Identity and function of key bacterial groups in Arctic deep-sea surface sediments

The deep-sea floor covers about 65% of the Earth s surface and benthic biomass is dominated by highly diverse bacterial communities. Bacterial carbon cycling in deep-sea sediments plays a crucial role in global biogeochemical cycles, and remineralization efficiency of organic carbon can be more than 97%. However, key bacteria relevant for carbon turnover and ecosystem functioning remain unknown. Benthic bacteria mainly depend on organic carbon supply from the surface ocean, and will therefore likely be affected by changing surface ocean conditions. The Arctic Ocean is already impacted by environmental changes more rapidly here than in any other ocean region and will be impacted even more in the future. This turns the Arctic Ocean into an important study site to understand the effects of environmental changes on bacterial communities and ecosystem functioning, such as carbon cycling. At the same time, the Arctic Ocean remains to a large extent understudied, and little is known about the identity of key bacterial groups, which could be useful as indicators to describe the state of the ecosystem and to monitor community response to changing environmental conditions. Consequently, the goals of this thesis include the identification of indigenous key bacteria in deep-sea sediments and their metabolic potential, as well as the development of a better understanding of the specific response of Arctic deep-sea bacterial communities to changes in the supply of organic matter. The Long-Term Ecological Research site HAUSGARTEN (HG) is one out of two open ocean, long-term observatories in a polar region, and therefore provided a unique opportunity to study key bacterial groups from Arctic deep-sea sediments. Chapters I and II present one of the first characterizations of a globally sequence-abundant sediment bacterial group, the JTB255 marine benthic group (JTB255). Cell counts with newly designed probes evidenced high cell abundances in coastal (Chapter I) and deep-sea sediments (Chapter II). Labeling experiments together with metatranscriptomic data suggested a chemolithoautotrophic lifestyle, with a potential high importance for sulfur-based carbon fixation in coastal sediments (Chapter II). Furthermore, genomic analyses of single cells emerged as a powerful means to provide first insights into the metabolic potential of JTB255 representatives in deep-sea sediments, suggesting a heterotrophic lifestyle with oxygen as terminal electron acceptor (Chapter II). Genomic analysis showed that JTB255 encode enzymes for the oxidative degradation of polymeric cell material such as membranes and cell walls, suggesting recalcitrant organic carbon sources in marine sediments. Therefore, it is hypothesized for the first time that some representatives of JTB255 might be involved in the cycling of a major class of refractory sediment organic matter, potentially explaining their global ecological success. In an ex situ experimental approach, the response of Arctic benthic bacterial deep-sea communities at HG to different types of detritus was explored (Chapter III). This is the first experimental study investigating the response of bacterial deep-sea communities to the addition of natural food sources by combining measurements of community function with the analysis of high resolution taxonomic community structure. Our results provide evidence that differences in organic matter composition lead to significant changes in bacterial community structure and function at the seafloor, which can affect carbon turnover and retention in the deep sea. In addition, opportunistic groups of bacteria were identified that may serve as indicator taxa for different organic matter sources at this site. In Chapter IV, a pilot study is presented which addresses an issue often discussed in deep-sea research, i.e. the unknown effects of sample retrieval from high-pressure environments on bacterial communities. Therefore, the influence of de- and recompression on deep-sea sediment bacteria, as inherently imposed during sediment retrieval and subsequent laboratory experiments, was studied in a small-scale experiment. Results indicated few effects of de- and recompression on bacterial community structure within the experimental time frame, but contained evidence for changes in the metabolic activity of specific taxa, after the retrieval of decompressed samples from the seafloor. These observations remain to be verified with further sample replication. In summary, this thesis contributes to the identification of candidate key bacterial groups. It further provides valuable insights into bacterial diversity and function in Arc-tic deep-sea sediments and will help to assess impacts of future climate scenarios on pelago-benthic coupling in the Arctic

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

Enhancing the usability of systematic reviews by improving the consideration and description of interventions

