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Bioproductivity and Biodiversity in Shallow

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BIOPRODUCTIVITY AND BIODIVERSITY IN SHALLOW FRESHWATER LAKES A DISSERTATION SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI‘I AT MĀNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN MOLECULAR BIOSCIENCES AND BIOENGINEERING DECEMBER 2012 By Tsu-Chuan Lee DISSERTATION COMMITTEE: Clark Liu, Chairperson Tao Yan Winston Su Yong Li Keywords: Lake Eutrophication, Biodiversity, Bioproductivity, DGGE ACKNOWLEDGEMENTS I would like to thank Dr. Clark Liu for his excellent advisces and support during my Ph D program. Without his support, it would not have been possible to complete my disserataion research successfully. I must offer my heartfelt thanks to committee members, Dr. Tao Yan, Dr. Winston Su, and Dr. Yong Li for their willingness to share their space, resource, criticism and recommendations. Dr. Yan provided me lab bench, materials, instruments and his lab notes. During my comprehensive examination, Dr. Su guided me an idea regarding the experiment on the behavior of algal transition. Dr. Li allowed me to use his instruments when I have problems in my lab. Many thanks are also extended to all of members for their assistance in the HOLME 286 lab. I express my gratitude to Bunnie and Joe for helping in lab works and Krispin and Card in field data collection. iii ABSTRACT To address the lake eutrophication problem, a research framework integrating molecular biotechnology with environmental engineering was developed. Initially, the lake-like microcosms (Trophic State-Classified Algal Reactors, TSCARs) were designed and constructed for using scenario assessment. As the results, several patterns of algal growth were observed under many replication experiments performed. By adjusting nutrient loading and hydraulic properties, TSCARs produced three classified trophic levels. The TSCARs’ treatments, based on the Vollenweider model in conjunction with the practical works of environmental engineering, were conducted to investigate the relationships between lake biodiversity (LB) and algal bioproductivity (AB). The Chlorophyll-based estimation was developed for assessing the AB. Based on the estimate of AB, the time-varying algal populations were quantified. The relationships between LB and AB were clearly demonstrated by DGGE (Denaturing Gradient Gel Electrophoresis) fingerprints. Data showed that the relationships were in agreement with previous studies. The Shannon index (H’) indicated that the eukaryotic biodiversity of mestrophic level was higher than that of oligo and eutrotrophic levels. The prokaryotic biodiversity of mestrophic level was lower than that iv of oligo and eutrotrophic levels. The similar trends were found in two sites of Lake Wilson under different trophic level. The phase-oriented concept of the algal growth is firstly proposed to explain the varying relationships between LB and AB by examining DGGE under time-varying analysis. Two relationships: positive relation following a hump shape pattern (eukaryotic assemblage) and negative relation following a U shape pattern (prokaryotic assemblage) were found and exhibited clear correlations between LB and AB. Results from time-varying analysis provided exciting insight into the lake biodiversity. These results showed that LB was deeply affected by the history of algal growth. Moreover, critical timing points of algal growth history in terms of Pr(t) predicted that a shift in LB was imminent. By conducting molecular cloning, four libraries were produced. The community structures sampled from the TSCARs were higher similarity in lakes. Finally, a minor finding is worthy of note in regard to the population dynamics of cryptophyta in lakes. It was found that the abundance of the cryptophyta was positively correlated with trophic levels in TSCARs. v TABLE OF CONTENTS ACKNOWLEDGEMENTS...............................................................................................iii ABSTRACT....................................................................................................................... iv TABLE OF CONTENTS................................................................................................... vi LIST OF TABLES............................................................................................................. ix LIST OF FIGURES ........................................................................................................... xi LIST OF ABBREVIATIONS .......................................................................................... xvi LIST OF SYMBOLS ....................................................................................................... xix CHAPTER 1. INTRODUCTION ....................................................................................... 1 CHAPTER 2. LITERATURE REVIEW............................................................................. 7 2.1 Lake eutrophication and algal bloom.................................................................... 7 2.2 Algal bioproductivity .......................................................................................... 13 2.3 Lake biodiversity ................................................................................................ 16 CHAPTER 3. METHODOLOGY .................................................................................... 23 3.1 Experimental design............................................................................................ 23 3.2 Estimates of algal bioproductivity ...................................................................... 28 3.3 Estimates of lake biodiversity............................................................................. 38 3.4 Discussion........................................................................................................... 48 vi CHAPTER 4. LAKE BIODIVERSITY UNDER DIFFERENT TROPHIC LEVELS..... 52 4.1 Laboratory investigation ..................................................................................... 52 4.1.1 Results of TSCARs experiments ............................................................. 53 4.1.2 Investigation of the lake biodiversity in TSCARs by DGGE .................. 63 4.2 Field investigation............................................................................................... 67 4.2.1 Results of field investigation in Lake Wilson.......................................... 68 4.2.2 Investigation of lake biodiversity in filed study ...................................... 75 4.3 Discussion........................................................................................................... 77 CHAPTER 5. LAKE BIODIVERSITY WITH TIME VARYING ALGAL BIOPRODUCTIVITY .............................................................................. 80 5.1 General variation in biodiversity ........................................................................ 81 5.2 Results of a time-varying experiment on the eutrophic TSCAR ........................ 82 5.2.1 Algal bloom in eutrophic TSCAR............................................................ 83 5.2.2 Time-varying lake biodiversity in eutrophic TSCAR.............................. 87 5.2.3 Relationships between lake biodiversity and algal bioproductivity ........ 94 5.3 Discussion......................................................................................................... 102 vii CHAPTER 6. MOLECULAR PHYLOGENY OF EUKARYOTIC ASSEMBLAGE UNDER VARYING TROPHIC LEVELS ...................................................................... 106 6.1 Results............................................................................................................... 106 6.1.1 Eukaryotic libraries in TSCARs ............................................................ 109 6.1.2 Prokaryotic library in eutrophic TSCAR ................................................111 6.2 Phylogenetic analyses ....................................................................................... 114 6.3 Discussion......................................................................................................... 132 CHAPTER 7. CONCLUSION........................................................................................ 135 Appendix A: Additional information for Chapter 3........................................................ 140 Appendix B: Supplement to Chapter 5 ........................................................................... 141 Appendix C: Supplement to Chapter 6 ........................................................................... 142 LITERATURE CITED.................................................................................................... 162 viii LIST OF TABLES 1.1 Spatial distribution of limiting nutrient analysis of Lake Wilson............................ 4 2.1 Typical trophic-state classification.......................................................................... 8 2.2 SRP and TP in lakes and laboratory experiments .................................................. 11 2.3 Phosphorus loading of Lake Wilson estimation..................................................... 12 3.1 Experimental parameters of TSCARs based on the Vollenweider plot dividing the three categories of trophic levels ............................................................................ 25 4.1 Trophic-state classification based on total phosphorus concentration................... 54 4.2 Parameters and coefficients of first-order kinetic SRP model in three trophic states based on the data of Figure4.1. ..............................................................................
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  • Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic 2 Distribution

    Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic 2 Distribution

    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436664; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Cation and anion channelrhodopsins: Sequence motifs and taxonomic 2 distribution 3 Elena G. Govorunova1, Oleg A. Sineshchekov1, Hai Li1, Yumei Wang1, Leonid S. Brown2, Alyssa 4 Palmateer2, Michael Melkonian3, Shifeng Cheng4, Eric Carpenter5, Jordan Patterson5, Gane K.-S. 5 Wong5,6, and John L. Spudich1# 6 1Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The 7 University of Texas Health Science Center at Houston McGovern Medical School, Houston, 8 Texas, USA 9 2Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, 10 Ontario, Canada 11 3Max Planck Institute for Plant Breeding Research, Integrative Bioinformatics, Cologne, 12 Germany 13 4Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 14 Shenzhen, China 15 5Departments of Biological Sciences and of Medicine, University of Alberta, Edmonton, Alberta, 16 Canada 17 6Beijing Genomics Institute-Shenzhen, Shenzhen, China 18 Running title: Cation and anion channelrhodopsins 19 #Address correspondence to John L. Spudich, [email protected]. 20 Word count Abstract: 227 21 Word count Text: 4,360 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436664; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 ABSTRACT 24 Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal 25 species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as 26 optogenetic tools to control cell membrane potential with light.