Diversity and ecology of bacterial communities at the deep seafloor

Understanding biodiversity and its distribution across space, time, and along environmental gradients, is crucial in order to assess the ecological functions of groups of organisms in the environment and gain insights into overall ecosystem functioning. In contrast to the distribution patterns of larger organisms, little is known about the structuring of bacterial communities in the environment. The reason being, that appropriate tools for the study of microbial ecology have only become available during the last decades. Today, molecular tools like fingerprinting or next-generation sequencing enable a time- and cost-effective, high-throughput processing of environmental samples to study bacterial diversity patterns. The application of such tools has revealed non-random patterns of bacterial diversity across space and time, and along environmental gradients in a variety of habitats. However, research on microbial community ecology is just starting to pick up pace, and entire ecosystems, such as the deep seafloor, remain largely uncharted. The deep sea represents the largest ecosystem on Earth and at the same time remains one of the least explored regions on our planet. Bacterial communities play an essential role for carbon and nutrient cycling in deep-sea sediments, and are thus an important component of benthic deep-sea ecosystems. Therefore, the specific investigation of bacterial diversity and its distribution at the deep seafloor in the context of environmental parameters were major objectives of this thesis. The influence of both spatial distance, as an indicator for dispersal limitation, and contemporary environmental factors on bacterial communities were investigated at different spatial scales

Variability in Benthic Ecosystem Functioning in Arctic Shelf and Deep-Sea Sediments: Assessments by Benthic Oxygen Uptake Rates and Environmental Drivers

Remineralization of organic matter at the seafloor is an important ecosystem function, as it drives carbon and nutrient cycling, supplying nutrients for photosynthetic production, but also controls carbon burial within the sediment. In the Arctic Ocean, changes in primary production due to rapid sea-ice decline and thinning affect the export of organic matter to the seafloor and thus, benthic ecosystem functioning. Due to the remoteness and difficult accessibility of the Arctic Ocean, we still lack baseline knowledge about patterns of benthic remineralization rates and their drivers in both shelf and deep-sea sediments. Particularly comparative studies across regions are scarce. Here, we address this knowledge gap by contrasting benthic diffusive and total oxygen uptake rates (DOU and TOU), both established proxies of the benthic remineralization function, between shelf and deep-sea habitats of the Barents Sea and the central Arctic Ocean, sampled during a RV Polarstern expedition in 2015. DOU and TOU were measured using ex situ porewater oxygen microprofiles and sediment core incubations, respectively. In addition, contextual parameters including organic matter availability and microbial cell numbers were determined as environmental predictors. Pan-Arctic regional comparisons were obtained by extending our analyses to previously published data from the Laptev and Beaufort Seas. Our results show that (1) benthic oxygen uptake rates and most environmental predictors varied significantly between shelf and deep-sea habitats; (2) the availability of detrital organic matter is the main driver for patterns in total as well as diffusive respiration, while bacterial abundances were highly variable and only a weak predictor of differences in TOU and DOU; (3) regional differences in oxygen uptake across shelf and deep-sea sediments were mainly related to organic matter availability and may reflect varying primary production regimes and distances to the nearest shelf. Our findings suggest that the expected decline in sea-ice cover and the subsequent increase in export of organic matter to the seafloor may particularly enhance remineralization in the deep seas of the Arctic Ocean, altering benthic ecosystem functioning in future climate scenarios

Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments

Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios

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

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front

Ultraslow spreading ridges account for one-third of the global mid-ocean ridges. Their impact on the diversity and connectivity of benthic deep-sea microbial assemblages is poorly understood, especially for hydrothermally inactive, magma-starved ridges. We investigated bacterial and archaeal diversity in sediments collected from an amagmatic segment (10°–17°E) of the Southwest Indian Ridge (SWIR) and in the adjacent northern and southern abyssal zones of similar water depths within one biogeochemical province of the Indian Ocean. Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. Our results show significant differences in microbial communities between stations outside and inside the SWIR, which were mostly explained by environmental selection. Community similarity correlated significantly with differences in chlorophyll a content and with the presence of upward porewater fluxes carrying reduced compounds (e.g., ammonia and sulfide), suggesting that trophic resource availability is a main driver for changes in microbial community composition. At the stations in the SWIR axial valley (3,655–4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g., SEEP-SRB1, Dehalococcoida, Atribacteria, and Woesearchaeota) and chemosynthetic environments (mainly Helicobacteraceae). The abyssal stations outside the SWIR communities (3,760–4,869 m water depth) were dominated by OM1 clade, JTB255, Planctomycetaceae, and Rhodospirillaceae. We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats

Impact of preservation method and storage period on ribosomal metabarcoding of marine microbes: Implications for remote automated samplings

Automated sampling technologies can enhance the temporal and spatial resolution of marine microbial observations, particularly in remote and inaccessible areas. A critical aspect of automated microbiome sampling is the preservation of nucleic acids over long-term autosampler deployments. Understanding the impact of preservation method on microbial metabarcoding is essential for implementing genomic observatories into existing infrastructure, and for establishing best practices for the regional and global synthesis of data. The present study evaluates the effect of two preservatives commonly used in autosampler deployments (mercuric chloride and formalin) and two extraction kits (PowerWater and NucleoSpin) on amplicon sequencing of 16S and 18S rRNA gene over 50 weeks of sample storage. Our results suggest the combination of mercuric chloride preservation and PowerWater extraction as most adequate for 16S and 18S rRNA gene amplicon-sequencing from the same seawater sample. This approach provides consistent information on species richness, diversity and community composition in comparison to control samples (nonfixed, filtered and frozen) when stored up to 50 weeks at in situ temperature. Preservation affects the recovery of certain taxa, with specific OTUs becoming overrepresented (SAR11 and diatoms) or underrepresented (Colwellia and pico-eukaryotes) after preservation. In case eukaryotic sequence information is the sole target, formalin preservation and NucleoSpin extraction performed best. Our study contributes to the design of long-term autonomous microbial observations in remote ocean areas, allowing cross-comparison of microbiome dynamics across sampling devices (e.g., water and particle samplers) and marine realms

