Alexander Harriet

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Alexander

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Harriet

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0000-0003-1308-8008

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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.
Keeping it light: (re)analyzing community-wide datasets without major infrastructure

(Oxford University Press, 2018-12-13) Alexander, Harriet ; Johnson, Lisa K ; Brown, C. Titus

DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

(Oxford University Press, 2019-04) Johnson, Lisa K. ; Alexander, Harriet ; Brown, C. Titus

Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
Sixty years of Sverdrup : a retrospective of progress in the study of phytoplankton blooms

(The Oceanography Society, 2014-03) Fischer, Alexis D. ; Moberg, Emily A. ; Alexander, Harriet ; Brownlee, Emily F. ; Hunter-Cevera, Kristen R. ; Pitz, Kathleen J. ; Rosengard, Sarah Z. ; Sosik, Heidi M.

One of the most dramatic large-scale features in the ocean is the seasonal greening of the North Atlantic in spring and summer due to the accumulation of phytoplankton biomass in the surface layer. In 1953, Harald Ulrik Sverdrup hypothesized a now canonical mechanism for the development and timing of phytoplankton blooms in the North Atlantic. Over the next 60 years, Sverdrup's Critical Depth Hypothesis spurred progress in understanding of bloom dynamics and offered a valuable theoretical framework on which to build. In reviewing 60 years of literature, the authors trace the development of modern bloom initiation hypotheses, highlighting three case studies that illuminate the complexity, including both catalysts and impediments, of scientific progress in the wake of Sverdrup's hypothesis. Most notably, these cases demonstrate that the evolution of our understanding of phytoplankton blooms was paced by access not only to technology but also to concurrent insights from several disciplines. This exploration of the trajectories and successes in bloom studies highlights the need for expanding interdisciplinary collaborations to address the complexity of phytoplankton bloom dynamics.
Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities?

(Oxford University Press, 2020-06-10) Johnson, Winifred M. ; Alexander, Harriet ; Bier, Raven L. ; Miller, Dan R. ; Muscarella, Mario E. ; Pitz, Kathleen J. ; Smith, Heidi

Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response

(Public Library of Science, 2012-03-29) Dyhrman, Sonya T. ; Jenkins, Bethany D. ; Rynearson, Tatiana A. ; Saito, Mak A. ; Mercier, Melissa L. ; Alexander, Harriet ; Whitney, LeAnn P. ; Drzewianowski, Andrea ; Bulygin, Vladimir V. ; Bertrand, Erin M. ; Wu, Zhijin ; Benitez-Nelson, Claudia R. ; Heithoff, Abigail

Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of <0.05, and a total of 136 proteins were differentially abundant (p<0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.
Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology

(Frontiers Media, 2022-01-10) Clayton, Sophie A. ; Alexander, Harriet ; Graff, Jason R. ; Poulton, Nicole J. ; Thompson, Luke R. ; Benway, Heather M. ; Boss, Emmanuel S. ; Martiny, Adam C.

In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.
Transcriptional shifts highlight the role of nutrients in harmful brown tide dynamics

(Frontiers Media, 2019-02-12) Wurch, Louie L. ; Alexander, Harriet ; Frischkorn, Kyle R. ; Haley, Sheean T. ; Gobler, Christopher J. ; Dyhrman, Sonya T.

Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.
A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae

(Inter Research, 2021-02-25) Fiore, Cara L. ; Alexander, Harriet ; Kido Soule, Melissa C. ; Kujawinski, Elizabeth B.

Phosphorus (P) limits primary production in regions of the surface ocean, and many plankton species exhibit specific physiological responses to P deficiency. The metabolic response of Micromonas pusilla, an ecologically relevant marine photoautotroph, to P deficiency was investigated using metabolomics and comparative genomics. The concentrations of some intracellular metabolites were elevated in the P-deficient cells (e.g. xanthine, inosine), and genes involved in the associated metabolic pathways shared a predicted conserved amino acid motif in the non-coding regions of each gene. The presence of the conserved motif suggests that these genes may be co-regulated, and the motif may constitute a regulatory element for binding a transcription factor, specifically that of Psr1 (phosphate starvation response). A putative phosphate starvation response gene ( psr1-like) was identified in M. pusilla with homology to well characterized psr1/ phr1 genes in algae and plants, respectively. This gene appears to be present and expressed in other marine algal taxa (e.g. Emiliania huxleyi) in field sites that are chronically P limited. Results from the present study have implications for understanding phytoplankton taxon-specific roles in mediating P cycling in the ocean.
The osmolyte ties that bind: genomic insights into synthesis and breakdown of organic osmolytes in marine microbes

(Frontiers Media, 2021-07-14) McParland, Erin L. ; Alexander, Harriet ; Johnson, Winifred M.

