luận văn the first report of myxomycetes amoebozoa in thai nguyen city northern vietnam rapid biodiversity assessment using tools in modern molecular era

THAI NGUYEN UNIVERSITY UNIVERSITY OF AGRICULTURE AND FORESTRY JOHN CARLO REDEÑA SANTOS THE FIRST REPORT OF MYXOMYCETES (AMOEBOZOA) IN THAI NGUYEN CITY, NORTHERN VIETNAM: RAPID BIODIVERSITY ASSESSMENT USING TOOLS IN MODERN MOLECULAR ERA BACHELOR THESIS Study Mode: Major: Faculty: Batch: Full-time Environmental Science and Management International Programs Office K45-AEP Thai Nguyen, 20/11/2017 n Thai Nguyen University of Agriculture and Forestry Degree Program Bachelor of Science in Environmental Science and Management Student name Student ID Thesis Title Supervisor (s) Abstract: John Carlo Redeña Santos DTN1454290051 The first report of Myxomycetes (Amoebozoa) in Thai Nguyen City, Northern Vietnam: Rapid biodiversity assessment using tools in modern molecular era Dr Duong Van Thao & Dr Nikki Heherson A Dagamac Myxomycetes are phagotrophic, fungus-like protists abundantly occurring as microbial predators in soil ecosystems However, in spite of their cosmopolitan distributions, limited studies were conducted in Southeast Asia In particular, gaps are found in Northern Vietnam which has no single reported studies that annotates myxomycetes In order to fill the missing voids, a three-phase rapid biodiversity assessment employing purely moist chamber cultures was carried out in Thai Nguyen City, Northern Vietnam using (i) traditional taxonomic survey, (ii) classical diversity measurement and estimation utilizing sophisticated statistical programming pipelines and (iii) modern molecular technique using DNA barcoding (partial 18s rRNA gene) technology These efforts showed: (1) agricultural plantations with specified leaf textural morphology are good microhabitat for leaflitter inhabiting myxomycetes, (2) protected and unprotected forests shares myxomycetes assemblages, (3) anthropogenic activities plays a role in spore dispersal, (4) confirmation that both at community and genetic level, dispersal ecology of myxomycetes are not affected by management strategies or forest type, ii n and (5) 54 species newly recorded for Northern Vietnam, of which are new records for the whole country, with possible species new to science As such, this study provided the very first baseline information on the biodiversity of myxomycetes for Northern Vietnam Keywords α and β diversity, barcoding, dispersal, forest management, slime molds, tropical plants Number of pages 143 pages Date of Submission September 25, 2017 Supervisor‘s signature iii n ACKNOWLEDGEMENT This body of work was made possible by a lot of people who participated in this endeavor in very different but significant ways Firstly, I would like to acknowledge my whole family for the unconditional support, especially to my parents (Nanay Annie & Tatay Jun), to whom I am beyond grateful as they invested not just money but also time and sweat for my education To my brothers (PJ, Paulo, Third) and my sister (Darla) in blood, a humongous shout-outs to the four of you I would also like to include a special note of ―hindi matatawarang pasasalamat‖ to Dr Nikki Heherson A Dagamac for not just being an adviser and fostering me for three months, but also for being my mentor in every aspect of life Without his untiring efforts and never-ending patience, I would not have finished this beautiful piece of work I would also like to express my gratitude to Prof Dr Martin Schnittler (University of Greifswald), Prof Dr Wilhelm Steingrube (SusEnMan Project, University of Greifswald) and Frau Katharina Schmitt (International Office, University of Greifswald) for the research scholarship, internship and field collection fundings, and to Dr Duong Van Thao, Frau Anja Klahr (Laboratory coordinator, Allgemeine und Spezielle Botanik), Dr Manuela Bog, Dr Hoang Hai Thanh, Dr Nguyen Dang Cuong (TUAF), Oriana Sanchez-Mahecha and Nguyen Thuy Linh for the technical assistance Big thanks to my friends (Nicole, Jose, Hong, Thao, Keraia, Pons, Tina, Colleene, Kenneth, Alex, Mishel, Kathleen, Jamba, Bojo, Tintin, CJ, Edwin) for the personal support, and to my Greifswald friends (Rafa, Kasia, Kemani, Oleg, Tim, Lukas, iv n Franzi, Jinny, Carlos, Brook, Christian, Paul, Sabine, Lorna, Dani, Julia) for keeping me stable during my research and internship in Germany Lastly, a very special mention to Ikkin, Ward and William for the Pizza party and Jenga session we shared during my stay in Germany v n TABLE OF CONTENTS List of Figures List