Seasonal and spatial patterns of eukaryotic phytoplankton communities in an urban river based on marker gene

The seasonal and spatial eukaryotic phytoplankton composition in the Fenhe River was investigated based on the 18S rDNA V4 region. The relationship between phytoplankton functional groups and environmental factors was explored to effectively capture the responses of these taxa to environmental gradients and their effects on ecosystem function. Our results indicated that the Chlorophyta and Bacillariophyta had higher relative abundance than other taxa, and their diversity and richness indices in spring were higher than those in other seasons. The linear discriminant analysis effect size (LEfSe) analyses detected that the potential seasonal biomarkers included Desmodesmus, Cyclotella, Pseudoschroederia, Discostella, Scenedesmus, Monoraphidium, and Nannochloropsis; the spatial biomarkers included Amphora, Neochloris, Hindakia, Pseudomuriella, Coccomyxa, Chloroidium, Scherffelia, Chromochloris, and Scotinosphaera. The systemic evolution and distribution characteristics of the first 50 representative sequences showed that the dominant genus included Desmodesmus in spring, Pseudopediastrum in summer, Mychonastes in autumn, and Monoraphidium in winter. Main seasonal variation of phytoplankton functional groups was as follows: spring (J + F + C + X1) → summer (J + F + X1 + X2) → autumn (J + F + X1 + C) → winter (X1 + J + B + X2). Pearson correlation, redundancy analysis, and variance partitioning analysis showed temperature and phosphate were the determining factors causing the changes of phytoplankton functional groups and community composition in the Fenhe River.

Genomic adaptation of the picoeukaryote Pelagomonas calceolata to temperate iron-poor oceans revealed by a chromosome-scale genome sequence.

Eukaryotic phytoplankton are key actors in marine ecosystems, they contribute to atmospheric CO2 sequestration and supply organic matter to the trophic network. Among them, Pelagophytes (Stramenopiles) algae are a diverse class with coastal species causative of harmful algal blooms while others are cosmopolites and abundant in open ocean ecosystems. Despite their ecological importance, only a few genomic references exist limiting our capacity to identify them and study their adaptation mechanisms in a changing environment. Here, we report the complete chromosome-scale assembled genome sequence of Pelagomonas calceolata. We identified unusual large low-GC and gene-rich regions potentially hosting centromeres. These particular genomic structures could be explained by the absence of genes necessary for an important recombination pathway in this species. We identified a large repertoire of genes involved in inorganic nitrogen sensing and uptake as well as many genes replacing iron-required proteins potentially explaining its ecological success in oligotrophic waters. Finally, based on this high-quality assembly, we evaluated P. calceolata relative abundance in all oceans using environmental Tara datasets. Our results suggest that P. calceolata is one of the most abundant eukaryote species in the oceans with a relative abundance driven by the high temperature and iron-poor conditions. Collectively, these findings bring new insights into the biology and ecology of P. calceolata and lay the foundation for the analysis of the adaptation and acclimation strategy of this picophytoplankton.

Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop

Meromictic Lake Cadagno, with its permanent stratification and persistent microbial bloom within the anoxic chemocline, serves as an ancient ocean analogue. Although the lake has been studied for over 25 years, the absence of simultaneous study of the bacteria, phytoplankton, and viruses, together with primary and secondary productivity, has hindered a comprehensive understanding of its microbial food web. This study evaluated the identities, abundances, and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified depths of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested high abundances of eukaryotic phytoplankton, primarily Chlorophyta, through the water column. Of these, a close relative of Ankyra judayi, a high-alpine adapted chlorophyte, peaked with oxygen in the mixolimnion, while Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. Chromatium, a genus of anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline, suggesting anoxygenic primary producers depended on heterotrophic nutrient remineralization. Virus-to-microbe ratios (VMR) peaked in the zone of high phytoplankton abundances, yet were at a minimum at the peak of Chromatium, dynamic trends that suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical dynamics of Lake Cadagno, this study provides a new perspective on the biological and geochemical connections that comprised the food webs of the Proterozoic ocean.

