Microbial Diversity of a Nature Reserve: Eukaryotic Microorganisms of Mere Sands Wood in N.W. England Angela Lyn Creevy
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MICROBIAL DIVERSITY OF A NATURE RESERVE: EUKARYOTIC MICROORGANISMS OF MERE SANDS WOOD IN N.W. ENGLAND ANGELA LYN CREEVY A thesis submitted in partial fulfilment of the requirements of Liverpool John Moores University for the degree of Master of Philosophy July 2013 CONTENTS LIST OF FIGURES AND TABLES ABSTRACT CHAPTER 1 - GENERAL INTRODUCTION ………………………………………..1 1.1 The diversity of distribution of eukaryotic microorganisms 1.2 Potential factors influencing microbial diversity and distribution 1.2.1 Terrestrial environments 1.2.2 Freshwater environments 1.3 Model organisms 1.3.1 Biology of Testate amoebae 1.3.2 Biology of Diatoms 1.4 Aims of this study CHAPTER 2 - STUDY SITE …………………………………………………………...15 2.1 Site description 2.2 Site history 2.3 Site character and ecology 2.3.1 Terrestrial habitats 2.3.2 Freshwater habitats CHAPTER 3 – METHODS ………………………………………………….............. 20 3.1 Field sampling design 3.2 Testate amoebae data collection 3.2.1 Laboratory preparation 3.2.2 Quantification and identification 3.3 Diatom data collection 3.3.1 Laboratory preparation 3.3.2 Quantification and identification 3.4 Environmental variables 3.4.1 Determination of organic matter content 3.4.2 Indicative pH measurements 3.5 Existing biological records 3.6 Data analysis 3.6.1 Margalef diversity index 3.6.2 Simpson diversity index 3.6.3 Shannon diversity index 3.6.4 LF Index CHAPTER 4 – RESULTS .................................................................................................29 4.1 Overview of biodiversity at Mere Sands Wood Nature Reserve 4.1.1 Comparison of microbial diversity with previously studied macroscopic organisms 4.1.2 Qualitative observations on the spatial distribution of testate amoebae and diatoms with previously studied macro-fungi 4.1.3 Microbial taxon and genus richness 4.2 Microbial diversity and distribution in terrestrial environments 4.2.1 Differences in microbial diversity between terrestrial microhabitats 4.2.2 Correlations between species richness and diversity of testate amoebae and diatoms 4.2.3 Correlations between species richness, diversity and environmental variables 4.2.4 Correlations between species richness and diversity indices 4.2.5. Differences between testate amoebae composition in litter and soil 4.2.6 Ratio of testate amoebae r-K strategists on an island in a shallow lake 4.3 Microbial diversity and distribution in aquatic environments 4.3.1 Differences in microbial diversity between terrestrial microhabitats 4.3.2 Correlations between species richness and diversity of testate amoebae and diatoms 4.3.3 Correlations between species richness, diversity and environmental variables 4.3.4 Correlations between species richness and diversity indices CHAPTER 5 – DISCUSSION .......................................................................................... 55 5.1 Overview of Biodiversity at Mere Sands Wood Nature Reserve - a wider context 5.1.1 A more balanced perspective of biodiversity? 5.1.2 Qualitative observations of testate amoebae, diatoms and macro fungi 5.2 The potential for surrogate measures in microbial diversity surveys 5.2.3 Can genus richness be used as a surrogate for species richness? 5.3 Terrestrial environments 5.3.1 Insights into potential factors influencing microbial diversity and distribution 5.3.2 The influence of humus forms 5.3.3 Vertical distribution in soils 5.3.4 Testate amoebae community assembly 5.3.5 Potential effects of animal disturbances 5.4 Freshwater environments 5.4.1 Insights into potential factors influencing microbial diversity and distribution 5.4.2 Potential effects of invasive species 5.4.3 The influence of sediment organic matter 5.4.4 Lake trophic status and condition 5.4.5 Lakes as complex, heterogeneous systems 5.5 Ecological hotspots 5.5.1 The terrestrial-aquatic interface and the potential for dispersal 5.6 Wider significance and directions for future research 5.6.1 Global change, biodiversity and biogeographies 5.6.2 Landscape systems ecology – micro to macro scale 5.6.3 Taxonomic uncertainty - reconciling environmental and molecular data 5.6.4 Evolutionary life strategies in Protists CHAPTER 6 – CONCLUSION ....................................................................................... 