Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros

Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.

Acclimation of the Marine Diatom Pseudo-nitzschia australis to Different Salinity Conditions: Effects on Growth, Photosynthetic Activity, and Domoic Acid Content1

Toxic Pseudo-nitzschia australis strains isolated from French coastal waters were studied to investigate their capacity to adapt to different salinities. Their acclimation to different salinity conditions (10, 20, 30, 35, and 40) was studied on growth, photosynthetic capacity, cell biovolume, and domoic acid (DA) content. The strains showed an ability to acclimate to a salinity range from 20 to 40, with optimal growth rates between salinities 30 and 40. The highest cell biovolume was observed at the lowest salinity 20 and was associated with the lowest growth rate. Salinity did not affect the photosynthetic activity; F_v /F_m values and the pigment contents remained high with no significant difference among salinities. An enhanced production of zeaxanthin was, however, observed in the late stationary and decline phases in all cultures except for those acclimated to salinity 20. In terms of cellular toxin content, DA concentrations were 2 to 3-fold higher at the lowest salinity (20) than at the other salinities and were combined with a low amount of dissolved DA. The fact that P. australis accumulate more DA per cell in less saline waters, illustrates that climate-related changes in salinity may affect Pseudo-nitzschia physiology through direct effects on growth, physiology, and toxin content.

Static allometry of unicellular green algae: scaling of cellular surface area and volume in the genus Micrasterias (Desmidiales)

The surface area-to-volume ratio of cells is one of the key factors affecting fundamental biological processes and, thus, fitness of unicellular organisms. One of the general models for allometric increase in surface-to-volume scaling involves fractal-like elaboration of cellular surfaces. However, specific data illustrating this pattern in natural populations of the unicellular organisms have not previously been available. This study shows that unicellular green algae of the genus Micrasterias (Desmidiales) have positive allometric surface-to-volume scaling caused by changes in morphology of individual species, especially in the degree of cell lobulation. This allometric pattern was also detected within most of the cultured and natural populations analysed. Values of the allometric S:V scaling within individual populations were closely correlated to the phylogenetic structure of the clade. In addition, they were related to species-specific cellular morphology. Individual populations differed in their allometric patterns, and their position in the allometric space was strongly correlated with the degree of allometric S:V scaling. This result illustrates that allometric shape patterns are an important correlate of the capacity of individual populations to compensate for increases in their cell volumes by increasing the surface area. However, variation in allometric patterns was not associated with phylogenetic structure. This indicates that the position of the populations in the allometric space was not evolutionarily conserved and might be influenced by environmental factors.

EXTREMAL PRINCIPLES WITH SPECIAL EMPHASIS ON EXERGY AND ASCENDENCY — THE MODERN APPROACH IN THEORETICAL ECOLOGY

Extremal principles or ecological orientors or goal functions are the most modern approach in theoretical ecology. There are many such principles proposed by different theoretical ecologists. In this paper, the most important extremal principles are discussed based on their theoretical backgrounds. Two widely accepted goal functions, i.e. exergy and ascendency are optimized and treated in a quantitative manner in an aquatic ecosystem model of planktonic and fish systems for their appropriateness. In the model varied body sizes of phytoplankton and zooplankton are considered. Parameter values varied according to the allometric principle with the body sizes. For self-organization of the model system two goal functions predict different results, however both are realistic.

EVALUATION OF SYSTEM PERFORMANCE THROUGH OPTIMIZING ASCENDENCY IN AN AQUATIC ECOSYSTEM MODEL

We develop a six-compartment model consisting of phosphorus, detritus, phytoplankton, zooplankton, planktonivorous fish and pisciphagous fish. In this model, we study the implications that the body sizes of phytoplankton and zooplankton have on the system dynamics. We use ascendency as a goal function or indicator of system performance. Ascendency quantifies growth and development of an ecosystem as a product of total system throughflow and the mutual information inherent in the pattern of internal system flows. Different physiological rate parameters of phytoplankton and zooplankton are assessed by means of allometric relationships applied to their body sizes. We let the phytoplankton body size range from 10 μm3to 107μm3and the zooplankton body size range from 10 μm3to 104μm3in volume. We also investigate the effects of phosphorus input conditions, corresponding to oligotrophic, mesotrophic and eutrophic systems on system dynamics. Ascendency (to be maximized over phytoplankton and zooplankton sizes) was computed after the system had reached a steady state. Since it always was a seasonal cycle, and the ascendency followed this behavior, we averaged the ascendency over 365 successive days (duration of one year) in the oscillatory phase. Under all types of nutrient conditions, the smallest phytoplankton size yielded the maximal values of the ascendency, while the corresponding zooplankton size varied. Under oligotrophic conditions, a phytoplankton size of 10 μm3combined with a zooplankton size of 101.25μm3to give the maximum value of the ascendency. Under mesotrophic and eutrophic conditions, maxima were obtained for zooplankton sizes 102.26μm3and 103.20μm3, respectively.

Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

BACKGROUND

Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions.

RESULTS

All isolates from the more regionally-localized population (population 2) possessed 1.94 +/- 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history.

CONCLUSIONS

The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms.

