A PHYLOGENETIC APPROACH TO THE ESTIMATION OF PHYTOPLANKTON TRAITS(1)

Assembly processes and functional diversity of marine protists and their rare biosphere

BACKGROUND

The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential.

RESULTS

Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions.

CONCLUSIONS

Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.

Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim

We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints.

Location

Finland.

Time period

1977-2017.

Major taxa

Phytoplankton.

Methods

We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a "region of common profile" approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development.

Results

We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities.

Main conclusions

Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.

Stochastic and Deterministic Processes Regulate Phytoplankton Assemblages in a Temperate Coastal Ecosystem

Assessing the relative contributions of the interacting deterministic and stochastic ecological processes for phytoplankton community assembly is crucial in understanding and predicting community organization and succession at different temporal and spatial scales. In this study, we hypothesized that deterministic and stochastic ecological processes regulating phytoplankton, present seasonal and repeating patterns. This hypothesis was explored during a 5-year survey (287 samples) conducted at a small spatial scale (~15km) in a temperate coastal ecosystem (eastern English Channel). Microscopy and flow cytometry quantified phytoplankton abundance and biomass, while metabarcoding data allowed an extended evaluation of diversity and the exploration of the ecological processes regulating phytoplankton using null model analysis. Alpha diversity of phytoplankton was governed by the effect of environmental conditions (environmental filtering). Temporal community turnover (beta diversity) evidenced a consistent interannual pattern that determined the phytoplankton seasonal structure. In winter and early spring (from January to March), determinism (homogeneous selection) was the major process in the phytoplankton community assembly. The overall mean in the year was 38%. Stochastic processes (ecological drift) prevailed during the rest of the year from April to December, where the overall mean for the year was 55%. The maximum values were recorded in late spring and summer, which often presented recurrent and transient monospecific phytoplankton peaks. Overall, the prevalence of stochastic processes rendered less predictable seasonal dynamics of phytoplankton communities to future environmental change. IMPORTANCE While ecological deterministic processes are conducive to modeling, stochastic ones are far less predictable. Understanding the overall assembly processes of phytoplankton is critical in tracking and predicting future changes. The novelty of this study was that it addressed a long-posed question, on a pluriannual scale. Was seasonal phytoplankton succession influenced by deterministic processes (e.g., abiotic environment) or by stochastic ones (e.g., dispersal, or ecological drift)? Our results provided strong support for a seasonal and repeating pattern with stochastic processes (drift) prevailing during most of the year and periods with monospecific phytoplankton peaks.

Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front

Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.

Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties

Our understanding on phytoplankton diversity has largely been progressing since the publication of Hutchinson on the paradox of the plankton. In this paper, we summarise some major steps in phytoplankton ecology in the context of mechanisms underlying phytoplankton diversity. Here, we provide a framework for phytoplankton community assembly and an overview of measures on taxonomic and functional diversity. We show how ecological theories on species competition together with modelling approaches and laboratory experiments helped understand species coexistence and maintenance of diversity in phytoplankton. The non-equilibrium nature of phytoplankton and the role of disturbances in shaping diversity are also discussed. Furthermore, we discuss the role of water body size, productivity of habitats and temperature on phytoplankton species richness, and how diversity may affect the functioning of lake ecosystems. At last, we give an insight into molecular tools that have emerged in the last decades and argue how it has broadened our perspective on microbial diversity. Besides historical backgrounds, some critical comments have also been made.

The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton

Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change.

Predicting West Nile virus transmission in North American bird communities using phylogenetic mixed effects models and eBird citizen science data

BACKGROUND

West Nile virus (WNV) is a mosquito-transmitted disease of birds that has caused bird population declines and can spill over into human populations. Previous research has identified bird species that infect a large fraction of the total pool of infected mosquitoes and correlate with human infection risk; however, these analyses cover small spatial regions and cannot be used to predict transmission in bird communities in which these species are rare or absent. Here we present a mechanistic model for WNV transmission that predicts WNV spread (R0) in any bird community in North America by scaling up from the physiological responses of individual birds to transmission at the level of the community. We predict unmeasured bird species' responses to infection using phylogenetic imputation, based on these species' phylogenetic relationships with bird species with measured responses.

RESULTS

We focused our analysis on Texas, USA, because it is among the states with the highest total incidence of WNV in humans and is well sampled by birders in the eBird database. Spatio-temporal patterns: WNV transmission is primarily driven by temperature variation across time and space, and secondarily by bird community composition. In Texas, we predicted WNV R0 to be highest in the spring and fall when temperatures maximize the product of mosquito transmission and survival probabilities. In the most favorable months for WNV transmission (April, May, September and October), we predicted R0 to be highest in the "Piney Woods" and "Oak Woods & Prairies" ecoregions of Texas, and lowest in the "High Plains" and "South Texas Brush County" ecoregions. Dilution effect: More abundant bird species are more competent hosts for WNV, and predicted WNV R0 decreases with increasing species richness. Keystone species: We predicted that northern cardinals (Cardinalis cardinalis) are the most important hosts for amplifying WNV and that mourning doves (Zenaida macroura) are the most important sinks of infection across Texas.

