The anchoring effect-long-term dormancy and genetic population structure

Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions

Diatoms can survive long periods in dark, anoxic sediments by forming resting spores or resting cells. These have been considered dormant until recently when resting cells of Skeletonema marinoi were shown to assimilate nitrate and ammonium from the ambient environment in dark, anoxic conditions. Here, we show that resting cells of S. marinoi can also perform dissimilatory nitrate reduction to ammonium (DNRA), in dark, anoxic conditions. Transmission electron microscope analyses showed that chloroplasts were compacted, and few large mitochondria had visible cristae within resting cells. Using secondary ion mass spectrometry and isotope ratio mass spectrometry combined with stable isotopic tracers, we measured assimilatory and dissimilatory processes carried out by resting cells of S. marinoi under dark, anoxic conditions. Nitrate was both respired by DNRA and assimilated into biomass by resting cells. Cells assimilated nitrogen from urea and carbon from acetate, both of which are sources of dissolved organic matter produced in sediments. Carbon and nitrogen assimilation rates corresponded to turnover rates of cellular carbon and nitrogen content ranging between 469 and 10,000 years. Hence, diatom resting cells can sustain their cells in dark, anoxic sediments by slowly assimilating and respiring substrates from the ambient environment.

Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist

Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.

Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System : Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System

The ecological importance of phytoplankton-benthic-propagules (PBP) from coastal sediments, except tropical monsoon-influenced rivers and estuaries, is well documented. PBP in such systems is often transported from upstream (near freshwater) to downstream (estuary) through freshwater discharges during monsoon and thereby experiences higher salinities (>30 PSU) and nutrients with varying light conditions due to reducing discharges during the monsoon-break/withdrawal-phase. However, the PBP responses (germination and subsequent growth) to such changes are unknown and are examined here at ~35 PSU salinity. For the study, macronutrients (nitrate, phosphate, silicate, and nitrate+phosphate+silicate) and light intensities were considered to assess the response of PBP representing estuarine, brackish, and near freshwater locations of monsoon-influenced Mandovi and Zuari rivers (Goa, India). Diatoms dominated the viable PBP community, but the maximum growth and sustained photosynthetic activity were observed when all macronutrients were supplied than individually. Here, variable fluorescence technique utility in PBP resurrection (detection of viability and responses) was also explored. The PBP growth was similar for macronutrients but increased with light intensity indicating a longer growth response during monsoon. For PBP (germination and photosynthetic activity), light intensities drive the rate of improvement/development, whereas the nutrients are essential for maintaining vegetative growth upon germination in the region. The PBP dominance of common planktonic species (Skeletonema and Thalassiosira) along the river also signifies the role of seawater intrusion (up to upstream locations) in distribution. Skeletonema and Thalassiosira, which contribute significantly to the total community, are light-sensitive with a similar response and cause single species blooms during monsoon and non-monsoon, respectively, depending on the species' tolerance to salinity.

Temporal and Spatial Signaling Mediating the Balance of the Plankton Microbiome

The annual patterns of plankton succession in the ocean determine ecological and biogeochemical cycles. The temporally fluctuating interplay between photosynthetic eukaryotes and the associated microbiota balances the composition of aquatic planktonic ecosystems. In addition to nutrients and abiotic factors, chemical signaling determines the outcome of interactions between phytoplankton and their associated microbiomes. Chemical mediators control essential processes, such as the development of key morphological, physiological, behavioral, and life-history traits during algal growth. These molecules thus impact species succession and community composition across time and space in processes that are highlighted in this review. We focus on spatial, seasonal, and physiological dynamics that occur during the early association of algae with bacteria, the exponential growth of a bloom, and its decline and recycling. We also discuss how patterns from field data and global surveys might be linked to the actions of metabolic markers in natural phytoplankton assemblages.

OUP accepted manuscript

Diatoms commonly set off the spring-bloom in temperate coastal environments. However, their temporal offset may change in regions subject to nutrient enrichment, and by peaking earlier, such populations can maintain their position in the vernal plankton succession. We tested whether the marine keystone diatom Skeletonema marinoi can accomplish this through thermal evolutionary adaptation. Eight geographically separated subpopulations, representing hydromorphologically and climatologically similar inlets displaying a range of trophic states, were compared in a common-garden experiment. At early-spring temperatures, both doubling times and variation coefficients thereof, correlated negatively with the trophic state of the environment of origin, indicating selection for fast growth due to eutrophication. At mid-spring temperatures, the relationships were reversed, indicating selection in the opposite direction. At late-spring temperatures, no significant relationships were detected, suggesting relaxed selection. Subsequent field observations reflected these findings, where blooming temperatures decreased with trophic state. Natural selection thus moves along with eutrophication towards colder temperatures earlier in the spring, favouring genotypes with the capacity to grow fast. The thermal niche shift demonstrated herein may be an evolutionary mechanism essentially leading to trophic changes in the local ecosystem.

