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Patterns of succession and functional groups
Focusing more on patterns of phytoplankton successions within lakes, Reynolds (1980) regrouped organisms in functional groups representative of lifeforms, that, he noticed, had also similar ecologies and physiologies (Figure 9). He hypothesized that these groups distinguished with further precision the various strategies adapted to gradients in turbulence and nutrients. The 14 functional groups contained: (1, 2).
Diatoms dominating the spring bloom (1 appeared in poor lakes, 2 in richer lakes) and (7, 8) other Diatoms occurring at the end of summer (7 appeared in poor lakes and 8 in richer lakes). When the waters started to stratify after the spring bloom of diatoms, the lakes were often dominated by green algae (3, 4, 5) with presence at the end of cyanobacteria (6). During harsh stratification, swimming dinoflagellates (10: Ceratium) or other cyanobacteria dominated (9: Microcystis). Other groups were
observed frequently but never dominated, notably the (11) small colonial Chlorophytes (Pediastrum) and the filamentous cyanobacteria Oscillatoria (12) that dominated during lower productivity periods, while other poorly identified nanoalgae (X) and Cryptomonads (Y) were present every time but at low abundances. As Margalef, Reynolds recognized that there were succession phases more repeatable than others and attributed these perturbations either to the allogenic changes in the physical environment or to predation. Later on, Reynolds used performance traits (i.e. measure of the success of a species in certain conditions) rather than functional trait (i.e. a selective advantage that impacts a species success) (Violle et al., 2007) and complicated even further his scheme, with the recognition of more than 31 functional groups of freshwater phytoplankton (Reynolds et al., 2002).
Beyond phytoplankton: heterotrophic protists
In parallel to these works on phytoplankton Fenchel (1980a, 1980b, 1982a, 1982b) helped to define the functional diversity of heterotrophic protists. In a first series of paper Fenchel focused on Ciliates (Fenchel, 1980a, 1980b). He noted that Ciliates had developed complex ways of feeding involving cilia that concentrated the suspended food close their mouth (i.e. cytosome). The efficiency of this mechanisms was involved in the clearance rate (food items ingested per predator per unit of time) of Ciliates. The optimal size of food items for ciliates was a function of the clearance rate, the size of the mouth of the ciliate species and food concentration. The success of heterotrophic protists in conditions of various prey abundance could thus be estimated by measurable morphological characters (Fenchel, 1980b). With help from the study of their functional response to small food items, Fenchel estimated that Ciliates could not be efficient removers of bacteria as proposed in the microbial loop concept (Pomeroy, 1974; Fenchel, 1980a). Instead, Fenchel studied the functional response of smaller heterotrophic flagellates and proposed them as regulators of bacteria in marine environments (Fenchel, 1982a). Within the small heterotrophs that he investigated, most fed with a flagellar apparatus that brought food particles towards their cytosome or to their pseudopodia. He noted that the size of their preferential food was determined by their clearance rates, distinct motile or attached ways of living, as well as the abundance, size and motility of their prey (Fenchel, 1982a). The functional response of small heterotrophic protists to small particle size indicated that they could feed on the natural bacterial abundances of the marine environment (Fenchel, 1982b). These results were later integrated to the microbial loop as depicted by Azam et al. (1983), where bacteria were eaten by small heterotrophic flagellates and ciliates were more efficient in the size range of preys such as small heterotrophic flagellates.
It is thus by using functional traits that researcher better understood protistan ecological strategies. The study of these strategies than improved the knowledge of the succession patterns, the composition and the functional roles of plankton communities.