Polysaccharide degradation potential of bacterial communities in Arctic deep-sea sediments (1200-5500 m water depth)

The majority of the Earth’s surface is covered by fine-grained deep-sea sediments, with bacteria dominating total benthic biomass. These benthic bacterial communities depend on organic matter input from the upper ocean, but as they comprise mostly unknown and uncultivated taxa, we have very limited knowledge of their enzymatic machinery to break down this material. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1000 to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA and metagenomic sequencing to elucidate total and active bacterial community composition, and the key functional potentials. Some sequence-dominant taxa of the total community (e.g. members of the Gamma- and Deltaproteobacteria) were underrepresented in the cDNA fraction, while other groups (e.g. Flavobacteriaceae; SAR202 clade) were overrepresented in the active fraction when compared to total community reads. We used the Carbohydrate Active Enzymes database (http://www.cazy.org) to identify protein families in the generated metagenomes, which are associated with polysaccharide degradation, e.g. glycoside hydrolases. We found the same families of glycoside hydrolases in all metagenomes, but their relative contribution to glycoside hydrolase-coding genes varied according to depth. A larger number of hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) was found at shallower depths, while those responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front

Ultraslow spreading ridges account for one-third of the global mid-ocean ridges. Their impact on the diversity and connectivity of benthic deep-sea microbial assemblages is poorly understood, especially for hydrothermally inactive, magma-starved ridges. We investigated bacterial and archaeal diversity in sediments collected from an amagmatic segment (10∘–17∘E) of the Southwest Indian Ridge (SWIR) and in the adjacent northern and southern abyssal zones of similar water depths within one biogeochemical province of the Indian Ocean. Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. Our results show significant differences in microbial communities between stations outside and inside the SWIR, which were mostly explained by environmental selection. Community similarity correlated significantly with differences in chlorophyll a content and with the presence of upward porewater fluxes carrying reduced compounds (e.g., ammonia and sulfide), suggesting that trophic resource availability is a main driver for changes in microbial community composition. At the stations in the SWIR axial valley (3,655–4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g., SEEP-SRB1, Dehalococcoida, Atribacteria, and Woesearchaeota) and chemosynthetic environments (mainly Helicobacteraceae). The abyssal stations outside the SWIR communities (3,760–4,869 m water depth) were dominated by OM1 clade, JTB255, Planctomycetaceae, and Rhodospirillaceae. We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats

Carbon and nitrogen turnover in the Arctic deep sea : in situ benthic community response to diatom and coccolithophorid phytodetritus

In the Arctic Ocean, increased sea surface temperature and sea ice retreat have triggered shifts in phytoplankton communities. In Fram Strait, coccolithophorids have been occasionally observed to replace diatoms as the dominating taxon of spring blooms. Deep-sea benthic communities depend strongly on such blooms, but with a change in quality and quantity of primarily produced organic matter (OM) input, this may likely have implications for deep-sea life. We compared the in situ responses of Arctic deep-sea benthos to input of phytodetritus from a diatom (Thalassiosira sp.) and a coccolithophorid (Emiliania huxleyi) species. We traced the fate of C-13- and N-15-labelled phytodetritus into respiration, assimilation by bacteria and infauna in a 4-day and 14-day experiment. Bacteria were key assimilators in the Thalassiosira OM degradation, whereas Foraminifera and other infauna were at least as important as bacteria in the Emiliania OM assimilation. After 14 days, 5 times less carbon and 3.8 times less nitrogen of the Emiliania detritus was recycled compared to Thalassiosira detritus. This implies that the utilization of Emiliania OM may be less efficient than for Thalassiosira OM. Our results indicate that a shift from diatom-dominated input to a coccolithophorid-dominated pulse could entail a delay in OM cycling, which may affect benthopelagic coupling

Journey to the deep sea: Do Arctic sea-ice bacteria hitchhike on ice-algal aggregates?

In 2012 Arctic sea ice declined to a record minimum. As a consequence of the melting, large sub-ice filaments of the diatom Melosira arctica were released and sank to the seafloor, resulting in a widespread deposition of fresh ice-algal material at 4400 m water depth. Elevated rates of oxygen consumption in sediments with algal deposits indicated remineralization by bacteria and evidenced a response of the entire ecosystem down to the deep sea to elevated carbon flux rates (Boetius et al. 2013, Science 339: 1430-1432). Bacteria play essential roles in carbon and nutrient cycling not only at the seafloor but also in the sea ice and in the water column, contributing significantly to Arctic ecosystem functioning. We sampled a wide range of Arctic environments from the surface to the deep sea, in order to compare bacterial communities from sea ice, melt ponds, surface seawater, deep-sea sediment with and without algal aggregates. Structure and composition of bacterial communities showed strong environmental specificity, with distinct differences between surface and deep-sea environments. Yet, some taxa were shared between algae aggregates from the surface and the seafloor, suggesting a transport of surface-derived bacteria to the deep ocean, as a consequence of rapid sea-ice melt