Seasonal genotype dynamics of a marine dinoflagellate: Pelagic populations are homogeneous and as diverse as benthic seed banks

Genetic diversity is the basis for evolutionary adaptation and selection under changing environmental conditions. Phytoplankton populations are genotypically diverse, can become genetically differentiated within small spatiotemporal scales and many species form resting stages. Resting stage accumulations in sediments (seed banks) are expected to serve as reservoirs for genetic information, but so far their role in maintaining phytoplankton diversity and in evolution has remained unclear. In this study we used the toxic dinoflagellate Alexandrium ostenfeldii (Dinophyceae) as a model organism to investigate if (i) the benthic seed bank is more diverse than the pelagic population and (ii) the pelagic population is seasonally differentiated. Resting stages (benthic) and plankton (pelagic) samples were collected at a coastal bloom site in the Baltic Sea, followed by cell isolation and genotyping using microsatellite markers (MS) and restriction site associated DNA sequencing (RAD). High clonal diversity (98%–100%) combined with intermediate to low gene diversity (0.58–0.03, depending on the marker) was found. Surprisingly, the benthic and pelagic fractions of the population were equally diverse, and the pelagic fraction was temporally homogeneous, despite seasonal fluctuation of environmental selection pressures. The results of this study suggest that continuous benthic–pelagic coupling, combined with frequent sexual reproduction, as indicated by persistent linkage equilibrium, prevent the dominance of single clonal lineages in a dynamic environment. Both processes harmonize the pelagic with the benthic population and thus prevent seasonal population differentiation. At the same time, frequent sexual reproduction and benthic–pelagic coupling maintain high clonal diversity in both habitats.

Principles of seed banks and the emergence of complexity from dormancy

Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.

Morpho-molecular description of a new HAB species, Pseudocochlodinium profundisulcus gen. et sp. nov., and its LSU rRNA gene based genetic diversity and geographical distribution

Harmful algal blooms (HABs) caused by an unknown dinoflagellate species have frequently occurred in the Pearl River Estuary, China Since 2006. These blooms were associated with severe water discoloration and economic losses, ranging from several km² to 300 km² with the maximum recorded cell density being 2.77 × 10⁷ cells⋅L^-1. This unknown dinoflagellate species was initially identified as Cochlodinium geminatum and subsequently reclassified as Polykrikos geminatus. However, after reviewing the original descriptions for Cochlodinium geminatum sensu Schütt (1895) and the genus Polykrikos, we considered this species is incongruent with their original descriptions. Further morphological examinations and particularly phylogenetic analyses based on the SSU and partial LSU rRNA genes of isolates and resting cysts from China and Japan prompted us to consider it a new species of a new genus. This new species was proposed to be Pseudocochlodinium profundisulcus gen. et sp. nov., based on its open comma-shaped apical structure complex (ASC), cingulum encircling the cell less than one and a half turns, a deep sulcus with a torsion of a half turn, either single cell or cell chain consisting of two cells with the same number of nuclei and zooids, the resting cyst bearing lobed ornaments, and the evolutionary distances from Polykrikos (and others) on the phylogenetic trees constructed using the concatenated SSU and partial LSU rRNA gene sequences. Metabarcoding investigation of surface sediment samples collected in China revealed that the species to be widely present along the entire Chinese coast with the highest abundance in the South China Sea. Further re-analysis of the Tara Oceans metabarcoding dataset targeting the SSU rRNA gene V9 domain suggested a global distribution of this new genus. Phylogenetic analyses on 46 OTUs (average length: ∼552 bases) of its LSU rRNA gene sequences (mainly D1-D2 domains) obtained from surface sediment samples revealed intraspecific genetic diversity of this species. Interestingly, based on the different distributions and the abundance of these OTUs along the coast of China, this species appeared to have expanded its distribution from the South China Sea to the northern Yellow Sea, or preferred a warm water habitat. We consider that the present work improves the taxonomy and provides important insights into the biogeography of Pseudocochlodinium profundisulcus.⋅.