Contemporaneous Functional Ecology
The functional approach gained wide interest among ecologists when Tilman et al. (1997) showed that functional diversity influenced more ecosystem functioning than species diversity. Gathering different plant traits, these authors regrouped species among functional groups and studied the effects of community structure on productivity. The results showed that species productivity was influenced more by the number of functional groups than by species diversity, however species diversity within functional groups, or functional redundancy, still increased productivity. By cumulating distinct strategies there was thus a better utilization of resources within the ecosystem which allowed to increase plants productivity. Since the work of Tilman and colleagues, the functional approach enriched by harvesting traits among various communities and this lead to recent publications about, among others: benthic systems (Rigolet et al., 2014), zooplankton community (Barnett et al., 2007; Kiørboe, 2011; Litchman et al., 2013; Benedetti et al., 2015), fishes (Mouillot et al., 2013, 2014; Villéger et al., 2013), microbial litter (Allison, 2012) or even amphibians (Tsianou and Kallimanis, 2015).
For marine plankton, there has been major reviews of relevant phytoplankton traits by Litchman & Klausmeier (2008), but also zooplankton traits (Litchman et al., 2013) and microbial traits (Litchman et al., 2015). The reviewing work of Litchman and colleagues gave much importance into sorting traits according to 1/ their typology (i.e. whether involving morphology, physiology, behavior or life-history) and 2/ their effect on ecological functions (i.e. reproduction, resource acquisition and avoidance of predation) (Figure 10). It is necessary to note the distinction between ecological function and functional role, for phytoplankton the functional role depending on the question can be e.g. primary production, while the ecological functions are proxies estimating the chance of a phytoplankton species to thrive, and to carry out primary production, under certain conditions (i.e. fitness, Violle et al., 2007). Another interesting focus of Litchman and colleagues was the recognition of trade-offs as an interrelation of traits, as they noted, the interdependence in these traits defined distinct ecological strategies based on investments into the distinct ecological functions (i.e. reproduction, resource acquisition and avoidance of predation). For example, a K strategy species have a long lifetime but this is only possible at the cost of a slower development.
Environmental characteristic of the sampled ecosystems
A total of 277 water samples were collected in a temporal and/or spatial manner across coasts of the north Atlantic Ocean (Figure 11), representing various environmental gradients (Table 1). Chemo-physical variables (temperature, salinity, and nutrients NO3 -, NO2 -, PO4 3-, NH4 + and Si(OH)4) were collected in all datasets, with the exception of Senegalese samples that lacked temperature and salinity measures, and the 2015 samples of the PI and PH cruises that lacked the whole environmental set. Principal Component Analysis (PCA; Figure S1) of this environmental dataset showed two major gradients. On the first PCA axis (PCA1, 39.92 % of the explained variance) samples were distributed along a gradient of nutrient concentrations. On the second axis of the PCA (PCA2, 34.14% of the explained variance) the samples were separated along a salinity-temperature gradient, distinguishing notably marine from estuarine waters.
Functional vs. taxonomical diversity of marine protists
The relationship between environmental variables, taxonomic and functional diversity, among pico-, nano- and micro-plankton communities was studied by the RV statistical coefficient of co-inertia, a multivariate generalization of the Pearson correlation coefficient (Borcard et al., 2011; Legendre and Legendre, 2012; Husson et al., 2018). Correlations (RV coefficient) between the taxonomical community table and environment variables were low but significant across all size-fraction (value for micro: 0.45, nano: 0.22 and picoplankton: 0.19, with p-value < 0.0001). Similarly, correlations between the functional community table and environmental variables were also low but significant (value for micro: 0.34, nano: 0.16 and picoplankton: 0.10, with p-value < 0.0001). For every size fraction, the correlations (RV coefficient) between the functional and the taxonomical community table were high and significant (values for micro-: 0.71, nano-: 0.46 and pico-plankton: 0.75, with p-value < 0.0001) meaning that taxonomic and functional diversity of marine protists were tightly coupled.
In order to study if protist communities different for their taxonomic composition were characterized by similar composition of our 6 functional groups, we computed a Non-metric Multi-Dimensional Scaling (NMDS) ordination separately for samples of micro-, nano- and pico-plankton on the basis of their OTUs composition. On each NMDS, samples were clustered together by an unsupervised best partitioning of samples using a k-mean method and a simple structure index (ssi) criterion. The relative abundances of the 6 functional groups within those samples and clusters were calculated. The overall aim was to compare the functional diversity across protistan communities distinct for their taxonomic composition (Figure 16). To study whether there was an effect of the environment on taxonomic and functional composition, environmental variables were projected as vectors onto each NMDS ordination space.
