Date of Award


Document Type



Edith Cowan University

Degree Name

Doctor of Philosophy


School of Science

First Supervisor

Professor Glenn Hyndes

Second Supervisor

Dr Annette Koenders

Third Supervisor

Dr Bonnie Laverock

Fourth Supervisor

Dr Christin Sawstrom


Microorganisms play a key role in facilitating the cycling of several elements in coastal environments, including nitrogen (N). N is a key component for maintaining high seagrass productivity and is often the limiting nutrient in marine environments. Seagrasses harbour an abundant and diverse microbial community (the ‘microbiome’), however their ecological and functional roles related to the seagrass host are still poorly understood, in particular regarding N cycling. Microorganisms capable of mineralising dissolved organic nitrogen (DON) may play a pivotal role in enhancing N availability in coastal environments such as seagrass meadows. Thus, the overall aim of my thesis was to enhance current understanding of abundance and diversity of the microbial community associated with seagrass meadows and their ecological role, with specific focus on N cycling. This was achieved by using molecular techniques together with 15N-enrichment experiments and nanoscale imaging techniques.

Firstly, I reviewed the literature on the potential effects that microorganisms associated with both the above- and belowground seagrass tissue may have on plant fitness and the relevance of the seagrass microbiome and I have highlighted literature gaps.

For my second chapter, I determined the abundance and community composition of bacteria and archaea associated with seagrass Posidonia sinuosa meadows in Marmion Marine Park, southwestern Australia. Data were collected from different seagrass meadows and meadow ‘microenvironments’, i.e. seagrass leaf surface, sediment and water column. I performed the quantitative polymerase chain reaction (q-PCR) targeting a series of bacterial and archaeal genes: 16S rRNA, ammonia oxidation genes (amoA) and genes involved in mineralisation of DON, via the urease enzyme (ureC). High-throughput sequencing was applied to 16S rRNA and amoA genes, to explore the diversity of these microbial assemblages related to P. sinuosa meadow microenvironments. Results from this chapter show that the P. sinuosa leaf biofilm represents a favourable habitat for microorganisms, as it hosts a significantly higher microbial abundance compared to the sediment and water. Moreover, 16S rRNA and amoA sequencing data indicate a high degree of compartmentalisation of functional microbial communities between the microenvironments of the seagrass meadow (leaf, sediment and water column), pointing towards the existence of a core seagrass leaf microbiome that could have specific interactions with the plant.

For my third chapter I determined the role that microorganisms inhabiting P. sinuosa seagrass leaves may play in the recycling of DON, and subsequent transfer of inorganic N (DIN) into plant tissues. To achieve this, I performed an experiment whereby seagrass leaves with and without microorganisms were incubated with DO15N, and I traced the fine-scale uptake and assimilation of microbially processed N into seagrass cells, using nanoscale secondary ion mass spectrometry (NanoSIMS). Results from this chapter show for the first time that seagrass leaf epiphytic microorganisms facilitated the uptake of 15N from DON, which was unavailable to the plant in the absence of epiphytes. This indicates that seagrass leaves have limited to no ability to take up DON, and the seagrass leaf microbiome could therefore play a much more significant role than previously thought in enhancing plant health and productivity.

Finally, I determined the net nitrification rates associated with ammoniaoxidising microorganisms (AOM) inhabiting P. sinuosa leaf surfaces, and explored whether AOM facilitated, or competed for, the plant’s N uptake. My findings show that AOM may compete with seagrasses for NH4 + uptake, but that their potential to outcompete seagrass epiphytic algae for DIN uptake indicates that AOM on seagrass leaves may serve as a ‘biocontrol’ over excess epiphytic algal growth.

In summary, the present thesis represents a significant advance in our understanding of the seagrass leaf-microbiome relationship and transformations of N within seagrass meadows. Moreover, it opens up new questions for future research not only on seagrass-microbiome interactions but other macrophytes in aquatic systems that may benefit from the presence of specific N-cycling microorganisms.


Paper Location