Research

OPAL Group research clusters around three main scientific questions:

1. How does intraspecific diversity structure marine phytoplankton communities and provide evidence for their future resilience to environmental change?
   • Past projects that support this emphasis area: Krinos et al. 2025 Ecology Letters, laboratory experiments with combined temperature and nutrient effects on strains
   • Current projects that support this emphasis area: forthcoming work to characterize coccolithophore intraspecific diversity
2. How do phytoplankton compete for resources in coastal ecosystems over temporal scales, and how does this result in changes in species succession?
   • Past projects that support this emphasis area: Krinos et al. 2026 (bioRxiv), Lake Mendota work
   • Current projects that support this emphasis area: Collaborative work with the Brisbin lab at USF, Collaborative work at the Salton Sea in California, Collaborative work with Bridge-to-PhD fellow Emily Hu
3. What is the relationship between taxonomic diversity and functional redundancy in marine microbes (or, eukaryotes)?
   • Past projects that support this emphasis area: EUKulele (Krinos et al. 2021), eukrhythmic (Krinos et al. 2023), tax-aliquots/cryptic taxonomic diversity (Krinos et al. 2024)
   • Current projects that support this emphasis area: using metatranscriptomic data to tune models with meaningful taxonomic subgroupings (Krinos et al. 2026 in prep), Multiscale modeling framework with C-CoMP, 2025 C-CoMP cruises data analysis

All

2026

Nutrient response strategies drive coastal range shifts of phytoplankton taxa

Arianna I. Krinos, Margaret Mars Brisbin, Amy Costa, Sara K. Shapiro, Michael J. Follows, Mara A. Freilich, Harriet Alexander

openRxiv  ·  14 Jan 2026  ·  doi:10.64898/2026.01.13.699386

2025

The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more

Danilo Di Leo, Emelie Nilsson, Arianna Krinos, Jarone Pinhassi, Daniel Lundin

PeerJ  ·  05 Dec 2025  ·  doi:10.7717/PEERJ.20328

A call for early-career teams in interdisciplinary microbiology research

Arianna I. Krinos, Daniel Muratore, Meriel J. Bittner, Preston Akenga, Leslie Wallace Auerbach, …, Edgart Flores, Naomi M. Levine, Thiago Monteiro, Camille Richon, Benjamin S. Twining

Nature Microbiology  ·  25 Aug 2025  ·  doi:10.1038/s41564-025-02097-2

Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture

Margaret Mars Brisbin, McCaela Acord, Rachel Davitt, