Krinos Quinn
Arianna I.
Krinos Quinn
Arianna I.
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ArticleMarine 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.
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ArticleReverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly(BMC, 2023-03-03) Krinos, Arianna I. ; Cohen, Natalie R. ; Follows, Michael J. ; Alexander, HarrietDiverse 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.
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ArticleVitamin 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.
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ThesisDecoding divergence in marine protistan communities: from strain diversity to basin biogeography(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Krinos Quinn, Arianna I. ; Follows, Michael J. ; Alexander, HarrietProtists (microbial eukaryotes) in the global ocean are critical components of primary productivity and nutrient recycling. Protists are genetically diverse and have distinctive ecological niches based on genetically-driven differences in physiological fitness. A deeper understanding of which dimensions of protistan genetic diversity translate to measurable phenotypic variation is needed to predict the impact of protists on marine biogeochemistry and protists’ environmental change sensitivity. I cultured twelve strains of the coccolithophore Gephyrocapsa huxleyi across temperatures, which revealed strain-specific differences in thermal optima and niche widths. I used traits measured during the experiments to design a Darwin ecosystem model simulation, which demonstrated basin-specific biogeography of thermal optima and niche widths (Chapter 2). For seven of the twelve strains, I sequenced transcriptomes at 3-5 temperatures to assess gene expression variation. Using the RNAseq data, I developed a regression modeling approach to identify proteome allocation model parameters. Combining differential expression analysis, gene abundance normalization, and the regression model to explore the proteome allocation model parameter space, I probed differences in modeled strategies of G. huxleyi strains in response to temperature (Chapter 3). Scalable workflows highlight the challenge and promise of meta-omic data to link community structure to physiology. I developed a pipeline for metatranscriptome analysis and taxonomic annotation to address the lack of tools built specifically for microbial eukaryotes, and created mock communities to assess recovery success in protistan metatranscriptome analysis workflows (Chapters 4 and 5). I applied these tools to a three-year metatranscriptomic dataset from Cape Cod Bay to investigate a recent emergence of a summer occolithophore population in the 20-year time series, tracking shifts in nutrient physiology to identify potential bottom-up controls (Chapter 6). This dissertation advances approaches to constrain the protistan taxonomic diversity that underlies shifts in global primary productivity and nutrient turnover. Specifically, strains of a single phytoplankton species revealed diversity relevant to a global ecosystem model. Future work will clarify variability in protistan gene content and expression that may underpin both protists’ present ecological niches and their future climate change response.
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ArticleEukaryotic 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, TaylorMetagenomics 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.
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ArticleProtistan community composition and metabolism in the North Pacific Subtropical Gyre: influences of mesoscale eddies and depth(Wiley, 2023-12-11) Gleich, Samantha J. ; Hu, Sarah K. ; Krinos, Arianna I. ; Caron, David A.Marine protists and their metabolic activities are intricately tied to the cycling of nutrients and the flow of energy through microbial food webs. Physiochemical changes in the environment, such as those that result from mesoscale eddies, may impact protistan communities, but the effects that such changes have on protists are poorly known. A metatranscriptomic study was conducted to investigate how eddies affected protists at adjacent cyclonic and anticyclonic eddy sites in the oligotrophic ocean at four depths from 25 to 250 m. Eddy polarity impacted protists at all depths sampled, although the effects of eddy polarity were secondary to the impact of depth across the depth range. Eddy-induced vertical shifts in the water column yielded differences in the cyclonic and anticyclonic eddy protistan communities, and these differences were the most pronounced at and just below the deep chlorophyll maximum. An analysis of transcripts associated with protistan nutritional physiology at 150 m revealed that cyclonic eddies may support a more heterotrophic community, while anticyclonic eddies promote a more phototrophic community. The results of this study indicate that eddies alter the metabolism of protists particularly in the lower euphotic zone and may therefore impact carbon export from the euphotic zone.