The production and consumption of organic matter by marine organisms plays a central role in the marine carbon cycle. Labile organic compounds (metabolites) are the major currency of energetic demands and organismal interaction, but these compounds remain elusive because of their rapid turnover and concomitant minuscule concentrations in the dissolved organic matter pool. Organic osmolytes are a group of small metabolites synthesized at high intracellular concentrations (mM) to regulate cellular osmolarity and have the potential to be released as abundant dissolved substrates. Osmolytes may represent an essential currency of exchange among heterotrophic prokaryotes and primary and secondary producers in marine food webs. For example, the well-known metabolite dimethylsulfoniopropionate (DMSP) is used as an osmolyte by some phytoplankton and can be subsequently metabolized by 60% of the marine bacterial community, supplying up to 13% of the bacterial carbon demand and 100% of the bacterial sulfur demand. While marine osmolytes have been studied for decades, our understanding of their cycling and significance within microbial communities is still far from comprehensive. Here, we surveyed the genes responsible for synthesis, breakdown, and transport of 14 key osmolytes. We systematically searched for these genes across marine bacterial genomes (n = 897) and protistan transcriptomes (n = 652) using homologous protein profiles to investigate the potential for osmolyte metabolisms. Using the pattern of gene presence and absence, we infer the metabolic potential of surveyed microbes to interact with each osmolyte. Specifically, we identify: (1) complete pathways for osmolyte synthesis in both prokaryotic and eukaryotic marine microbes, (2) microbes capable of transporting osmolytes but lacking complete synthesis and/or breakdown pathways, and (3) osmolytes whose synthesis and/or breakdown appears to be specialized and is limited to a subset of organisms. The analysis clearly demonstrates that the marine microbial loop has the genetic potential to actively recycle osmolytes and that this abundant group of small metabolites may function as a significant source of nutrients through exchange among diverse microbial groups that significantly contribute to the cycling of labile carbon.
Marine microeukaryotem metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications

(Frontiers Media, 2022-06-28) Cohen, Natalie R. ; Alexander, Harriet ; Krinos, Arianna I. ; Hu, Sarah K. ; Lampe, Robert H.

Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.
Identifying reference genes with stable expression from high throughput sequence data

(Frontiers Media, 2012-11-09) Alexander, Harriet ; Jenkins, Bethany D. ; Rynearson, Tatiana A. ; Saito, Mak A. ; Mercier, Melissa L. ; Dyhrman, Sonya T.

Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability < 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

(BMC, 2023-03-03) Krinos, Arianna I. ; Cohen, Natalie R. ; Follows, Michael J. ; Alexander, Harriet

Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity.Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach.We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
Defining the ecological and physiological traits of phytoplankton across marine ecosystems

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2016-02) Alexander, Harriet

Marine phytoplankton are central players in the global carbon cycle, responsible for nearly half of global primary production. The identification of the factors controlling phytoplankton ecology, physiology, and, ultimately, bloom dynamics has been a central problem in the field of biological oceanography for the past century. Molecular approaches enable the direct examination of species-specific metabolic profiles in mixed, natural communities, a task which was previously intractable. In this thesis, I developed and applied novel analytical tools and bioinformatic pipelines to characterize the physiological response of phytoplankton to their environment at various levels of taxonomic grouping. An in silico Bayesian statistical approach was designed to identify stable reference genes from high-throughput sequence data for use in RT-qPCR assays or metatranscriptome studies. Using a metatranscriptomic approach, the role of resource partitioning in the coexistence of two closely related diatom species in an estuarine system was examined. This study demonstrated that co-occurring diatoms in a dynamic coastal system have apparent differences in their capacity to use nitrogen and phosphorus, and that these differences may facilitate the diversity of the phytoplankton. The second field study focused on the diatom, haptophyte, and dinoflagellate functional groups, using simulated blooms to characterize the traits that govern the magnitude and timing of phytoplankton blooms in the oligotrophic ocean. The results indicated that blooms form when phytoplankton are released from limitation by resources and that the mechanistic basis for the success of one functional group over another may be driven by how efficiently the transcriptome is modulated following a nutrient pulse. The final study looked at the sub-species level, examining the balance of phenotypic plasticity and strain diversity in the success of the coccolithophore Emiliania huxleyi. Results indicated strong control of nitrogen on the species complex and showed that nutrient resupply shifted the strain composition as well as transcript abundance of key biogeochemical genes involved in nutrient acquisition and the life stage of the population. Together, these studies demonstrate the breadth of information that can be garnered through the integration of molecular approaches with traditional biological oceanographic surveys, with each illuminating fundamental questions around phytoplankton ecology and bloom formation.
Vitamin B12 conveys a protective advantage to phycosphere-associated bacteria at high temperatures

(Oxford University Press, 2023-08-25) Mars Brisbin, Margaret ; Schofield, Alese ; McIlvin, Matthew R. ; Krinos, Arianna I. ; Krinos, Arianna I. ; Saito, Mak A.

Many marine microbes require vitamin B12 (cobalamin) but are unable to synthesize it, necessitating reliance on other B12-producing microbes. Thus, phytoplankton and bacterioplankton community dynamics can partially depend on the production and release of a limiting resource by members of the same community. We tested the impact of temperature and B12 availability on the growth of two bacterial taxa commonly associated with phytoplankton: Ruegeria pomeroyi, which produces B12 and fulfills the B12 requirements of some phytoplankton, and Alteromonas macleodii, which does not produce B12 but also does not strictly require it for growth. For B12-producing R. pomeroyi, we further tested how temperature influences B12 production and release. Access to B12 significantly increased growth rates of both species at the highest temperatures tested (38 °C for R. pomeroyi, 40 °C for A. macleodii) and A. macleodii biomass was significantly reduced when grown at high temperatures without B12, indicating that B12 is protective at high temperatures. Moreover, R. pomeroyi produced more B12 at warmer temperatures but did not release detectable amounts of B12 at any temperature tested. Results imply that increasing temperatures and more frequent marine heatwaves with climate change will influence microbial B12 dynamics and could interrupt symbiotic resource sharing.
Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

(American Society for Microbiology, 2023-11-10) Alexander, Harriet ; Hu, Sarah K. ; Krinos, Arianna I. ; Pachiadaki, Maria G. ; Tully, Benjamin J. ; Neely, Christopher J. ; Reiter, Taylor

Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.

Alexander Harriet

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