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Title: Characterisation of Marine Gel Particles and Associated Bacterial Communities
Authors: Al-Wahaibi, Aisha Salim Mohammed
Issue Date: 2020
Publisher: Newcastle University
Abstract: Gel particles including biopolymers, microgels, transparent exoploymeric particles (TEP), and other classes of exopolymeric substances (EPS) are ubiquitous in the marine environment. Despite the different names for these gel particles in the literature they represent closely related materials and will be referred to simply as marine gel particles (MGPs). MGPs have a natural ability to aggregate, forming large particles of ‘marine snow’ that play an important role in the carbon flux to the ocean floor and the biogeochemical cycling of carbon in the sea. MGP aggregates are also a habitat for bacteria and their metabolic activities can affect the structure and dynamics of the MGPs. Extracellular DNA (eDNA) as an abundant element in the marine environment. eDNA is a key component in the structural integrity of some biofilms, and likewise could have similar effect on the structure of MGP aggregates. Hence, it is hypothesized here that extracellular DNA (eDNA) is present in MGPs as a result of bacterial growth and lysis. Therefore, the aim of this study was to investigate the presence of eDNA in MGPs. In addition, to characterise the bacterial community associated with MGPs and to examine their functional potential focusing on the occurrence of nuclease genes. A further aim was to investigate the production of deoxyribonuclease (DNase) by marine bacteria isolated from free living and attached bacteria. Seawater samples collected from the North Sea and filtered through a 100-μm sieve and a 0.4 μm polycarbonate filters to collect MGPs. eDNA occurrence was probed by bioimaging with cell-impermeant fluorescent DNA dyes YOYO-1 and TOTO-3. For the bacterial community structure and function analysis, MGPs were subjected to total DNA extraction and sequencing of the V4 region of the 16S rRNA gene using illumina MiSeq. Marine bacterial isolates were also investigated for DNase secretion on methyl green DNase test agar, with genome sequencing being carried out for the most productive DNase isolate. Results of the bioimaging analysis and quantification of the MGP composition demonstrated for the first time the presence of eDNA in MGPs. Proteobacteria dominated the bacterial community structure within MGPs, where Pseudoalteromonas and Vibrio were the most abundant genera. The bioinformatics based functional predictions of the bacterial community using KEGG analysis also affirmed the presence of numerous nuclease genes. The results from studies of isolated strains reported for the first time DNase secreting bacteria associated with MGPs in the North Sea. Additionally, there are 43 nuclease genes present in the genome of the prolific DNase producer Serratia marcescens. In conclusion, the co- occurrence of eDNA and DNases in the MGPs indicate important implications for understanding the dynamics and properties of MGP in the world’s oceans. This work can contribute to a further understanding of the role of the bacterial activities in MGPs formation, degradation and sedimentation processes.
Description: PhD Thesis
Appears in Collections:School of Natural and Environmental Sciences

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