Table of contents :
INTRODUCTION
1) Preamble: Ecology
2) Marine Protistan Diversity
3) Marine Protistan Ecology: State of the Art
a) Everything is everywhere but the environment selects
b) Redfield Ratio
c) Trophic Ecology
d) Competitive Exclusion and the Paradox of the Plankton
e) Plankton species successions and ecosystem maturity
f) The microbial loop
g) Transitions in pelagic ecosystems
h) Neutral theory and dispersal
i) Conclusion
4) Methodological developments in the sampling of marine protists
5) A perspective for marine protists: functional ecology
a) Strategies of marine protists in aquatic ecosystems
b) Lifeforms and successions
c) Patterns of succession and functional groups
d) Beyond phytoplankton: heterotrophic protists
e) Contemporaneous Functional Ecology
6) Marine Coastal Ecosystems
OVERVIEW AND OBJECTIVES
CHAPTER I: COUPLING BETWEEN TAXONOMIC AND FUNCTIONAL DIVERSITY IN PROTISTAN COASTAL
1) Introduction
2) Results
a) Environmental characteristic of the sampled ecosystems
b) Genetic diversity
c) Functional diversity
d) Functional vs. taxonomical diversity of marine protists
3) Discussion
a) Patterns of genetic diversity of coastal protist communities
b) From a genetic to a functional diversity approach in protists: limits and potential development .
c) Patterns of functional diversity of coastal protist communities
d) Coupling between functional roles and taxonomy among marine protistan communities
4) Conclusions
5) Experimental Procedures
a) Sampling strategy
b) Genetic procedures
c) Sequence data cleaning, filtering and clustering into OTUs and taxa
d) Functional approach
e) Statistical Analyses
6) Supplementary Material
CHAPTER II: PATTERNS OF PROTISTAN DIVERSITY OVER A COASTAL TIDAL FRONT
A. PATTERNS OF PHYTOPLANKTON DIVERSITY OVER A COASTAL TIDAL FRONT
1) Introduction
2) Material and methods
a) Oceanographic context and sampling strategy
b) Genetic procedures
c) Bioinformatics analyses
d) Phytoplankton Diversity analyses
e) Functional diversity analyses
3) Results
a) Oceanographic Context
b) Metabarcoding of the Protistan Community
c) Phytoplankton Diversity Patterns
d) Functional Diversity
4) Discussion
a) Phytoplankton community composition
b) Phytoplankton diversity and environmental drivers
c) Phytoplankton ecological strategies and environmental drivers
5) Conclusion
6) Supplementary Material
B. HETEROTROPHIC PROTISTS: DYNAMIC AND DIVERSITY OVER A COASTAL TIDAL FRONT
1) Introduction
2) Material and methods
3) Results
a) The heterotrophs/phototrophs ratio
b) Heterotrophic protists diversity
c) Abundant heterotrophic protists and their traits
4) Discussion
a) Trophic ratio of marine protists
b) Heterotrophic protisan community
c) Heterotrophic protistan diversity
5) Conclusions
6) Perspective
CHAPTER III: THE FUNCTIONAL ROLE OF PARASITISM IN A COASTAL ECOSYSTEM
1) Introduction
2) Material and Methods
a) Sampling strategy
b) Genetic procedures
c) Bioinformatics analyses
d) Detection of A. minutum
e) Parasites of A. minutum
f) Ecological analysis
3) Results
a) Protist community diversity across the A. minutum blooms
b) Identification and dynamic of Alexandrium minutum
c) Identification and dynamics of known parasitic interactions
d) Other potential host-parasite interactions
4) Discussion
a) Metabarcoding approach for the study of the dynamic of Alexandrium minutum
b) Known parasites of A. minutum and their dynamic
c) Other potential parasitic interactions
5) Conclusion
6) Supplementary Material
CONCLUSION AND PERSPECTIVES
REFERENCES
