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Nastassia Denis Thesis Spatiotemporal microbial community composition in the subsurface sediments of tropical peat- draining rivers in Sarawak, Malaysia Nastassia Denis 101760198 A thesis submitted in fulfilment of the requirement for the degree of Doctor of Philosophy (by Research) (PhD) Faculty of Engineering, Computing & Science Swinburne University of Technology, Sarawak Campus June 2019 ABSTRACT Our initial study in March 2014 demonstrated high abundance of Acidobacteria, Proteobacte- ria, and Terrabacteria at all sampling stations and advocated the possibility that the microbial diversity and enzyme activity is linked to the low CO2 emissions. In August 2015 and January 2016, we investigated the occurrence of shared and unique core and rare taxa in the pristine peat-draining rivers (Maludam river) and the disturbed peat-draining rivers (Sebuyau and Simunjan rivers) using 16S rRNA amplicon sequencing. Most of the bacterial core taxa found were members of the Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, Aci- dobacteria and Planctomyctes, all of which are commonly found in peatland ecosystems and are degraders related to amino acid processes. Alphaproteobacteria usually prevail in meth- ane-emitting wetlands and these bacteria are mainly composed of methanotrophs from Methy- locystaceae. Firmicutes, Bacteroidetes and Actinobacteria are plant-degrading microbes de- graders. Deltaproteobacteria belong to phylogenetic lineages from the genera Syntrophobac- ter and Geobacter which prevail in wetlands with high sulfate levels (Baker, Lazar et al. 2015). The sediment Archaea 16S revealed the core archaea communities composed of Cre- narchaeota, Euryarchaeota and Thaumarchaeota. Crenarchaeota were detected in low se- quence reads and relative abundance in all rivers during both dry and monsoon seasons. The sediments in all the rivers were enriched with Euryarchaeota. Most of the euryarchaeal OTUs detected in the peat-draining rivers were related to Methanosarcinales. Fungi (under the phylum Opisthokonta) were the major group of Eukaryotes for all the three peat-draining rivers. Opistokhonta and Alveolata were the most dominant Eukaryotes. The most dominant lineages under Opistokhonta were Nucletmycea followed by Holozoa. The rare Eukaryotes were Discosea, Gracilipodida, Tubulinea, Chloroplastida, Centrohelida, Discoba, D 1, SAR and Stramenopiles. Both the pristine and anthropogenically influenced peat-draining rivers were dominated by Bacillariophyceae. (consisting of Stramenopiles and Ciliophara). The bacterial abundance and composition increased in the pristine peat-draining river and de- creased in disturbed peat-draining rivers. This pattern is supported by the increased of enzyme activities in the disturbed rivers indicating due to the increase of organic matter from the soil run-off. This study highlights the impact of anthropogenic activities to the microbial commu- nity and activities in the three peat-draining rivers in Sarawak. !1 ACKNOWLEDGEMENT Firstly, I would like to express my sincere gratitude to my supervisor Prof. Moritz Mueller for the continuous support of my Ph.D study and related research, for his patience, motivation, and immense knowledge. His guidance helped me in all the time of research and writing of this thesis. I could not have imagined having a better advisor and mentor for my Ph.D study. Besides my advisor, I would like to thank the rest of my thesis committee: Dr Aazani Mu- jahid, Dr Lik Fong and Dr Daniel Tan for their insightful comments and encouragement, but also for the hard question which incented me to widen my research from various perspectives. My sincere thanks also goes to Professor Justus Notholt, Dr Thorsten Warnecke and Dr Denise Mueller provided me an opportunity to collaborate this research with them. Dr Aazani Mujahid who gave access to the laboratory facilities in UNIMAS. Dr David Pearce for en- couraging this research. Dr Lim Poh Teen who granted temporary research in IOES, Bachok, Kelantan. Without their precious support it would not be possible to conduct this research. I thank Prof Wallace Wong, Dr Lim Hong Chang, Dr Tan Toh Hii, Swinburne staff, UNIMAS staff and students, Bremen University staff and students, Sarawak Forestry Coorperation staff and AQUES members for assisting in my research for the last four years. Also, I thank my friends in Inno Biologics Sdn Bhd. In particular, I am grateful to Datuk Dr Mohd Nazlee Ka- mal, Dr. Heilly Chong, Dr Shivraj Dasari and Miss Serena Ganesan for enlightening me the first glance of research. Last but not the least, I would like to thank my parents, my family and friends for supporting me throughout my PhD journey and my life in