Phytoplankton surveys in the Arctic Fram Strait demonstrate the tiny eukaryotic alga Micromonas and other picoprasinophytes contribute to deep sea export

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bachy, C., Sudek, L., Choi, C. J., Eckmann, C. A., Nöthig, E.-M., Metfies, K., & Worden, A. Z. Phytoplankton surveys in the Arctic Fram Strait demonstrate the tiny eukaryotic alga Micromonas and other picoprasinophytes contribute to deep sea export. Microorganisms, 10(5), (2022): 961, https://doi.org/10.3390/microorganisms10050961.Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears to constitute a large, but variable, proportion of the phytoplankton in these waters. Here, we analyze 81 samples from the upper 100 m of the water column from the Fram Strait collected over multiple years (2009–2015). We also analyze sediment trap samples to examine picophytoplankton contributions to export, using both 18S rRNA gene qPCR and V1-V2 16S rRNA Illumina amplicon sequencing to assess the Micromonas abundance within the broader diversity of photosynthetic eukaryotes based on the phylogenetic placement of plastid-derived 16S amplicons. The material sequenced from the sediment traps in July and September 2010 showed that 11.2 ± 12.4% of plastid-derived amplicons are from picoplanktonic prasinophyte algae and other green lineage (Viridiplantae) members. In the traps, Micromonas dominated (83.6 ± 21.3%) in terms of the overall relative abundance of Viridiplantae amplicons, specifically the species Micromonas polaris. Temporal variations in Micromonas abundances quantified by qPCR were also observed, with higher abundances in the late-July traps and deeper traps. In the photic zone samples, four prasinophyte classes were detected in the amplicon data, with Micromonas again being the dominant prasinophyte, based on the relative abundance (89.4 ± 8.0%), but with two species (M. polaris and M. commoda-like) present. The quantitative PCR assessments showed that the photic zone samples with higher Micromonas abundances (>1000 gene copies per mL) had significantly lower standing stocks of phosphate and nitrate, and a shallower average depth (20 m) than those with fewer Micromonas. This study shows that despite their size, prasinophyte picophytoplankton are exported to the deep sea, and that Micromonas is particularly important within this size fraction in Arctic marine ecosystems.This research was supported by funding from the National Science Foundation (NSF) DEB-1639033, Gordon and Betty Moore Foundation Marine Investigator Award grant 3788, and fellowships from the Radcliffe Institute for Advanced Research at Harvard University and the Hanse-Wissenschaftskolleg for Marine and Climate Science, awarded to A.Z.W. Contribution to HGF POF-IV 6.1, 6.3, and 6.4

The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

Photosynthesis in eukaryotes first arose through phagocytotic processes wherein an engulfed cyanobacterium was not digested, but instead became a permanent organelle. Other photosynthetic lineages then arose when eukaryotic cells engulfed other already photosynthetic eukaryotic cells. Some of the resulting lineages subsequently lost their ability for phagocytosis, while many others maintained the ability to do both processes. These mixotrophic taxa have more complicated ecological roles, in that they are both primary producers and consumers that can shift more towards producing the organic matter that forms the base of aquatic food chains, or towards respiring and releasing CO2. We still have much to learn about which taxa are predatory mixotrophs as well as about the physiological consequences of this lifestyle, in part, because much of the diversity of unicellular eukaryotes in aquatic ecosystems remains uncultured. Here, we discuss existing methods for studying predatory mixotrophs, their individual biases, and how single-cell approaches can enhance knowledge of these important taxa. The question remains what the gold standard should be for assigning a mixotrophic status to ill-characterized or uncultured taxa—a status that dictates how organisms are incorporated into carbon cycle models and how their ecosystem roles may shift in future lakes and oceans

Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae

Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46  ±  24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans

Transitions in eukaryotic algae distributions and physiology from subtropical to tropical environments

The seasonal and geographical dynamics of phytoplankton have important implications for primary production, carbon sequestration, and predicting future ocean change. The distribution of phytoplankton is influenced by their environmental needs and preferences and can be examined at various levels, from strain or species to size class or broad taxonomic grouping. The first two chapters of this thesis focus on phytoplankton distribution by taxonomic group as determined by 16S and 18S rRNA gene amplicon sequencing. In chapter one, a time-series study of the seasonally oligotrophic northwestern Sargasso Sea underscores the importance of prasinophytes, a polyphyletic group of green algae. Prasinophytes (mostly Class II Mamiellophyceae) comprised approximately half the eukaryotic phytoplankton amplicons during the time of year where deep mixing brings nutrients to the surface. At the end of the deep mixing, the mixed layer shoaled quickly, which could lead to carbon export when the algae were trapped at depth. The focus of the second chapter is expanded to include other phytoplankton groups in addition to prasinophytes. This chapter explores the eukaryotic phytoplankton communities of various tropical habitats, from the green-algae-dominated salt ponds to the mangroves, reefs, and offshore habitats where stramenopiles become more relatively abundant. The Stramenopile group dictyochophytes were examined at high taxonomic resolution previously not reported for this region, with much of that group found to be comprised of uncultured environmental clades. The third chapter moves from the field to the laboratory, measuring the cell quotas of cultured representatives of Mamiellophyceae under nutrient replete, limiting, and starved conditions. Together, these chapters seek to increase the knowledge of prasinophytes across geographic areas and environmental parameters

Transitions in eukaryotic algae distributions and physiology from subtropical to tropical environments

