Eukaryotic phytoplankton community spatiotemporal dynamics as identified through gene expression within a eutrophic estuary

Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples

Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.

Nutrient-imbalanced conditions shift the interplay between zooplankton and gut microbiota

Background

Nutrient stoichiometry of phytoplankton frequently changes with aquatic ambient nutrient concentrations, which is mainly influenced by anthropogenic water treatment and the ecosystem dynamics. Consequently, the stoichiometry of phytoplankton can markedly alter the metabolism and growth of zooplankton. However, the effects of nutrient-imbalanced prey on the interplay between zooplankton and their gut microbiota remain unknown. Using metatranscriptome, a 16 s rRNA amplicon-based neutral community model (NCM) and experimental validation, we investigated the interactions between Daphnia magna and its gut microbiota in a nutrient-imbalanced algal diet.

Results

Our results showed that in nutrient-depleted water, the nutrient-enriched zooplankton gut stimulated the accumulation of microbial polyphosphate in fecal pellets under phosphorus limitation and the microbial assimilation of ammonia under nitrogen limitation. Compared with the nutrient replete group, both N and P limitation markedly promoted the gene expression of the gut microbiome for organic matter degradation but repressed that for anaerobic metabolisms. In the nutrient limited diet, the gut microbial community exhibited a higher fit to NCM (R² = 0.624 and 0.781, for N- and P-limitation, respectively) when compared with the Control group (R² = 0.542), suggesting increased ambient-gut exchange process favored by compensatory feeding. Further, an additional axenic grazing experiment revealed that the growth of D. magna can still benefit from gut microbiota under a nutrient-imbalanced diet.

Conclusions

Together, these results demonstrated that under a nutrient-imbalanced diet, the microbes not only benefit themselves by absorbing excess nutrients inside the zooplankton gut but also help zooplankton to survive during nutrient limitation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07333-z.

Disentangling effects of river inflow and marine diffusion in shaping the planktonic communities in a heavily polluted estuary

Estuarine ecosystems are important in terms of biodiversity processes because there are intense interactions between the river and sea environments. Phytoplankton and zooplankton have been shown to be ecological indicators of the water quality status in estuary ecosystems. Therefore, a comprehensive evaluation of the effects that multiple pressures have on the phytoplankton and zooplankton communities in estuarine ecosystems is essential. In this study, water samples from 29 stations were collected from the Liaohe Estuary over three different seasons, and biotic factors (i.e., phytoplankton and zooplankton) were obtained and compared. The results showed that there were significant temporal and spatial variations in the phytoplankton and zooplankton communities from the Liaohe Estuary. The correlation analyses showed that water temperature was the most important factor regulating the variation in phytoplankton communities, whereas the main driving force for the zooplankton was nutrient concentrations. Large amounts of nutrients entered the estuary in spring and summer due to intensive human activities in the Liaohe River basin. The inflows by the Liaohe River introduced some phytoplankton and zooplankton into the estuary, such as Coscinodicus asteromphalus, Chaetoceros decipiens, and Schmacheria poplesia. The impacts of Liaohe inflows on the estuary region gradually decreased as the distance from the inlet increased and this change was mediated by marine diffusion. The results from this study will improve knowledge about planktonic communities in estuarine ecosystems and provide a theoretical foundation for estuary environmental management.

Phytoplankton composition in a eutrophic estuary: Comparison of multiple taxonomic approaches and influence of environmental factors

To assess the comparability between taxonomic identification methods for phytoplankton, multiple approaches were used to characterize phytoplankton community composition within the Neuse River Estuary (NRE), North Carolina. Small subunit 18S rRNA gene sequencing and accessory pigment analysis displayed similar trends, indicating chlorophytes were the dominant microalgal group during most of the year, whereas results from microscopic cell counts, biovolume analysis and metatranscriptomics suggested diatom and dinoflagellate-dominated communities. Spatial environmental gradients drove variation in taxonomic composition due to preferences for specific environmental conditions among different microalgal groups. Cryptophytes were a greater proportion of the phytoplankton community within high nutrient, fresher environments whereas diatoms and dinoflagellates dominated higher salinity sections of the estuary. This study provides a detailed examination of phytoplankton communities associated with environmental gradients present in the NRE. The high level of taxonomic resolution offered by DNA sequencing (i.e., species to sub-species level) provides a better understanding of population dynamics at the base of estuarine food webs.

Species specific gene expression dynamics during harmful algal blooms

Harmful algal blooms are caused by specific members of microbial communities. Understanding the dynamics of these events requires comparing the strategies developed by the problematic species to cope with environmental fluctuations to the ones developed by the other members of the community. During three consecutive years, the meta-transcriptome of micro-eukaryote communities was sequenced during blooms of the toxic dinoflagellate Alexandrium minutum. The dataset was analyzed to investigate species specific gene expression dynamics. Major shifts in gene expression were explained by the succession of different species within the community. Although expression patterns were strongly correlated with fluctuation of the abiotic environment, and more specifically with nutrient concentration, transcripts specifically involved in nutrient uptake and metabolism did not display extensive changes in gene expression. Compared to the other members of the community, A. minutum displayed a very specific expression pattern, with lower expression of photosynthesis transcripts and central metabolism genes (TCA cycle, glucose metabolism, glycolysis…) and contrasting expression pattern of ion transporters across environmental conditions. These results suggest the importance of mixotrophy, cell motility and cell-to-cell interactions during A. minutum blooms.

Decadal monitoring reveals an increase in Vibrio spp. concentrations in the Neuse River Estuary, North Carolina, USA

A decade long study was conducted to investigate the ecological, biological, and temporal conditions that affect concentrations of Vibrio spp. bacteria in a well-studied lagoonal estuary. Water samples collected from the Neuse River Estuary in eastern North Carolina from 2004-2014 (with additional follow-up samples from Fall of 2018) were analyzed to determine Vibrio spp. concentrations, as well as the concentrations of inorganic and organic nutrients, fecal indicator bacteria, phytoplankton biomass, and a wide range of other physio-chemical estuarine parameters. A significant increase in Vibrio spp. was observed to occur in the estuary over the examined period. Strikingly, over this long duration study period, this statistically significant increase in total culturable Vibrio spp. concentrations does not appear to be correlated with changes in salinity, temperature, or dissolved oxygen, the three most commonly cited influential factors that predict estuarine Vibrio spp. abundance. Furthermore, shorter term (~3 years) data on specific Vibrio species (V. vulnificus and V. parahaemolyticus)show that while Vibrio spp. are increasing overall as a genus, the numbers of some key potentially pathogenic species are decreasing as a part of the total population, further supporting the concept that quantification of the entire genus is not a worthwhile use of resources toward predicting levels of specific potentially pathogenic species of public health concern. The significant increase in this concentration of Vibrio spp. in the studied estuary appears to be related to nitrogen and carbon in the system, indicating a continued need for further research.