1 Introduction
This chapter is included in this thesis to provide background information for Chapter II and to validate the newly designed CARD-FISH JTB255 probe sets.
*KH performed comparative counts between her newly designed CARD-FISH probe set and the probe set developed by SD and MM on, both, coastal and deep-sea sediments. KH performed double hybridizations between the two sets of new JTB-probes, the gammaproteobacterial probe (GAM42a), and the Xanthomonadales probe (GAM42a_T1038). KH generated cell images of JTB from coastal and deep-sea sediments. KH discussed CARD-FISH results with SD and MM.
Contribution of the PhD candidate in % of the total work load (100% for each of the following categories): Experimental concept and design: ca. 0%; Acquisition of (experimental) data: ca. 8%; Data analysis and interpretation: ca. 5%; Preparation of Figures and Tables: ca. 5%; Writing of the manuscript: ca. 0%.
Chapter II ‘Diversity and metabolism of the JTB255 clade (Gammaproteobacteria), a global member of deep-sea sediment communities’
Preliminary author list: Katy Hoffmann, Christina Bienhold, Katrin Knittel, Pier L.
Buttigieg, Rafael Laso-Pérez, Eduard Fadeev, Josephine Z. Rapp, Antje Boetius, and Pierre Offre.
Planned for submission to The ISME Journal
We combined a diverse set of cultivation-independent and molecular ‘omics’ tec h-niques, with cultivation-dependent methods to progress on the characterization of the core bacterial group from deep-sea surface sediments: JTB255. This study confirmed the abundance and ubiquitous distribution of JTB255 in deep-sea sediments globally. It refined the phylogenetic position of the JTB255 clade within the Gammaproteobacteria, and suggested a grouping into five sequence clusters. Furthermore, we analyzed JTB255`s microdiversity for different marine environments such as sediments, deep-sea water, and polymetallic nodules, indicating a preferential association of sub-groups with certain types of environments. Furthermore, we found strong indications for a hetero-trophic lifestyle of JTB255 in deep-sea sediments through the encoding of diverse
pep-The study was designed by KH, CB, AB, and PO. KH and JZR collected samples.
KH performed lab work. KH and KK designed CARD-FISH probes. KH and CB de-signed the cultivation experiments. JZR provided the assembled HAUSGARTEN meta-genome. KH, RLP, and EF binned JTB255 genomes from the metagenome and anlyzed them. PLB applied oligotyping. KH and PO analyzed the data. KH, PO, and CB dis-cussed the data. KH, PO, and CB wrote the manuscript. The manuscript was edited by all co-authors.
Contribution of the PhD candidate in % of the total work load (100% for each of the following categories): Experimental concept and design: ca. 60%; Acquisition of (experimental) data: ca. 75%; Data analysis and interpretation: ca. 60%; Preparation of Figures and Tables: ca. 80%; Writing of the manuscript: ca. 60%.
Chapter III ’Response of bacterial communities to different detritus compositions in Arctic deep-sea sediments’
Katy Hoffmann, Christiane Hassenrück, Verena Salman-Carvalho, Moritz Holtappels, and Christina Bienhold
Frontiers in Aquatic Microbiology (published in February 2017; doi:
10.3389/fmicb.2017.00266)
In this experimental approach, we combined measurements of community function with high-resolution taxonomic community structure, and statistical methods, in order to evaluate the response of a complex bacterial community from Arctic deep-sea sedi-ments to the input of various organic matter sources. The results were evaluated in the light of a changing Arctic Ocean and provided evidence that differences in organic mat-ter composition led to significant changes in bacmat-terial community structure and function at the seafloor, which may affect carbon turnover and retention in the deep sea. In addi-tion, we identified opportunistic groups of bacteria that may serve as indicator taxa for different organic matter sources in this region.
KH and CB designed experiments. KH performed the experiments. KH, CH, and CB analysed data, and VS-C assisted in data interpretation. MH performed oxygen sen-sor data analysis and modelling. KH, VS-C, and CB wrote the manuscript with support and input from all co-authors. The manuscript was edited by all co-authors.
1 Introduction
Contribution of the PhD candidate in % of the total work load (100% for each of the following categories): Experimental concept and design: ca. 85%; Acquisition of (experimental) data: ca. 100%; Data analysis and interpretation: ca. 75%; Preparation of Figures and Tables: ca. 80%; Writing of the manuscript: ca. 65%.
Chapter IV ‘The effect of hydrostatic de- and recompression on bacterial communities sampled from deep-sea sediments’
Katy Hoffmann, Christiane Hassenrück, and Christina Bienhold
In preparation for submission to FEMS Microbiology Letters as a short communication In this study, we used molecular and statistical methods to assess the influence of de- and recompression on bacterial communities retrieved from high-pressure deep-sea surface sediments at the LTER HAUSGARTEN. Results indicated that hydrostatic pressure changes potentially affected the metabolic activity of bacteria, based on ob-served altered enzymatic activities and bacterial composition pattern of the actively transcribing bacterial groups (16S rRNA) for certain taxa within the Proteobacteria and Bacteroidetes. Total community structure (16S rDNA) and total cell numbers remained rather unaffected over short time periods of decompression and over repeated de- and recompression cycles. However, these observations remain to be verified through fur-ther sample replication.
KH and CB designed this study. KH did the sampling and laboratory work. KH an-alyzed the data with input from CH. KH interpreted and discussed the data with input from CH, and CB. KH, CH, and CB wrote the manuscript.
Contribution of the PhD candidate in % of the total work load (100% for each of the following categories): Experimental concept and design: ca. 90%; Acquisition of (experimental) data: ca. 100%; Data analysis and interpretation: ca. 85%; Preparation of Figures and Tables: ca. 80%; Writing of the manuscript: ca. 85%.