The seasonal and geographical dynamics of phytoplankton have important implications for primary production, carbon sequestration, and predicting future ocean change. The distribution of phytoplankton is influenced by their environmental needs and preferences and can be examined at various levels, from strain or species to size class or broad taxonomic grouping. The first two chapters of this thesis focus on phytoplankton distribution by taxonomic group as determined by 16S and 18S rRNA gene amplicon sequencing. In chapter one, a time-series study of the seasonally oligotrophic northwestern Sargasso Sea underscores the importance of prasinophytes, a polyphyletic group of green algae. Prasinophytes (mostly Class II Mamiellophyceae) comprised approximately half the eukaryotic phytoplankton amplicons during the time of year where deep mixing brings nutrients to the surface. At the end of the deep mixing, the mixed layer shoaled quickly, which could lead to carbon export when the algae were trapped at depth. The focus of the second chapter is expanded to include other phytoplankton groups in addition to prasinophytes. This chapter explores the eukaryotic phytoplankton communities of various tropical habitats, from the green-algae-dominated salt ponds to the mangroves, reefs, and offshore habitats where stramenopiles become more relatively abundant. The Stramenopile group dictyochophytes were examined at high taxonomic resolution previously not reported for this region, with much of that group found to be comprised of uncultured environmental clades. The third chapter moves from the field to the laboratory, measuring the cell quotas of cultured representatives of Mamiellophyceae under nutrient replete, limiting, and starved conditions. Together, these chapters seek to increase the knowledge of prasinophytes across geographic areas and environmental parameters

Are deterministic descriptions and indeterministic descriptions observationally equivalent?

The central question of this paper is: are deterministic and indeterministic descriptions observationally equivalent in the sense that they give the same predictions? I tackle this question for measure-theoretic deterministic systems and stochastic processes, both of which are ubiquitous in science. I first show that for many measure-theoretic deterministic systems there is a stochastic process which is observationally equivalent to the deterministic system. Conversely, I show that for all stochastic processes there is a measure-theoretic deterministic system which is observationally equivalent to the stochastic process. Still, one might guess that the measure-theoretic deterministic systems which are observationally equivalent to stochastic processes used in science do not include any deterministic systems used in science. I argue that this is not so because deterministic systems used in science even give rise to Bernoulli processes. Despite this, one might guess that measure-theoretic deterministic systems used in science cannot give the same predictions at every observation level as stochastic processes used in science. By proving results in ergodic theory, I show that also this guess is misguided: there are several deterministic systems used in science which give the same predictions at every observation level as Markov processes. All these results show that measure-theoretic deterministic systems and stochastic processes are observationally equivalent more often than one might perhaps expect. Furthermore, I criticize the claims of some previous philosophy papers on observational equivalence

Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a ‘copiotrophic’ module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an ‘oligotrophic’ module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4–10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300–750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed

SAR324 16S rRNA gene reference tree identifies novel clades and distributions.

Shown is the ML reconstruction with percent relative abundance of SAR324 clade members out of total SAR324 amplicons at the study sites shown to the right of the tree topology. All clades retained support >90% apart from clades II and IV (82 and 88%, respectively; see also S5 Fig). Amplicons were phylogenetically placed on the SAR324 reconstruction developed herein using PhyloAssigner [17] after initial assignment and retrieval using a global 16S rRNA gene reference tree [17]. Heat map columns represent individual samples ordered by hierarchical clustering based on the Bray-Curtis similarities of the SAR324 composition. White in the heat map indicates not detected. Stations (color) and sampling dates (shape) are indicated as is sample depth (m) for each column.</p

Abundance and diversity of bacteria and cyanobacteria across depth and sample periods.

(A) Cell abundance of Prochlorococcus (closed symbols) and Synechococcus (open symbols) in the upper 200 m as enumerated by flow cytometry; cyanobacterial cells were not detected below this depth. (B) Heterotrophic bacterial cell abundance (i.e., non-pigmented; analyzed by flow cytometry after SYBR Green I staining) decreased with depth by 1.5 orders of magnitude. Replicates from individual sampling dates revealed a variance of 16% (n = 8) that can be attributed to methodology. (C) Shannon diversity indices for all sequenced samples and depth profiles as calculated from V1-V2 16S rRNA gene ASV data. September 2015 (squares), May 2016 (triangles), and September 2016 (circles) sampling dates are indicated, while stations are represented by color for all panels. Horizontal dotted lines (plots B and C) represent the bottom depth for the respective stations.</p

Phylogeny and distributions of Pelagibacterales.

The 16S rRNA gene phylogenetic reconstruction utilized full-length sequences and identifies 10 recognized subclades and 3 previously unrecognized subclades, all with bootstrap support >90% (1,000 replicates) except subclade IIb (86% support; see also S4 Fig). Note that dashed lines indicate LCA placements at unsupported nodes, some with relatively few amplicons. For example, that demarked ‘Clade V’—with a dashed line comprised >0.01% of amplicons . Some others with dashed lines were notable, but lacked full length sequences and therefore references sequences were not in the reconstruction. Also shown is the relative abundance of Pelagibacterales subclades as percent of all Pelagibacterales ASVs in each sample for the Monterey Bay Stations and depths sampled. Pelagibacter amplicons were first retrieved using PhyloAssigner and a global 16S rRNA gene reference tree [17]. These amplicons were then run in PhyloAssigner using the above Pelagibacterales reference tree. Heat map columns represent individual samples ordered by hierarchical clustering based on the Bray-Curtis similarities of the Pelagibacterales community composition. White in the heat map indicates not detected. Stations (color) and sampling dates (shape) are indicated as is sample depth (m) for each column.</p