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Using the PCI-LF - a Draft User Guide

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Using the PCI-LF - a Draft User Guide Using the PCI-LF - a draft user guide Paul Tett Napier University, Edinburgh (v1.2) 2006 This document explains how to use the Matlab script PCI1ED2 and provides some explanatory material to help users of the PCI-LF tool. It is best read before using the script and tool, but you may go directly to the practical instructions (section 5) and run the script with the test data provided, reading the explanatory material afterwards. A licensed copy of Matlab version 7 or later is needed in order to run the script. Table of contents 1. Phytoplankton and sources of phytoplankton data.......................................................2 2. What is phytoplankton community structure and what is a PCI? .................................3 3. The PCI-LF explained.................................................................................................4 4. Lifeform theory ..........................................................................................................8 5. Using the Matlab script PCI1ED2 to calculate the PCI..............................................10 Overview..................................................................................................................10 Running the Matlab script.........................................................................................11 Data file preparation .................................................................................................12 Preparing the run control file ....................................................................................12 Problems...................................................................................................................13 6. Interpreting the PCI-LF.............................................................................................14 7. Acknowledgements...................................................................................................16 8. References................................................................................................................17 Figures and Tables will be found on the page(s) following their legend(s) 1. Phytoplankton and sources of phytoplankton data Phytoplankton is the community of pelagic photosynthetic micro-organisms. Typically, this community includes many species: these, and individual organisms, are referred to as phytoplankters. The species, as exemplified in Figure 11, belong to several high-level taxa, such as the diatoms (Baccillariophyta), dinoflagellates (Dinophyta) and prymnesiophyte flagellates (Haptophyta). Views on the status and relationship of these high-level taxa are rapidly changing as a result of sequencing of the nucleic acids that dictate the genotypes of the member species. Table 1* gives a current summary. Species are sometimes also categorized according to lifeform, exemplified here by pelagic diatoms - those members of the Bacillariophyta living in the water column, in contrast to benthic diatoms, found in or on the seabed. Phytoplankton abundance and species composition is highly variable in time and space. This variability can be monitored in two main ways. The major taxa differ in their photosynthetic pigments, and it has been argued that chemical measurements of the concentrations of these pigments in samples of seawater, or measurements of ocean colour (by remote, or in-water, sensing) or pigment-specific fluorescence emission (in flow cytometers), can be used for efficient monitoring. However, with the exception of flow cytometry for the smallest members of the phytoplankton, such methods have not yet replaced microscopic analysis as the main source of phytoplankton data. In the Uttermohl microscopic method, a water sample is preserved with Lugol's iodine. Phytoplankters present in a few millilitres (or decilitres) of the sample are allowed to sink onto the transparent base of a sedimentation chamber and there identified and counted using an inverted microscope. Alternatively, a sample is collected by a fine-mesh net. Such a net is used, in the form of a moving band, called a silk, in the Continuous Plankton Recorder (CPR). As part of the CPR Survey, recorders are towed behind ships of opportunity, unit length of the silk corresponding to a certain distance towed. As each instrument is towed, its 1 Figure 1. Example phytoplankters, drawn living material in samples from Scottish west coast waters (modified from Tett, 1992). 