Giovannoni Stephen J.

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Giovannoni

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Stephen J.

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0000-0002-2431-4296

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Identification of possible source markers in marine dissolved organic matter using ultrahigh resolution mass spectrometry

( 2009-04-30) Kujawinski, Elizabeth B. ; Longnecker, Krista ; Blough, Neil V. ; Del Vecchio, Rossana ; Finlay, Liam ; Kitner, Joshua B. ; Giovannoni, Stephen J.

Marine dissolved organic matter (DOM) is one of the most heterogeneous and largest pools of reactive carbon on earth, rivaling in mass the carbon in atmospheric carbon dioxide. Nevertheless, the molecular-level composition of marine DOM has eluded detailed description, impeding inquiry into the specific mechanisms that add or remove compounds from the DOM pool. Here we describe the molecular-level composition of C18-extracted DOM along an east-west transect of the North Atlantic Ocean. We examine the changes in DOM composition along this transect with ultrahigh resolution mass spectrometry and multivariate statistics. We use indicator species analysis (ISA) to identify possible source markers for photochemical degradation and heterotrophic bacterial metabolism. The inclusion of ISA in statistical evaluation of DOM mass spectral data allows investigators to determine the m/z values associated with significant changes in DOM composition. With this technique, we observe indicator m/z values in estuarine water that may represent components of terrestrially-derived chromophoric DOM subject to photo-chemical degradation. We also observe a unique set of m/z values in surface seawater and show that many of these are present in pure cultures of the marine α-proteobacterium Candidatus Pelagibacter ubique when grown in natural seawater. These findings indicate that a complex balance of abiotic and biotic processes controls the molecular composition of marine DOM to produce signatures that are characteristic of different environments.
Experimental results and survey of biogeochemical and microbial data collected on the R/V Atlantic Explorer (AE1516) at the Bermuda Atlantic Time-series study site during 2015 (Bacterial DOC cycling project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-09-30) Giovannoni, Stephen

This dataset is a log of samples collected on AE1516 at the Bermuda Atlantic Time-series study site (BAT) Hydrostation S. The samples were analyzed for microbial diversity, dissolved organic carbon (DOC), total DOC, single celled genomics, and an osmolyte inculation experiment. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/616269
Growth behaviors of diatom monoculture and diatom-bacteria co-cultures in the lab

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-12-16) Halsey, Kimberly ; Giovannoni, Stephen

This dataset represents the growth behaviors of diatom (Phaeodactylum tricornutum) monoculture and diatom-bacteria co-cultures in the lab. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/856200
Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1620 in the Bermuda Atlantic Time-series Study site from Sept 2016

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-09-30) Giovannoni, Stephen ; Carlson, Craig

Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1620 in the Bermuda Atlantic Time-series Study site from Sept 2016. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/753624
Seasonal and geographical transitions in eukaryotic phytoplankton community structure in the Atlantic and Pacific Oceans

(Frontiers Media, 2020-09-30) Choi, Chang Jae ; Jimenez, Valeria ; Needham, David M. ; Poirier, Camille ; Bachy, Charles ; Alexander, Harriet ; Wilken, Susanne ; Chavez, Francisco P. ; Sudek, Sebastian ; Giovannoni, Stephen J. ; Worden, Alexandra Z.

