Microbial populations associated with the Irish brown seaweeds, Ascophyllum nodosum and Laminaria digitata, and their biotechnological applications

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Ihua, Maureen W.
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Brown macroalgae or seaweeds which belong to the class Phaeophyta arose around 200 million years ago and have since become one of the most ecologically remarkable and commercially relevant marine species. Brown seaweeds such as Ascophyllum nodosum and Laminaria digitata are a rich source of polysaccharides including fucoidan, alginate, laminarin and ascophyllan which have a variety of functional biotechnological applications. These seaweeds are well known to harbour a diverse range of bacteria which exert both beneficial and detrimental effects on their algal host. Some of the positive ecological functions of the associated microbiome include modulating the normal morphology of their host as well as contributing to antifouling defence. Marine microorganisms associated with algae are also known to produce diverse hydrolytic enzymes such as polysaccharidases which improve algal nutrient uptake and development while also contributing to algal defence from potential grazers. These diverse and complex bacterial communities thus represent a potential source of novel enzymes with biotechnological applications that could include their use in enzyme-assisted extraction (EAE) strategies, resulting in the improvement of the yields of algal components with cosmeceutical, functional food, and nutraceutical and biopharmaceutical applications. Several environmental and non-environmental factors, including seasonal variations and the physiological (fresh or decayed) state of macroalgae, can influence the composition and abundance of algal-associated epibacterial communities. The original work presented in this study aims at describing the microbial populations that are associated with the two brown seaweeds, namely Ascophyllum nodosum and Laminaria digitata and to examine the hydrolytic potential of their cultivable surface microbiota which may display useful biotechnological applications. Chapter 1 presents an overview of macroalgae and macroalgal-microbial interactions and of the diversity of algal-associated microbial communities and key interactions with the algal host. In addition, it describes the complex nature of brown algal cell walls and the potential for their exploitation. Chapter 2 describes the use of both metagenomic and culture-based approaches to investigate the effect of algal decay on the composition and abundance of Ascophyllum nodosum associated bacterial population. Three batches of fresh Ascophyllum nodosum samples were incubated in artificial seawater under sterile conditions in the laboratory for a period of six weeks, each at a different temperature (18 °C, 25 °C and 30 °C) to induce decay. Over 800 bacterial isolates were cultured from the intact and decaying macroalga using both traditional cultivation methods including the novel ichip in-situ cultivation method. Distinct differences between the bacterial populations associated with the seaweed before and during decay were observed. We also identified over 50 bacterial isolates which are capable of producing algal cell wall polysaccharide degrading enzymes of interest, some of which were tested for their biotechnological application and were proven to be successful, with 11-13% yield in the enzyme-assisted extraction of phenolics from a brown seaweed. Similarly, using culture dependent and independent methods, Chapter 3 describes how the induced decay of the brown seaweed Laminaria digitata resulted in changes in its associated microbial communities. We incubated the seaweed in the laboratory for four weeks at 20 °C, 25 °C and 30 °C. Our results show that the cultivable surface microbiota of the macroalga is enriched with algal cell wall degradation enzymes, with over 50% of the bacterial isolates being found to produce at least one of the enzymes tested. The study presented in chapter 4 further describes how morphological niches and seasonal variations drive the structure and composition of Laminaria digitata associated bacterial communities. Using Illumina sequencing of the 16S rRNA genes, the metagenomic populations of the four different parts (holdfast, stipe, meristem, blades) of the seaweed were examined over a ten month period, with samples being collected in April 2016, July 2016, November 2016 and January 2017. The data obtained revealed that the seaweed appears to lack a core microbial community, and that the month of November and the holdfast region harbour the most diverse bacterial population. Finally, the study ends with chapter 5 with a general discussion of the relevance of the results obtained and a look at some possible future prospects.
Ascophyllum nodosum , Laminaria digitata , Algal cell wall degrading enzymes , Algae , Enzyme-assisted extraction , Seaweed bacteria
Ihua, M. W. 2019. Microbial populations associated with the Irish brown seaweeds, Ascophyllum nodosum and Laminaria digitata, and their biotechnological applications. PhD Thesis, University College Cork.