Revisiting the 'bank of microscopic forms' in macroalgal-dominated ecosystems

Theoretical ecological models, such as succession and facilitation, were defined in terrestrial habitats, and subsequently applied to marine and freshwater habitats in intertidal and then subtidal realms. One such model is the soil seed bank, defined as all viable seeds (or fruits) found near the soil surface that facilitate community restoration/recovery. "Banks of microscopic forms" have been hypothesized in aquatic habitats and recent work from aquaculture has highlighted dormancy in algal life cycle stages. To reinvigorate the discussions about these algal banks, we discuss differences in life cycles, dispersal, and summarize research on banks of macroalgal stages in aquatic ecosystems that may be easier to explore with modern advances in molecular technology. With focus on seminal work in global kelp forest ecosystems, we present a pilot study in northern California as proof of concept that Nereocystis luetkeana and Alaria marginata stages can be detected within kelp forests in the biofilm of rocks and bedrock using targeted primers long after zoospore release. Considering the increased interest in algae as an economic resource, [blue] carbon sink, and as ecosystem engineers, the potential for "banking" macroalgal forms could be a mechanism of resilience and recovery in aquatic populations that have complex life cycles and environmental cues for reproduction. Molecular barcoding is becoming an important tool for identifying banks of macroalgal forms in marine communities. Understanding banks of macroalgal stages, especially in deforested habitats with intense disturbance and grazer pressure, will allow researchers and marine resource managers to facilitate this natural process in recovery of the aquatic system.

Regulation of Seed Dormancy and Germination Mechanisms in a Changing Environment

Environmental conditions are the basis of plant reproduction and are the critical factors controlling seed dormancy and germination. Global climate change is currently affecting environmental conditions and changing the reproduction of plants from seeds. Disturbances in germination will cause disturbances in the diversity of plant communities. Models developed for climate change scenarios show that some species will face a significant decrease in suitable habitat area. Dormancy is an adaptive mechanism that affects the probability of survival of a species. The ability of seeds of many plant species to survive until dormancy recedes and meet the requirements for germination is an adaptive strategy that can act as a buffer against the negative effects of environmental heterogeneity. The influence of temperature and humidity on seed dormancy status underlines the need to understand how changing environmental conditions will affect seed germination patterns. Knowledge of these processes is important for understanding plant evolution and adaptation to changes in the habitat. The network of genes controlling seed dormancy under the influence of environmental conditions is not fully characterized. Integrating research techniques from different disciplines of biology could aid understanding of the mechanisms of the processes controlling seed germination. Transcriptomics, proteomics, epigenetics, and other fields provide researchers with new opportunities to understand the many processes of plant life. This paper focuses on presenting the adaptation mechanism of seed dormancy and germination to the various environments, with emphasis on their prospective roles in adaptation to the changing climate.

Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species

Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32 Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.

Resting Stages of Skeletonema marinoi Assimilate Nitrogen From the Ambient Environment Under Dark, Anoxic Conditions

The planktonic marine diatom Skeletonema marinoi forms resting stages, which can survive for decades buried in aphotic, anoxic sediments and resume growth when re-exposed to light, oxygen, and nutrients. The mechanisms by which they maintain cell viability during dormancy are poorly known. Here, we investigated cell-specific nitrogen (N) and carbon (C) assimilation and survival rate in resting stages of three S. marinoi strains. Resting stages were incubated with stable isotopes of dissolved inorganic N (DIN), in the form of ¹⁵ N-ammonium (NH₄⁺ ) or -nitrate (NO₃^- ) and dissolved inorganic C (DIC) as ¹³ C-bicarbonate (HCO₃^- ) under dark and anoxic conditions for 2 months. Particulate C and N concentration remained close to the Redfield ratio (6.6) during the experiment, indicating viable diatoms. However, survival varied between <0.1% and 47.6% among the three different S. marinoi strains, and overall survival was higher when NO₃^- was available. One strain did not survive in the NH₄⁺ treatment. Using secondary ion mass spectrometry (SIMS), we quantified assimilation of labeled DIC and DIN from the ambient environment within the resting stages. Dark fixation of DIC was insignificant across all strains. Significant assimilation of ¹⁵ N-NO₃^- and ¹⁵ N-NH₄⁺ occurred in all S. marinoi strains at rates that would double the nitrogenous biomass over 77-380 years depending on strain and treatment. Hence, resting stages of S. marinoi assimilate N from the ambient environment at slow rates during darkness and anoxia. This activity may explain their well-documented long survival and swift resumption of vegetative growth after dormancy in dark and anoxic sediments.