Lake warming favours small-sized planktonic diatom species

Diatoms contribute to a substantial portion of primary production in the oceans and many lakes. Owing to their relatively heavy cell walls and high nutrient requirements, planktonic diatoms are expected to decrease with climate warming because of reduced nutrient redistribution and increasing sinking velocities. Using a historical dataset, this study shows that diatoms were able to maintain their biovolume with increasing stratification in Lake Tahoe over the last decades; however, the diatom community structure changed. Increased stratification and reduced nitrogen to phosphorus ratios selected for small-celled diatoms, particularly within the Cyclotella genus. An empirical model showed that a shift in phytoplankton species composition and cell size was consistent within different depth strata, indicating that altered nutrient concentrations were not responsible for the change. The increase in small-celled species was sufficient to decrease the average diatom size and thus sinking velocity, which strongly influences energy transfer through the food web and carbon cycling. Our results show that within the diverse group of diatoms, small-sized species with a high surface area to volume ratio were able to adapt to a decrease in mixing intensity, supporting the hypotheses that abiotic drivers affect the size structure of planktonic communities and that warmer climate favours small-sized diatom cells.

A mechanistic approach for modeling temperature-dependent consumer-resource dynamics

Paramount to our ability to manage and protect biological communities from impending changes in the environment is an understanding of how communities will respond. General mathematical models of community dynamics are often too simplistic to accurately describe this response, partly to retain mathematical tractability and partly for the lack of biologically pleasing functions representing the model/environment interface. We address these problems of tractability and plausibility in community/environment models by incorporating the Boltzmann factor (temperature dependence) in a bioenergetic consumer-resource framework. Our analysis leads to three predictions for the response of consumer-resource systems to increasing mean temperature (warming). First, mathematical extinctions do not occur with warming; however, stable systems may transition into an unstable (cycling) state. Second, there is a decrease in the biomass density of resources with warming. The biomass density of consumers may increase or decrease depending on their proximity to the feasibility (extinction) boundary. Third, consumer biomass density is more sensitive to warming than resource biomass density (with some exceptions). These predictions are in line with many current observations and experiments. The model presented and analyzed here provides an advancement in the testing framework for global change scenarios and hypotheses of latitudinal and elevational species distributions.

Size distribution in ultraphytoplankton: a comparative analysis of counting methods

Water samples taken at three depth layers from the offshore oligotrophic Cretan Sea were analyzed for ultraphytoplankton size fractionation using different methods: (a) sequential filtration on filters of pore size 5, 1 and 0.2 microm, (b) separate filtration using filters 5 and 0.2 microm as well as 1 and 0.2 microm and (c) direct filtration on 0.2 microm filters after staining of the samples with DAPI. Total abundance of photosynthetic organisms as well as the abundance of different groups such as flagellates and cyanobacteria measured by means of sizing after DAPI staining were significantly higher than those obtained by the other methods. This indicates that although there were no significant differences between the estimates provided by the separate and sequential filtration, both these methods underestimated total abundance by at least 25-50%. The estimates for the size fractions were also found to range from relatively imprecise to completely unreliable depending on the group and the size range. Although size fractionation through direct observation after staining largely depends on the expertise of the observer, this study suggests that it may provide more informative estimates than the other two methods. Although it is difficult to generalize the results of this study in a global context, the paper provides strong indications on the limitations of the sequential and separate methods for size fractionation of photosynthetic organisms and implies that their results are likely to be less accurate than is presently believed.

Invariant scaling relationships for interspecific plant biomass production rates and body size

The allometric relationships for plant annualized biomass production ("growth") rates, different measures of body size (dry weight and length), and photosynthetic biomass (or pigment concentration) per plant (or cell) are reported for multicellular and unicellular plants representing three algal phyla; aquatic ferns; aquatic and terrestrial herbaceous dicots; and arborescent monocots, dicots, and conifers. Annualized rates of growth G scale as the 3/4-power of body mass M over 20 orders of magnitude of M (i.e., G proportional to M(3/4)); plant body length L (i.e., cell length or plant height) scales, on average, as the 1/4-power of M over 22 orders of magnitude of M (i.e., L proportional to M(1/4)); and photosynthetic biomass M(p) scales as the 3/4-power of nonphotosynthetic biomass M(n) (i.e., M(p)proportional to M(n)3/4). Because these scaling relationships are indifferent to phylogenetic affiliation and habitat, they have far-reaching ecological and evolutionary implications (e.g., net primary productivity is predicted to be largely insensitive to community species composition or geological age).

Certain Aspects of Production and Standing Stock of Particulate Matter in the Surface Waters of the Northwest Atlantic Ocean

Samples collected during January and October 1968 from 44° to 19°N in the western North Atlantic were analysed for particulate organic carbon, ATP, DNA, chlorophyll a, and total particulate volume between 1 and 40 μ diameter. Although the ratio of chlorophyll to ATP decreased from north to south, the ratio of particulate carbon to ATP did not show any systematic trend. A good correlation was found between ATP and DNA even though the DNA concentration was too great to be entirely representative of living material. Growth or production of particulate material as measured by the Coulter Counter method was higher than that measured by C-14 method. A trend was noted towards higher specific growth rate with smaller standing crop in southern waters.