Assessment of phytoplankton group composition in the Golden Horn Estuary (Sea of Marmara, Turkey) determined with pigments measured by HPLC-CHEMTAX analyses and microscopy

Phtytoplankton group composition determined by microscopy was compared with high performance liquid chromatography (HPLC) derived from pigment signatures in surface water samples taken bi-weekly and monthly between October 2018 and September 2019 in the Golden Horn Estuary (Sea of Marmara). A total of 80 eukaryotic phytoplankton taxa belonging to eight algal classes were identified in surface water during the study period. Forty-three taxa (54%) were diatoms, 29 taxa (36%) were dinoflagellates and eight taxa (10%) were other phytoflagellates. The average contribution of diatoms to total phytoplankton abundance decreased considerably (41 to 25%), while the average contribution of dinoflagellates and other phytoflagellates increased markedly (59 to 75%) from the lower to the middle estuary. Chlorophyll-a and seven other group-specific pigments, including fucoxanthin, peridinin, chlorophyll-c1 + c2, alloxanthin, 19′-hexanoyloxyfucoxanthin, 19′-butanoyloxyfucoxanthin and divinyl chlorophyll-a were identified in the study area. The relative contribution of the major phytoplankton groups to chlorophyll-a was estimated on three different initial ratio matrices by CHEMTAX. The results obtained were compared with those from microscopic examination. It was concluded that the CHEMTAX method was not accurate enough to characterize the phytoplankton community in the Golden Horn Estuary ecosystem and microscopic analysis was essential to determine the major contributing species to chlorophyll-a.

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.

Freshwater dissolved oxygen dynamics: changes due to glyphosate, 2,4-D and their mixture, both under clear and turbid-organic conditions.

We performed two independent outdoor mesocosm experiments where we measured the variation of DO saturation (DO%) in freshwater after a single input of Roundup Max (G) (glyphosate-based formulation), AsiMax 50 (2,4-D) (2,4-D-based formulation) and their mixture (M). Two concentration levels were tested; 0.3 mg/L G and 0.135 mg/L 2,4-D (Low; L) and 3 mg/L G and 1.35 mg/L 2,4-D (High; H). We assayed consolidated microbial communities coming from a system in organic turbid eutrophic status and a system in clear mesotrophic status during 21 and 23 days, respectively. A sample of phytoplankton (micro+nano, pico-eukaryotes, pico-cyanobacteria), mixotrophic algae and heterotrophic bacteria was collected to determine abundances at each of four sampling dates. The clear and turbid systems showed similar, but not synchronized, patterns of daily DO% changes in relation to the controls (DO%v), after exposure to both single and combined formulations. Under glyphosate scenarios (GL, GH, ML and MH), the two types of systems showed similar DO%v but different microbial abundances, being associated to an increase in the micro+nano and pico-eukaryotic phytoplankton fractions for the clear system. In contrast, in the turbid system changes were associated with increased pico-cyanobacteria and decreased mixotrophic algae. Effects of 2,4-D were only observed in the turbid system, leading to decreased micro+nano phytoplankton abundances. Under the turbid scenario, the herbicide mixture at high concentration had a synergistic effect on DO%v and recovery was not detected by the end of the experiment. Our results revealed that herbicides inputs induced changes in phytoplankton abundances that leads to measurable DO variations.

Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus

Small eukaryotic phytoplankton are major contributors to global primary production and marine biogeochemical cycles. Many taxa are thought to be mixotrophic, but quantitative studies of phagotrophy exist for very few. In addition, little is known about consumers of Prochlorococcus, the abundant cyanobacterium at the base of oligotrophic ocean food webs. Here we describe thirty–nine new phytoplankton isolates from the North Pacific Subtropical Gyre (Station ALOHA), all flagellates ~2–5 μm diameter, and we quantify their ability to graze Prochlorococcus. The mixotrophs are from diverse classes (dictyochophytes, haptophytes, chrysophytes, bolidophytes, a dinoflagellate, and a chlorarachniophyte), many from previously uncultured clades. Grazing ability varied substantially, with specific clearance rate (volume cleared per body volume) varying over ten–fold across isolates and six–fold across genera. Slower grazers tend to create more biovolume per prey biovolume consumed. Using qPCR we found that the haptophyte Chrysochromulina was most abundant among the isolated mixotrophs at Station ALOHA, with 76–250 cells mL-1 across depths in the upper euphotic zone. Our results show that within a single ecosystem the phototrophs that ingest bacteria come from many branches of the eukaryotic tree, and are functionally diverse, indicating a broad range of strategies along the spectrum from phototrophy to phagotrophy.