Much is known about how broad eukaryotic phytoplankton groups vary according to nutrient availability in marine ecosystems. However, genus- and species-level dynamics are generally unknown, although important given that adaptation and acclimation processes differentiate at these levels. We examined phytoplankton communities across seasonal cycles in the North Atlantic (BATS) and under different trophic conditions in the eastern North Pacific (ENP), using phylogenetic classification of plastid-encoded 16S rRNA amplicon sequence variants (ASVs) and other methodologies, including flow cytometric cell sorting. Prasinophytes dominated eukaryotic phytoplankton amplicons during the nutrient-rich deep-mixing winter period at BATS. During stratification (‘summer’) uncultured dictyochophytes formed ∼35 ± 10% of all surface plastid amplicons and dominated those from stramenopile algae, whereas diatoms showed only minor, ephemeral contributions over the entire year. Uncultured dictyochophytes also comprised a major fraction of plastid amplicons in the oligotrophic ENP. Phylogenetic reconstructions of near-full length 16S rRNA sequences established 11 uncultured Dictyochophyte Environmental Clades (DEC). DEC-I and DEC-VI dominated surface dictyochophytes under stratification at BATS and in the ENP, and DEC-IV was also important in the latter. Additionally, although less common at BATS, Florenciella-related clades (FC) were prominent at depth in the ENP. In both ecosystems, pelagophytes contributed notably at depth, with PEC-VIII (Pelagophyte Environmental Clade) and (cultured) Pelagomonas calceolata being most important. Q-PCR confirmed the near absence of P. calceolata at the surface of the same oligotrophic sites where it reached ∼1,500 18S rRNA gene copies ml–1 at the DCM. To further characterize phytoplankton present in our samples, we performed staining and at-sea single-cell sorting experiments. Sequencing results from these indicated several uncultured dictyochophyte clades are comprised of predatory mixotrophs. From an evolutionary perspective, these cells showed both conserved and unique features in the chloroplast genome. In ENP metatranscriptomes we observed high expression of multiple chloroplast genes as well as expression of a selfish element (group II intron) in the psaA gene. Comparative analyses across the Pacific and Atlantic sites support the conclusion that predatory dictyochophytes thrive under low nutrient conditions. The observations that several uncultured dictyochophyte lineages are seemingly capable of photosynthesis and predation, raises questions about potential shifts in phytoplankton trophic roles associated with seasonality and long-term ocean change.
Virioplankton abundance using FISH probe at BATS site in the western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-05-11) Carlson, Craig ; Giovannoni, Stephen

Virioplankton abundances were measured from samples collected from January 2000 to December 2011 as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/). This dataset reports abundances quantified using FISH (Fluorescence in situ hybridization). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543828
Newly discovered deep-branching marine plastid lineages are numerically rare but globally distributed

(Elsevier, 2017-01-09) Choi, Chang Jae ; Bachy, Charles ; Spiro Jaeger, Gualtiero ; Poirier, Camille ; Sudek, Lisa ; Sarma, V. V. S. S. ; Mahadevan, Amala ; Giovannoni, Stephen J. ; Worden, Alexandra Z.

Ocean surface warming is resulting in an expansion of stratified, low-nutrient environments, a process referred to as ocean desertification. A challenge for assessing the impact of these changes is the lack of robust baseline information on the biological communities that carry out marine photosynthesis. Phytoplankton perform half of global biological CO2 uptake, fuel marine food chains, and include diverse eukaryotic algae that have photosynthetic organelles (plastids) acquired through multiple evolutionary events. While amassing data from ocean ecosystems for the Baselines Initiative (6,177 near full-length 16S rRNA gene sequences and 9.4 million high-quality 16S V1-V2 amplicons) we identified two deep-branching plastid lineages based on 16S rRNA gene data. The two lineages have global distributions, but do not correspond to known phytoplankton. How the newly discovered phytoplankton lineages contribute to food chains and vertical carbon export to the deep sea remains unknown, but their prevalence in expanding, low nutrient surface waters suggests they will have a role in future oceans.
Impact of instrument and experiment parameters on reproducibility of ultrahigh resolution ESI FT-ICR mass spectra of natural organic matter

( 2010-04-09) Kido Soule, Melissa C. ; Longnecker, Krista ; Giovannoni, Stephen J. ; Kujawinski, Elizabeth B.

Natural dissolved organic matter (OM) is a complex heterogeneous mixture of compounds that have defied traditional characterization using standard analytical methods. Electrospray ionization mass spectrometry, particularly ultrahigh resolution mass spectrometry, has provided a new platform for compositional assessment of this important pool of the Earth’s reduced carbon. Here, we propose a framework for optimization of instrument and experiment parameters for high quality data acquisition using Fourier‐transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS). We report the impact of these parameters on reproducibility of peak detection and repeatability of peak height in replicate injections of Suwannee River fulvic acid (FA), a common terrestrial OM standard. In addition, we examine the variability in peak detection and peak height among different types of experimental replicates of dissolved OM derived from laboratory cultures of Candidatus Pelagibacter ubique, a ubiquitous marine α‐ proteobacterium.
Sugar concentrations from the BATS site in the Sargasso Sea, 2001-2004 (Ocean Microbial Observatory project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-05-11) Carlson, Craig ; Giovannoni, Stephen