Generalist Life Cycle Aids Persistence of Alexandrium ostenfeldii (Dinophyceae) in Seasonal Coastal Habitats of the Baltic Sea

In seasonal environments, strong gradients of environmental parameters can shape life cycles of phytoplankton. Depending on the rate of environmental fluctuation, specialist or generalist strategies may be favored, potentially affecting life cycle transitions. The present study examined life cycle transitions of the toxin producing Baltic dinoflagellate Alexandrium ostenfeldii and their regulation by environmental factors (temperature and nutrients). This investigation aimed to determine whether genetic recombination of different strains is required for resting cyst formation and whether newly formed cysts are dormant. Field data (temperature and salinity) and sediment surface samples were collected from a site with recurrent blooms and germination and encystment experiments were conducted under controlled laboratory conditions. Results indicate a lack of seasonal germination pattern, set by an endogenous rhythm, as commonly found with other dinoflagellates from the Baltic Sea. Germination of quiescent cysts was triggered by temperatures exceeding 10°C and combined nutrient limitation of nitrogen and phosphorus or a drop in temperature from 16 to 10°C triggered encystment most efficiently. Genetic recombination was not mandatory for the formation of resting cysts, but supported higher numbers of resistant cysts and enhanced germination capacity after a resting period. Findings from this study confirm that A. ostenfeldii follows a generalist germination and cyst formation strategy, driven by strong seasonality, which may support its persistence and possibly expansion in marginal environments in the future, if higher temperatures facilitate a longer growth season.

Spatiotemporal genetic structure of regional-scale Alexandrium catenella dinoflagellate blooms explained by extensive dispersal and environmental selection

Paralytic Shellfish Poisoning (PSP) caused by the dinoflagellate Alexandrium catenella is a well-known global syndrome that negatively impacts human health and fishery economies. Understanding the population dynamics and ecology of this species is thus important for identifying determinants of blooms and associated PSP toxicity. Given reports of extensive genetic heterogeneity in the toxicity and physiology of Alexandrium species, knowledge of genetic population structure in harmful algal species such as A. catenella can also facilitate the understanding of toxic bloom development and ecological adaptation. In this study we employed microsatellite markers to analyze multiple A. catenella strains isolated from several sub-regions in the Gulf of Maine (GoM) during summer blooms, to gain insights into the sources and dynamics of this economically important phytoplankton species. At least three genetically distinct clusters of A. catenella were identified in the GoM. Each cluster contained representatives from different sub-regions, highlighting the extent of connectivity and dispersal throughout the region. This shared diversity could result from cyst beds created by previous coastal blooms, thereby preserving the overall diversity of the regional A. catenella population. Rapid spatiotemporal genetic differentiation of A. catenella populations was observed in local blooms, likely driven by natural selection through environmental conditions such as silicate and nitrate/nitrite concentrations, emphasizing the role of short-term water mass intrusions and biotic processes in determining the diversity and dynamics of marine phytoplankton populations. Given the wide-spread intraspecific diversity of A. catenella in GoM and potentially elsewhere, harmful algal blooms will likely persist in many regions despite global warming and changing environmental conditions in the future. Selection of different genetic lineages through variable hydrological conditions might impact toxin production and profiles of future blooms, challenging HAB control and prediction of PSP risk in the future.

Microalgae biotechnology in Nordic countries - the potential of local strains

Climate change, energy use and food security are the main challenges that our society is facing nowadays. Biofuels and feedstock from microalgae can be part of the solution if high and continuous production is to be ensured. This could be attained in year-round, low cost, outdoor cultivation systems using strains that are not only champion producers of desired compounds but also have robust growth in a dynamic climate. Using microalgae strains adapted to the local conditions may be advantageous particularly in Nordic countries. Here, we review the current status of laboratory and outdoor-scale cultivation in Nordic conditions of local strains for biofuel, high-value compounds and water remediation. Strains suitable for biotechnological purposes were identified from the large and diverse pool represented by saline (NE Atlantic Ocean), brackish (Baltic Sea) and fresh water (lakes and rivers) sources. Energy-efficient annual rotation for cultivation of strains well adapted to Nordic climate has the potential to provide high biomass yields for biotechnological purposes.