UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Intertidal benthic diatoms of the Tagus estuary: Taxonomic composition and spatial-temporal variation (Volume 1) Lourenço Luís Cardoso Soares Ribeiro DOUTORAMENTO EM BIOLOGIA Especialidade Biodiversidade 2010 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Intertidal benthic diatoms of the Tagus estuary: Taxonomic composition and spatial-temporal variation (Volume 1) Lourenço Luís Cardoso Soares Ribeiro Tese orientada por: Prof. Doutora Vanda Brotas e Prof. Doutor Yves Rincé DOUTORAMENTO EM BIOLOGIA Especialidade Biodiversidade 2010 à Laura e ao Luís Alberto O apanhador de nabos aponta o caminho com um nabo Issa Kobayashi, séc. XVIII-XIX. versão de Jorge Sousa Braga, in “Primeira Neve”, Ed. Assírio & Alvim INDEX Acknowledgements ................................................................................................................................................ iii Summary ................................................................................................................................................................. v Resumo .................................................................................................................................................................. vii 1. Introduction ................................................................................................................................................... 3 2. Study area..................................................................................................................................................... 15 2.1. Tagus estuary ..................................................................................................................................... 15 2.2. Alcochete intertidal flats .................................................................................................................... 19 2.2.1. Sediment characterisation and environmental parameters ....................................................... 20 2.2.2. MPB biomass, MPB pigment and microalgal composition ........................................................ 23 3. Material and methods ................................................................................................................................. 29 3.1. Sampling and slide preparation ........................................................................................................ 29 3.1.1. Diatom sampling, extraction, and preservation .......................................................................... 29 3.1.2. Diatom cleaning procedures and slide preparation .................................................................... 31 3.1.3. Diatom identification and cell counting ....................................................................................... 32 3.2. Data screening: species datasets ....................................................................................................... 33 3.3. Diversity .............................................................................................................................................. 34 3.4. Multivariate data analysis ................................................................................................................. 36 3.4.1. Similarity measurement: Bray-Curtis Similarity ....................................................................... 36 3.4.2. Classification: CLUSTER ............................................................................................................. 37 3.4.3. Ordination: MDS ........................................................................................................................... 38 3.4.4. Hypothesis testing for differences between groups of samples: ANOSIM ................................ 38 3.4.5. Species similarities percentage analysis: SIMPER ..................................................................... 39 3.4.6. Linking multivariate community structure to environmental variables: BIOENV ................ 40 3.5. Terminology of functional-groups, life-forms and size-classes ...................................................... 42 4. Results ........................................................................................................................................................... 49 4.1. Diversity .............................................................................................................................................. 49 4.2. Diatom community structure: biotic and environmental multivariate patterns (ANOSIM, MDS, CLUSTER, BIOENV) .......................................................................................................................... 51 4.3. Diatom community structure: taxonomic composition of the assemblages (SIMPER) ............... 57 4.4. Diatom community physiognomy: spatial distribution of size-classes, functional-groups and life-forms .......................................................................................................................................................... 61 4.4.1. Size-classes ...................................................................................................................................... 61 4.4.2. Functional groups and Life-forms ................................................................................................ 63 4.5. Temporal variation of diatom assemblages and individual species ............................................... 65 5. Discussion ..................................................................................................................................................... 73 5.1. Spatial variation and the role of sediment texture .......................................................................... 73 i 5.2. Two main types of communities ........................................................................................................ 76 5.2.1. Epipsammon-dominated community ........................................................................................... 77 5.2.2. Epipelon-dominated community .................................................................................................. 82 5.3. Temporal variation in both types of communities ........................................................................... 88 5.3.1. Epipsammon ................................................................................................................................... 89 5.3.2. Epipelon .......................................................................................................................................... 91 5.4. Diversity .............................................................................................................................................. 95 6. Assessing alternative approaches to species abundance-by-sample community structure description in intertidal benthic diatoms ......................................................................................................... 101 6.1. Introduction ...................................................................................................................................... 101 6.2. Methods ............................................................................................................................................. 104 6.2.1. Matrix selection and data transformation ................................................................................. 104 6.2.2. Matrix comparison and multivariate analyses .......................................................................... 105 6.3. Results ............................................................................................................................................... 107 6.3.1. Higher taxonomical resolution: species presence/absence matrix ........................................... 109 6.3.2. Higher taxonomical resolution: species relative biovolume matrix ......................................... 109 6.3.3. Lower taxonomical resolution: genera matrices ....................................................................... 110 6.3.4. Alternative classifications: size-classes and life-forms matrices .............................................. 113 6.4. Discussion .......................................................................................................................................... 114 6.4.1. Rare species exclusion ................................................................................................................. 114 6.4.2. Qualitative analysis: species presence-absence ......................................................................... 115 6.4.3. Species relative biovolume analysis ............................................................................................ 116 6.4.4. Taxonomic sufficiency: genus-level analyses ............................................................................. 118 6.4.5. Taxonomic surrogacy: size-classes and life-forms analysis ...................................................... 120 6.5. Conclusion......................................................................................................................................... 122 7. Diatom Identification Guide ..................................................................................................................... 127 7.1. Introduction .....................................................................................................................................