The importance of adequate intervention descriptions in minimising research waste and improving research usability and reproducibility has gained attention in the past few years. Nearly all focus to date has been on intervention reporting in randomised trials. Yet clinicians are encouraged to use systematic reviews, whenever available, rather than single trials to inform their practice. This article explores the problem and implications of incomplete intervention details during the planning, conduct, and reporting of systematic reviews and makes recommendations for review authors, peer reviewers, and journal editors

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Identität und Funktion von bakteriellen Schlüsselgruppen in den Oberflächensedimenten der arktischen Tiefsee

The deep-sea floor covers about 65% of the Earth s surface and benthic biomass is dominated by highly diverse bacterial communities. Bacterial carbon cycling in deep-sea sediments plays a crucial role in global biogeochemical cycles, and remineralization efficiency of organic carbon can be more than 97%. However, key bacteria relevant for carbon turnover and ecosystem functioning remain unknown. Benthic bacteria mainly depend on organic carbon supply from the surface ocean, and will therefore likely be affected by changing surface ocean conditions. The Arctic Ocean is already impacted by environmental changes more rapidly here than in any other ocean region and will be impacted even more in the future. This turns the Arctic Ocean into an important study site to understand the effects of environmental changes on bacterial communities and ecosystem functioning, such as carbon cycling. At the same time, the Arctic Ocean remains to a large extent understudied, and little is known about the identity of key bacterial groups, which could be useful as indicators to describe the state of the ecosystem and to monitor community response to changing environmental conditions. Consequently, the goals of this thesis include the identification of indigenous key bacteria in deep-sea sediments and their metabolic potential, as well as the development of a better understanding of the specific response of Arctic deep-sea bacterial communities to changes in the supply of organic matter. The Long-Term Ecological Research site HAUSGARTEN (HG) is one out of two open ocean, long-term observatories in a polar region, and therefore provided a unique opportunity to study key bacterial groups from Arctic deep-sea sediments. Chapters I and II present one of the first characterizations of a globally sequence-abundant sediment bacterial group, the JTB255 marine benthic group (JTB255). Cell counts with newly designed probes evidenced high cell abundances in coastal (Chapter I) and deep-sea sediments (Chapter II). Labeling experiments together with metatranscriptomic data suggested a chemolithoautotrophic lifestyle, with a potential high importance for sulfur-based carbon fixation in coastal sediments (Chapter II). Furthermore, genomic analyses of single cells emerged as a powerful means to provide first insights into the metabolic potential of JTB255 representatives in deep-sea sediments, suggesting a heterotrophic lifestyle with oxygen as terminal electron acceptor (Chapter II). Genomic analysis showed that JTB255 encode enzymes for the oxidative degradation of polymeric cell material such as membranes and cell walls, suggesting recalcitrant organic carbon sources in marine sediments. Therefore, it is hypothesized for the first time that some representatives of JTB255 might be involved in the cycling of a major class of refractory sediment organic matter, potentially explaining their global ecological success. In an ex situ experimental approach, the response of Arctic benthic bacterial deep-sea communities at HG to different types of detritus was explored (Chapter III). This is the first experimental study investigating the response of bacterial deep-sea communities to the addition of natural food sources by combining measurements of community function with the analysis of high resolution taxonomic community structure. Our results provide evidence that differences in organic matter composition lead to significant changes in bacterial community structure and function at the seafloor, which can affect carbon turnover and retention in the deep sea. In addition, opportunistic groups of bacteria were identified that may serve as indicator taxa for different organic matter sources at this site. In Chapter IV, a pilot study is presented which addresses an issue often discussed in deep-sea research, i.e. the unknown effects of sample retrieval from high-pressure environments on bacterial communities. Therefore, the influence of de- and recompression on deep-sea sediment bacteria, as inherently imposed during sediment retrieval and subsequent laboratory experiments, was studied in a small-scale experiment. Results indicated few effects of de- and recompression on bacterial community structure within the experimental time frame, but contained evidence for changes in the metabolic activity of specific taxa, after the retrieval of decompressed samples from the seafloor. These observations remain to be verified with further sample replication. In summary, this thesis contributes to the identification of candidate key bacterial groups. It further provides valuable insights into bacterial diversity and function in Arc-tic deep-sea sediments and will help to assess impacts of future climate scenarios on pelago-benthic coupling in the Arctic