83 ACKNOWLEDGEMENTS ...............................................................................................85 REFERENCE LIST .............................................................................................................86 APPENDICES .....................................................................................................................94 MANUSCRIPT Page List of figures number 1 Photographs of sampled lakes 18 2 Sketch maps of lakes 19 3 Nested sampling design 20 4 GIS map of study site, boundary, sampling locations 21 5 Taxon sampling curve 23 6 Taxonomic composition of biodiversity at MSW 29 7 Qualitative spatial data for testate amoebae, diatoms and macro-fungi 31 8 Distribution of testate amoebae species per genus 33 9 Distribution of diatom species per genus 34 10 Number of testate and diatom taxa in terrestrial microhabitats 39 11 Number of testate taxa under different stages of vegetation succession 40 12 Correlation between number of testate taxa and mor humus organic matter 42 13 Correlation between number of testate taxa and mull humus organic matter 42 14 Relative abundance of lobose testate amoebae in fresh and soil organic matter 43 15 Correlation between the proportion of filose testate amoebae and stained tests 44 16 Ratio of testate r-K strategists in fresh organic matter 46 17 Ratio of testate r-K strategists in soil organic matter 46 18 Number of testate amoebae and diatom taxa in drainage ditch sediment 49 19 Number of testate amoebae and diatom taxa in the sediment of four lakes 50 20 Correlation between diatom species richness and lake sediment organic matter 54 21 Diatom assemblage in soil beneath bryophytes 62 22 Nematode worm in bryophyte litter 65 23 Desmids in litter and soil on an island in a shallow lake 74 24 Unidentified organisms 80 Page List of tables number 1 Relative abundance and number of testate amoebae genera 33 2 Relative abundance and number of diatom genera 34 3 Summary of taxon and genus richness in terrestrial microhabitats 35 4 Summary of taxon and genus richness in aquatic microhabitats 36 5 Pearson’s correlation between taxon and genus richness 37 6 Summary of environmental variables for terrestrial habitats 37 7 Testate amoebae summary table for terrestrial microhabitats 45 8 Summary of environmental variables for aquatic habitats 47 9 Differences in mean testate diversity in aquatic microhabitats 48 10 Differences in mean diatom diversity in aquatic microhabitats 49 11 Differences in diatom taxon richness between lakes and substrate type 51 12 Differences in testate taxon richness between lakes and substrate type 51 13 Testate amoebae summary table for aquatic microhabitats 52 ABSTRACT The idea of incorporating eukaryotic microorganisms into biological surveys is a new idea in nature conservation. Using Testate amoebae and Diatoms as model organisms, this study aimed at expanding the Wildlife Trust’s knowledge of biodiversity at its Mere Sands Wood Nature Reserve by describing and quantifying microbial diversity and distribution using traditional protist taxonomy based on morphology. The methods employed were similar to that adopted in the studies of macroscopic organisms, allowing for a comparison between the diversity of microscopic and previously studied macroscopic organisms. The results of this study highlighted the dramatic increase in species richness estimates by incorporating just two groups of eukaryotic microorganisms. Species richness was a useful measure of diversity and these results were largely consistent with diversity indices. Terrestrial soil and lake sediment microhabitats supported distinct assemblages of testate amoebae and diatom communities which enabled inferences to be made about the potential factors influencing microbial diversity and distribution in terrestrial and aquatic habitats. Lower microbial diversity was found in lake sediment associated with invasive aquatic plants and native monocultures. Taxon richness and diversity varied between different microhabitats and also at the replicate scale within a 1m2 quadrat, further highlighting the small-scale variability in microbial communities. The lack of correlation between different microbial groups demonstrated the complexities in understanding the structure of microbial communities. The relationship between species and genus richness highlighted the potential for using surrogate measures for future rapid biodiversity surveys. The use of evolutionary life strategies in protists is an area for future study which may provide useful insights into nature conservation management for microscopic organisms in habitats prone to disturbance and stress. This study illustrates the potential for incorporating eukaryotic microorganisms into biodiversity surveys. It would be useful to extend this research to other nature reserves and representative habitats using a nested design, facilitating replication and randomisation. CHAPTER ONE GENERAL INTRODUCTION 1.1 The diversity of distribution of eukaryotic microorganisms The diversity and distribution of free-living microbial eukaryotes is a vastly understudied question in classical ecology (Wilkinson 2007). Ecologists have focused much attention on trying to explain broad patterns of biodiversity, yet published literature on, for instance, the loss of