1-3 are diatoms (Bacillariophyta); 4 - 6 are dinoflagellates (Dinophyta); 7-9 are ' flagellates', 7 being an euglenoid (Euglenophyceae), 8 a cryptomonad (Cryptophyta), and 9 a set of 'small flagellates' including at least one member of the Haptophyta. * Table 1. Taxonomy of photosynthetic organisms. Using the PCI-LF page 2 2/7/06 Figure 1 Table 1: Taxonomy of photosynthetic organisms Originally based on Margulis (1993) who put most groups at the level of a phylum, with name ending in -[phyt]a) and the algal taxonomy of Tomas (ed.) (1997), who put most groups at the level of a class, with name ending in -[phyc]eae. However, the high-level taxonomy has been revised according to the 'Tree of Life' web project (Patterson & Sogin, 2001) and the NCBI taxonomy browser (Wheeler et al., 2000; NCBI, 2002). In the 'Group' column the names of the highest-order taxa, which may be considered Kingdoms, are given in CAPITALS; a colon (:) shows hierarchy, a slash (/) separates alternative names. Group typical marine phytoplanktonic forms example marine genera Prokaryote Domain (EU)BACTERIA CYANOBACTERIA cyanobacteria: 'blue-green algae', mostly contain Trichodesmium, / Cyanophyta/ phycobiliprotein; filiamentous or otherwise colonial Synechococcus, Cyanophyceae Oscillatoriales and heterocystous Nostocales include Prochlorococcus N-fixers; there picoplanktonic members in Chroococcales and Chloroxybacteria (without phycobiliprotein) Domain EUCARYA/EUKARYOTA, grade PROTOCTISTA EUGLENOZOA: elastic-bodied uni- or bi- euglenoid flagellates Eutreptiella Euglenida/ -phyceae ALVEOLATA: ciliates: functionally photoautotrophic Mesodinium with Mesodinium = Ciliophora symbiotic cryptomonads Myrionecta Dinophyta/ dinoflagellates: 2 dissimilar flagella; many heterotrophic pr Dinophysis, -phyceae obably originally photoautotrophic by secondary symbiosis w Prorocentrum, ith alga. (a) Dinophysidae, (b) Prorocentrales, Gyrodinium, (c) Gymnodiniales, (d) Gonyaulacales, (h) Pyrocystales. Gonyaulax, Ceratium Cryptophyta/ crytomonads: flagellates with phycobiliprotein, arisen by Cryptomonas -phycea symbiosis between heterorophic flagellate and red alga STRAMEN- diatoms: cells with box-like silicified wall, often forming Asterionella, OPHILES loose chains, photoautotrophic by secondary symbiosis Chaetoceros, (HETEROKONTS): with alga, (a) Coscinodiscophyceae, centric diatoms - radiall Leptocylindrus, y symetrical Skeletonema, Bacillariophyta/ (b) Fragilariophyceae - araphid, pennate diatoms; Thalassiosira, -phyceae (c) Bacillariophyceae- raphid, pennate diatoms, bilaterally Pseudo-nitzschia symmetrical Chrysophyta/ small uni- or bi- flagellates including silicoflagellates with sil Ochromonas, -phyceae icified scales or cases. (a) Ochromonodales, (b) Synurales Dinobryon Dictyochophyceae silicoflagellates with many chloroplasts and semi-internal Dictyocha silica skeleton Eustigmatophyta/ very small coccoid algae and small flagellates Nannochloropsis -phyceae Pelagophyceae small or picoplanktonic coccoid algae Aureococcus, Raphidophyta/ small bi-flagellates with many chloroplasts Chatonella, -phyceae Heterosigma Haptophyta/ small, bi-flagellates with haptonema: (a) Coccosphaerales, Pavlova, -phyceae or and (b) Isochrysidales, are flagellates, often with coccoliths Chrysochromulina, Prymesiophyta/ and/or spiny organic scales; (c) Pavlovales: flagellates; Emiliana, Phaeocystis -phyceae (d) Prymnesiales: flagellates, some colonial. VIRIDIOPLANTAE green algae: (a) Volvocales: small flagellates with 1, 2,4,8 fl Brachiomonas, : Chlorophyta: agella, some forming flagellated colonies; Dunaliella, Chlorophyceae (b) Chlorococcales: small coccoid cells Nannochloris Chlorophyta: small flagellates with 1,2,4,8.. stiff flagella and organic Pyramimonas, Tetra- Prasinophyceae scales; some colonial. selmis, Halosphaera silk is wound into a tank of formaldehyde preservative. Subsequently, back in the SAHFOS laboratory, the silk is unwound beneath a microscope, allowing the retained phytoplankters to be identified and counted. 2. What is phytoplankton community structure and what is a PCI? Some biological communities, such as woods and coral reefs, have recognizable physical structure as well as a diversity of primary producers, and both can be seen as contributing to community structure. Thus in the case of temperate deciduous woodland, the member species are seen as belonging to tree, shrub (or understorey) and herb (or ground) layers of vegetation. In the case of the phytoplankton, what we mean by 'community structure' includes the diversity of phytoplankters but not the physical structure element - which is absent, phytoplankters by definition being passively dispersed through the watery medium. Instead, the seasonal changes in dominant species can be considered as fulfilling the same ecological function as layers in woodland. As in the case of the herb, shrub and tree lifeforms that characterize these layers, phytoplankters can be categorized into lifeform types. The exact basis for this is part of the challenge of devising PCIs, but it can be exemplified by the customary distinction between diatoms and other phytoplankters.
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