The effect of hydrostatic de- and re-compression events on deep-sea bacterial communities

This work focuses on the effect of decompression on bacterial communities from deep-sea surface sediments. We evaluated the effects of slow and fast decompression (within hours and seconds, respectively), and repeated de-re-compression (up to 10 times) on the abundance and extracellular enzymatic activity of bacterial communities as well as their taxonomic composition using next generation sequencing of the 16S rRNA and rRNA gene. Decompression due to sample retrieval from the seafloor with a push corer or a pressure corer showed minor effects on bacterial cell numbers and enzymatic activity patterns. It however showed an initial effect on bacterial activity patterns based on 16S rRNA (cDNA) community analysis. This signal vanished during a few hours standing at atmospheric pressure. The results reported here may be useful to provide ideas for future research as to how bacterial communities react to the procedure of sample retrieval from a high pressure environment

Response of Arctic benthic bacterial deep-sea communities to different detritus composition during an ex-situ high pressure experiment

In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from 2,500 m water depth at the Long-Term Ecological Research Observatory HAUSGARTEN (stationPS93/050-5 and 6), were retrieved using a TV-guided multiple corer. Surface sediments (0 - 2 cm) of 16 cores were mixed with sterile filtered deep-sea water to a final sediment dilution of 3.5 fold. The slurries were split and supplemented with five different types of habitat-related detritus: chitin, as the most abundant biopolymer in the oceans, and four different naturally occurring Arctic algae species, i.e. Thalassiosira weissflogii, Emiliania huxleyi, Bacillaria sp. and Melosira arctica. Incubations were performed in five replicates, at in situ temperature and at atmospheric pressure, as well as at in situ pressure of 250 atm. At the start of the incubation and after 23 days, changes in key community functions, i.e. extracellular enzymatic activity, oxygen respiration and secondary production of biomass (bacterial cell numbers and biomass), were assessed along with changes in the bacterial community composition based on 16S rRNA gene and 16S rRNA Illumina sequencing. 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

Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named “JTB255-Marine Benthic Group” (now the candidate order Woeseiales), accounts for 1–22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and specific ecological niches in the deep sea, which constitutes the largest biome globally. Here, we characterized the phylogeny, environmental distribution patterns, abundance, and metabolic potential of Woeseiales bacteria with a focus on representatives from the deep sea. From a phylogenetic analysis of publicly available 16S rRNA gene sequences (≥1400 bp, n = 994), we identified lineages of Woeseiales with greater prevalence in the deep sea than in coastal environments, a pattern corroborated by the distribution of 16S oligotypes recovered from 28 globally distributed sediment samples. Cell counts revealed that Woeseiales bacteria accounted for 5 ± 2% of all microbial cells in deep-sea surface sediments at 23 globally distributed sites. Comparative analyses of a genome, metagenome bins, and single-cell genomes suggested that members of the corresponding clades are likely to grow on proteinaceous matter, potentially derived from detrital cell membranes, cell walls, and other organic remnants in marine sediments

Diversity and metabolism of the JTB255 clade in deep-sea sediments

The present study aimed at a first characterization of the enigmatic JTB255 marine benthic group in deep-sea sediments, by: i) confirming the abundance and ubiquitous distribution of JTB255 in deep-sea sediments globally, ii) refining the phylogenetic positioning of the JTB255 clade within the \u03b3-Proteobacteria, iii) distinguishing potential ecotypes within the JTB255 clade, iv) providing first insights into the metabolic potential of deep-sea representatives of this clade. Therefore, two single cell genomes from Arctic HAUSGARTEN deep-se surface sediments were obtained and CARD-FISH counts of total cells, y-Proteobacteria and the JTB255 marine benthic group performed