CONCLUSIONS

Despite some data limitations, we demonstrate the power of phylogenetic imputation in predicting disease transmission in heterogeneous host communities. Our mechanistic modeling framework shows promise both for assisting future analyses on transmission and spillover in heterogeneous multispecies pathogen systems and for improving model transparency by clarifying assumptions, choices and shortcomings in complex ecological analyses.

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth

Background: The phyllosphere hosts a variety of microorganisms, including bacteria, which can play a positive role in the success of the host plant. Bacterial communities in the phylloplane are influenced by both biotic and abiotic factors, including host plant surface topography and chemistry, which change in concert with microbial communities as the plant leaves develop and age.

Methods: We examined how the Zea mays L. leaf microbial community structure changed with plant age. Ribosomal spacer length and scanning electron microscopic imaging strategies were used to assess microbial community composition across maize plant ages, using a novel staggered experimental design.

Results: Significant changes in community composition were observed for both molecular and imaging analyses, and the two analysis methods provided complementary information about bacterial community structure within each leaf developmental stage.

Conclusions: Both taxonomic and cell-size trait patterns provided evidence for niche-based contributions to microbial community development on leaves.

A light-induced shortcut in the planktonic microbial loop

Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light.

Bridging the gap between theoretical ecology and real ecosystems: modeling invertebrate community composition in streams

For the first time, we combine concepts of theoretical food web modeling, the metabolic theory of ecology, and ecological stoichiometry with the use of functional trait databases to predict the coexistence of invertebrate taxa in streams. We developed a mechanistic model that describes growth, death, and respiration of different taxa dependent on various environmental influence factors to estimate survival or extinction. Parameter and input uncertainty is propagated to model results. Such a model is needed to test our current quantitative understanding of ecosystem structure and function and to predict effects of anthropogenic impacts and restoration efforts. The model was tested using macroinvertebrate monitoring data from a catchment of the Swiss Plateau. Even without fitting model parameters, the model is able to represent key patterns of the coexistence structure of invertebrates at sites varying in external conditions (litter input, shading, water quality). This confirms the suitability of the model concept. More comprehensive testing and resulting model adaptations will further increase the predictive accuracy of the model.

Phytoplankton-specific response to enrichment of phosphorus-rich surface waters with ammonium, nitrate, and urea

Supply of anthropogenic nitrogen (N) to the biosphere has tripled since 1960; however, little is known of how in situ response to N fertilisation differs among phytoplankton, whether species response varies with the chemical form of N, or how interpretation of N effects is influenced by the method of analysis (microscopy, pigment biomarkers). To address these issues, we conducted two 21-day in situ mesocosm (3140 L) experiments to quantify the species- and genus-specific responses of phytoplankton to fertilisation of P-rich lake waters with ammonium (NH₄⁺), nitrate (NO₃⁻), and urea ([NH₂]₂CO). Phytoplankton abundance was estimated using both microscopic enumeration of cell densities and high performance liquid chromatographic (HPLC) analysis of algal pigments. We found that total algal biomass increased 200% and 350% following fertilisation with NO₃⁻ and chemically-reduced N (NH₄⁺, urea), respectively, although 144 individual taxa exhibited distinctive responses to N, including compound-specific stimulation (Planktothrix agardhii and NH₄⁺), increased biomass with chemically-reduced N alone (Scenedesmus spp., Coelastrum astroideum) and no response (Aphanizomenon flos-aquae, Ceratium hirundinella). Principle components analyses (PCA) captured 53.2–69.9% of variation in experimental assemblages irrespective of the degree of taxonomic resolution of analysis. PCA of species-level data revealed that congeneric taxa exhibited common responses to fertilisation regimes (e.g., Microcystis aeruginosa, M. flos-aquae, M. botrys), whereas genera within the same division had widely divergent responses to added N (e.g., Anabaena, Planktothrix, Microcystis). Least-squares regression analysis demonstrated that changes in phytoplankton biomass determined by microscopy were correlated significantly (p<0.005) with variations in HPLC-derived concentrations of biomarker pigments (r² = 0.13–0.64) from all major algal groups, although HPLC tended to underestimate the relative abundance of cyanobacteria. Together, these findings show that while fertilisation of P-rich lakes with N can increase algal biomass, there is substantial variation in responses of genera and divisions to specific chemical forms of added N.

Evidence for a three-way trade-off between nitrogen and phosphorus competitive abilities and cell size in phytoplankton

Trade-offs among functional traits are essential for explaining community structure and species coexistence. While two-way trade-offs have been investigated in many systems, higher-dimensional trade-offs remain largely hypothetical. Here we demonstrate a three-way trade-off between cell size and competitive abilities for nitrogen and phosphorus in marine and freshwater phytoplankton. At a given cell size, competitive abilities for N and P are negatively correlated, but as cell size increases, competitive ability decreases for both nutrients. The relative importance of the two trade-off axes appears to be environment dependent, suggesting different selective pressures: freshwater phytoplankton separate more along the N vs. P competition axis, and marine phytoplankton separate more along the nutrient competition vs. cell size axis. Our results demonstrate the multidimensional nature of key trade-offs among traits and suggest that such trade-offs may drive species interactions and structure ecological communities.