of Tables 10 List of Abbreviations 11 Part I Introduction 12 1.1 Research Rationale 12 1.2 Research Questions and Hypotheses 15 1.2.1 Occurrence of myxomycetes in homogenous vegetation 15 1.2.2 α and β diversity in a heterogeneous vegetation 16 1.2.3 Genetic diversity 17 1.3 Research Objectives 18 1.4 Scope and Limitations 20 1.5 Definition of terms 21 Part II Literature Review 25 2.1 Natural Classification history of myxomycetes 25 2.2 Economic and ecological importance 26 2.3 Cutting edge technologies applied in studying the diversity and ecology of myxomycetes 31 Part III Methodology 37 3.1 Occurrence of myxomycetes in homogenous vegetation 37 3.1.1 Collection of substrates and preparation of moist chambers 37 3.1.2 Characterization and identification of fruiting bodies 38 3.1.3 Calculation of productivity and myxomycete occurrence 39 3.2 α and β diversity in a heterogeneous vegetation 40 3.2.1 Collecting localities 40 3.2.2 Collection of substrates, laboratory isolation method and myxomycetes characterization 41 3.2.3 Data evaluation 43 3.3 Genetic diversity 46 3.3.1 Specimen acquisition 46 vi n 3.3.2 DNA Extraction, amplification and sequencing 47 3.3.3 Sequence alignment, tree construction and genetic analysis 49 Part IV Results and Discussion 51 4.1 Occurrence of myxomycetes in homogenous vegetation 51 4.1.1 Results 51 4.1.2 Discussion 55 4.2 α and β diversity in a heterogeneous vegetation 57 4.2.1 Results 58 4.2.2 Discussion 73 4.3 Genetic diversity 78 4.3.1 Results 78 4.3.2 Discussion 80 PART V Conclusion 83 References 88 Appendices 104 vii n LIST OF FIGURES Figure 1: The study area: Thai Nguyen City, Thai Nguyen Province showing the sampling location of the three agricultural plantations 37 Figure 2: Schematic diagram for the methodology of the first phase of this research study 40 Figure 3: Sampling locations for the two community forests in Thai Nguyen City, Thai Nguyen Province 41 Figure 4: Schematic diagram for the methodology of the second phase of this research study 46 Figure 5: Schematic diagram for the methodology of the third phase of this research study 50 Figure 6: The 2D bar graph shows (a) percentages of positive moist chambers between the aerial (AL) and ground leaf (GL) litter substrates in three different agricultural plantations and (b) percentages of positive moist chambers between Superorder Lucisporidia (bright-spored) and Superorder Fuscisporidia (dark-spored) in three different agricultural plantations 51 Figure 7: (a) Rarefaction curves for two different forest type and generated species accumulation curves from Chao estimator for the (b) both community forests; (c) for protected forest; (d) for unprotected forest .58 Figure 8: Box plot showing the comparison of six different diversity indices (Alpha = Fisher‘s alpha; Shannon = Shannon‘s H index; Simpson = Simpson‘s diversity index; N0 = species richness only, N1 = exponent of the Shannon diversity, N2= inverse of the Simpson diversity) 71 n luan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.era Figure 9: Non-metric multidimensional scaling (NMDS) of species occurrence between two community forests Black dots represent the position of myxomycetes species in the ordination space Colored circles represent the forest type; colored ellipses denote dispersion based on standard deviation of point scores 72 Figure 10: Phylogenetic tree of Diderma hemisphaericum: based on partial SSU sequences of the 13 successfully amplified specimens .79 n luan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.era luan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.era LIST OF TABLES Table 1: Occurrence of myxomycetes: The table shows the list of myxomycetes and their average pH ±, - max values as measured on every positive moist chamber A species recorded as rare (1 record) uses only the pH value of the sole moist chamber where it was found The color on the left side of the species indicates their Superorder (yellow=bright-spored, Superorder Lucisporidia; brown=dark-spored, Superorder Fucisporidia) The abundance index (AI) in accordance to Stephenson et al (2013), and their total number of records is further reported on this table The distribution of records for substrates (AL or GL) and agricultural plants are also enumerated .52 Table 2: Computed values using Analysis of Molecular Variance 80 10 n luan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.eraluan.van.the.first.report.of.myxomycetes.amoebozoa.in.thai.nguyen.city.northern.vietnam.rapid.biodiversity.assessment.using.tools.in.modern.molecular.era