Sugar concentrations and dissolved combined neutral sugar (DCNS) dynamics were measured from samples for DCNS collected monthly to bimonthly between 2001 and 2004 at the BATS study site aboard the R/V Weatherbird II, Western Sargasso Sea. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543771
Virioplankton abundance from multiple cruises at the Bermuda AtlanticTime Series Station (BATS), Western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-05-11) Carlson, Craig ; Giovannoni, Stephen

Virioplankton abundances were measured from samples collected from January 2000 to December 2011 at the Bermuda Atlantic Time Series Station (BATS), Western Sargasso Sea, as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543808
Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013 (Ocean Microbial Observatory project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-05-11) Carlson, Craig ; Giovannoni, Stephen

Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013. This dataset includes water samples collected from 2009-2013 at the Bermuda Hydrostation that were analyzed for DOC, POC, bacterial abundance, leucine, and thymidine incorporation. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543314
Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1703 in the Bermuda Atlantic Time-series Study site from Mar/April 2016

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-09-30) Giovannoni, Stephen ; Carlson, Craig

Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1703 in the Bermuda Atlantic Time-series Study site from Mar/April 2016. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/753679
Genomes from uncultivated Pelagiphages reveal multiple phylogenetic clades exhibiting extensive auxiliary metabolic genes and cross-family multigene transfers

(American Society for Microbiology, 2022-08-16) Wittmers, Fabian ; Needham, David M. ; Hehenberger, Elisabeth ; Giovannoni, Stephen J. ; Worden, Alexandra Z.

For the abundant marine Alphaproteobacterium Pelagibacter (SAR11), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pan-genome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter, they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts.
Linkages among dissolved organic matter export, dissolved metabolites, and associated microbial community structure response in the northwestern Sargasso Sea on a seasonal scale

(Frontiers Media, 2022-03-08) Liu, Shuting ; Longnecker, Krista ; Kujawinski, Elizabeth B. ; Vergin, Kevin ; Bolaños, Luis M. ; Giovannoni, Stephen J. ; Parsons, Rachel J. ; Opalk, Keri ; Halewood, Elisa ; Hansell, Dennis A. ; Johnson, Rodney J. ; Curry, Ruth G. ; Carlson, Craig A.

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
Different carboxyl-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea

(Wiley, 2020-01-23) Liu, Shuting ; Parsons, Rachel J. ; Opalk, Keri ; Baetge, Nicholas ; Giovannoni, Stephen J. ; Bolaños, Luis M. ; Kujawinski, Elizabeth B. ; Longnecker, Krista ; Lu, YueHan ; Halewood, Elisa ; Carlson, Craig A.

Marine dissolved organic matter (DOM) varies in its recalcitrance to rapid microbial degradation. DOM of varying recalcitrance can be exported from the ocean surface to depth by subduction or convective mixing and oxidized over months to decades in deeper seawater. Carboxyl‐rich alicyclic molecules (CRAM) are characterized as a major component of recalcitrant DOM throughout the oceanic water column. The oxidation of CRAM‐like compounds may depend on specific bacterioplankton lineages with oxidative enzymes capable of catabolizing complex molecular structures like long‐chain aliphatics, cyclic alkanes, and carboxylic acids. To investigate the interaction between bacteria and CRAM‐like compounds, we conducted microbial remineralization experiments using several compounds rich in carboxyl groups and/or alicyclic rings, including deoxycholate, humic acid, lignin, and benzoic acid, as proxies for CRAM. Mesopelagic seawater (200 m) from the northwest Sargasso Sea was used as media and inoculum and incubated over 28 d. All amendments demonstrated significant DOC removal (2–11 μmol C L−1) compared to controls. Bacterioplankton abundance increased significantly in the deoxycholate and benzoic acid treatments relative to controls, with fast‐growing Spongiibacteracea, Euryarcheaota, and slow‐growing SAR11 enriched in the deoxycholate treatment and fast‐growing Alteromonas, Euryarcheaota, and Thaumarcheaota enriched in the benzoic acid treatment. In contrast, bacterioplankton grew slower in the lignin and humic acid treatments, with oligotrophic SAR202 becoming significantly enriched in the lignin treatment. Our results indicate that the character of the CRAM proxy compounds resulted in distinct bacterioplankton removal rates of DOM and affected specific lineages of bacterioplankton capable of responding.
Pangenomics analysis reveals diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria

(American Society for Microbiology, 2020-01-07) Saw, Jimmy H. W. ; Nunoura, Takuro ; Hirai, Miho ; Takaki, Yoshihiro ; Parsons, Rachel ; Michelsen, Michelle ; Longnecker, Krista ; Kujawinski, Elizabeth B. ; Stepanauskas, Ramunas ; Landry, Zachary ; Carlson, Craig A. ; Giovannoni, Stephen J.

