal and spatial resolution