general. Danke! !2 AUTHOR DECLARATION I hereby declare that this thesis entitled “Spatiotemporal microbial community composi- tion in the subsurface sediments of tropical peat- draining rivers in Sarawak, Malaysia” is the result of my own research work except for quotations and citations which have been duly acknowledged. I also declare that is, it has not been previously or concurrently submitted for any other Master/PhD students at Swinburne University of Technology (Sarawak Campus). Name: Nastassia Denis ID No.101760198 Date: 6th June 2019 !3 LISTS OF JOURNAL AND CONFERENCES PUBLICA- TIONS Work carried out during this PhD project (but not covered in this thesis) has led to the fol- lowing co-authored paper: Müller, D., T. Warneke, T. Rixen, M. Müller, S. Jamahari, N. Denis, A. Mujahid and J. Notholt (2015). "Lateral carbon fluxes and CO2 outgassing from a tropical peat-draining riv- er." Biogeosciences 12(20): 5967-5979. List of conference presentations i. Nastassia Denis, Aazani Mujahid and Moritz Mueller ‘Potential use of oil palm waste for microbial fuel cell’ World Hybrid conference 2013, UNIMAS, Kuching, Malaysia (Poster presentation) ii. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Is Archaea linked to Methane production in Sarawakian rivers?’ 9th International WESTPAC Scientific Conference 2014, Nha Trang, Vietnam (Poster presentation) iii. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Assessment of the microbial diversity in tropical peat-draining rivers in Sarawak, Malaysia using 16s rRNAa pyrosequencing’ 15th International Peat Congress 2016, Kuching, Malaysia (Poster presentation) iv. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Assessment of the microbial diversity in tropical peat-draining rivers in Sarawak, Malaysia using 16s rRNAa pyrosequencing’ 10th International WESTPAC Scientific Conference 2017, Qing Dao, China (Oral presentation) v. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Environmental viral community in the subsurface of peat-drain- ing rivers in Sarawak, Malaysia’ 23rd International Symposium on Environmental Biogeochemistry 2017, Cairns, Australia (Poster presentation) !4 vi. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Microbial community in the subsurface of peat-draining rivers in Sarawak, Malaysia’ 23rd International Symposium on Environmental Biogeochem- istry 2017 Cairns, Australia (Oral presentation) vii. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Microbial community in the subsurface of peat-draining rivers in Sarawak, Malaysia’ The International Society for Subsurface Microbiology (ISSM) 2017 Conference, Rotorua, New Zealand (Oral presentation) viii. Nastassia Denis, Denise Mueller, Moritz Mueller, Aazani Mujahid,Thorsten War- necke, Justus Notholt ‘Environmental viral community in the subsurface of peat-drain- ing rivers in Sarawak, Malaysia’ The International Society for Subsurface Microbiolo- gy (ISSM) 2017 Conference, Rotorua, New Zealand (Poster presentation) !5 Table of Contents !6 ABSTRACT ...............................................................................................................................1 ACKNOWLEDGEMENT ..........................................................................................................2 AUTHOR DECLARATION .......................................................................................................3 LISTS OF JOURNAL AND CONFERENCES PUBLICATIONS ...........................................4 Overview ....................................................................................................................................1 Chapter 1 .....................................................................................................................................3 1.0 Introduction ..........................................................................................................................4 1.1 Microbial communities ....................................................................................................4 1.2 Rivers ................................................................................................................................5 1.3 Peatland ............................................................................................................................5 1.4 Tropical peatland and peat-draining rivers .......................................................................6 1.5 The microbiology of peatlands .........................................................................................8 Chapter 2 ...................................................................................................................................12
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