It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns. IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.
Marine particle size-fractionation indicates organic matter is processed by differing microbial communities on depth-specific particles

(Oxford University Press, 2024-07-12) Comstock, Jacqueline ; Henderson, Lillian C. ; Close, Hilary G. ; Liu, Shuting ; Vergin, Kevin L. ; Worden, Alexandra Z. ; Wittmers, Fabian ; Halewood, Elisa ; Giovannoni, Stephen J. ; Carlson, Craig A.

Passive sinking flux of particulate organic matter in the ocean plays a central role in the biological carbon pump and carbon export to the ocean’s interior. Particle-associated microbes colonize particulate organic matter, producing “hotspots” of microbial activity. We evaluated variation in particle-associated microbial communities to 500 m depth across four different particle size fractions (0.2–1.2, 1.2–5, 5–20, >20 μm) collected using in situ pumps at the Bermuda Atlantic Time-series Study site. In situ pump collections capture both sinking and suspended particles, complementing previous studies using sediment or gel traps, which capture only sinking particles. Additionally, the diagenetic state of size-fractionated particles was examined using isotopic signatures alongside microbial analysis. Our findings emphasize that different particle sizes contain distinctive microbial communities, and each size category experiences a similar degree of change in communities over depth, contradicting previous findings. The robust patterns observed in this study suggest that particle residence times may be long relative to microbial succession rates, indicating that many of the particles collected in this study may be slow sinking or neutrally buoyant. Alternatively, rapid community succession on sinking particles could explain the change between depths. Complementary isotopic analysis of particles revealed significant differences in composition between particles of different sizes and depths, indicative of organic particle transformation by microbial hydrolysis and metazoan grazing. Our results couple observed patterns in microbial communities with the diagenetic state of associated organic matter and highlight unique successional patterns in varying particle sizes across depth.
Toward a synthesis of phytoplankton communities composition methods for global-scale application

(Association for the Sciences of Limnology and Oceanography (ASLO), 2024-02-23) Kramer, Sasha J. ; Bolanos, Luis M. ; Catlett, Dylan ; Chase, Alison P. ; Behrenfeld, Michael J. ; Boss, Emmanuel S. ; Crockford, E. Taylor ; Giovannoni, Stephen J. ; Graff, Jason R. ; Haentjens, Nils ; Karp-Boss, Lee ; Peacock, Emily E. ; Roesler, Collin S. ; Sosik, Heidi M. ; Siegel, David A.

The composition of the marine phytoplankton community has been shown to impact many biogeochemical processes and marine ecosystem services. A variety of methods exist to characterize phytoplankton community composition (PCC), with varying degrees of taxonomic resolution. Accordingly, the resulting PCC determinations are dependent on the method used. Here, we use surface ocean samples collected in the North Atlantic and North Pacific Oceans to compare high-performance liquid chromatography pigment-based PCC to four other methods: quantitative cell imaging, flow cytometry, and 16S and 18S rRNA amplicon sequencing. These methods allow characterization of both prokaryotic and eukaryotic PCC across a wide range of size classes. PCC estimates of many taxa resolved at the class level (e.g., diatoms) show strong positive correlations across methods, while other groups (e.g., dinoflagellates) are not well captured by one or more methods. Since variations in phytoplankton pigment concentrations are related to changes in optical properties, this combined dataset expands the potential scope of ocean color remote sensing by associating PCC at the genus- and species-level with group- or class-level PCC from pigments. Quantifying the strengths and limitations of pigment-based PCC methods compared to PCC assessments from amplicon sequencing, imaging, and cytometry methods is the first step toward the robust validation of remote sensing approaches to quantify PCC from space.
Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae

(Nature Research, 2024-05-20) Eckmann, Charlotte A. ; Bachy, Charles ; Wittmers, Fabian ; Strauss, Jan ; Blanco-Bercial, Leocadio ; Vergin, Kevin L. ; Parsons, Rachel J. ; Kudela, Raphael M. ; Johnson, Rod ; Bolanos, Luis M. ; Giovannoni, Stephen J. ; Carlson, Craig A. ; Worden, Alexandra Z.

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.

Giovannoni Stephen J.

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