Microbial loop of a Proterozoic ocean analogue

Meromictic Lake Cadagno, an ancient ocean analogue, is known for its permanent stratification and persistent anoxygenic microbial bloom within the chemocline. Although the anaerobic microbial ecology of the lake has been extensively studied for at least 25 years, a comprehensive picture of the microbial food web linking the bacterial layer to phytoplankton and viruses, with explicit measures of primary and secondary production, is still missing. This study sought to understand better the abundances and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified zones of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested the presence of eukaryotic phytoplankton through the water column. Evidence supported high abundances of Ankyra judayi, a high-alpine adapted chlorophyte, in the oxic mixolimnion where oxygenic-primary production peaked. Through the low- and no-oxygen chemocline and monimolimnion, chlorophytes related to Closteriopsis acicularis, a known genus of meromictic lakes, and Parachlorella kessleri were observed. Chromatium, anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline suggesting primary producers depend on heterotrophs for nutrient remineralization. As previously observed, sulfur-reducing bacteria (SRBs), especially Desulfocapsa and Desulfobulbus, were present in the chemocline and anoxic monimolimnion. Virus-to-microbe ratios (VMR) peaked in the zone of phytoplankton yet were at a minimum at the peak of Chromatium. These dynamic trends suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno and other permanently stratified systems.ImportanceAs a window to the past, the study offers insights into the role of microbial guilds of Proterozoic ocean chemoclines in the production and recycling of organic matter of sulfur- and ammonia-containing ancient oceans. The new observations described here suggest that eukaryotic algae were persistent in the low oxygen upper-chemocline in association with purple and green sulfur bacteria in the lower half of the chemocline. Further, this study provides the first insights into Lake Cadagno viral ecology. High viral abundances suggested viruses may be essential components of the chemocline where their activity may result in the release and recycling of organic matter. The framework developed in this study through the integration of diverse geochemical and biological data types lays the foundation for future studies to quantitatively resolve the processes performed by discrete populations comprising the microbial loop in this early anoxic ocean analogue.

Influence of Estuarine Water on the Microbial Community Structure of Patagonian Fjords

Fjords are sensitive areas affected by climate change and can act as a natural laboratory to study microbial ecological processes. The Chilean Patagonian fjords (41–56°S), belonging to the Subantarctic ecosystem (46–60°S), make up one of the world’s largest fjord systems. In this region, Estuarine Water (EW) strongly influences oceanographic conditions, generating sharp gradients of oxygen, salinity and nutrients, the effects of which on the microbial community structure are poorly understood. During the spring of 2017 we studied the ecological patterns (dispersal and oceanographic factors) underlying the microbial community distribution in a linear span of 450 km along the estuarine-influenced Chilean Patagonian fjords. Our results show that widespread microbial dispersion existed along the fjords where bacterioplankton exhibited dependence on the eukaryotic phytoplankton community composition. This dependence was particularly observed under the low chlorophyll-a conditions of the Baker Channel area, in which a significant relationship was revealed between SAR11 Clade III and the eukaryotic families Pyrenomonadaceae (Cryptophyte) and Coccomyxaceae (Chlorophyta). Furthermore, dissolved oxygen and salinity were revealed as the main drivers influencing the surface marine microbial communities in these fjords. A strong salinity gradient resulted in the segregation of the Baker Channel prokaryotic communities from the rest of the Patagonian fjords. Likewise, Microbacteriaceae, Burkholderiaceae and SAR11 Clade III, commonly found in freshwater, were strongly associated with EW conditions in these fjords. The direct effect of EW on the microbial community structure and diversity of the fjords exemplifies the significance that climate change and, in particular, deglaciation have on this marine region and its productivity.

Equatorial to Polar genomic variability of the microalgae Bathycoccus prasinos

The importance of marine phytoplankton in food webs and biogeochemical cycles makes the study of prokaryotic and eukaryotic phytoplankton species essential to understand changes in the global ecosystem. As plankton is transported by ocean currents, its community composition varies. Some species are abundant in contrasting environments, which raises the question of the genomic basis of their adaptation. Here we exploit the cosmopolitan distribution of the eukaryotic picoalgae Bathycoccus prasinos to investigate its genomic variations among temperate and polar populations. Using multiple metagenomic data, we found that ~5% of genomic positions of B. prasinos are variable, with an overwhelming majority of biallelic patterns. Cold and temperate waters are clearly associated with changes in variant occurrences including striking differences at some non-synonymous positions of several genes. Data from transitional waters showed more balanced polymorphism at most of these positions. The comparison of mesophilic and psychrophilic gene variants of this species suggests that its adaptation to cold waters may involve few amino acid changes at positions of protein structures critical for physical and functional properties. These results provide new insights into the genomic diversity and temperature-associated amino acid changes of a cosmopolitan eukaryotic planktonic species.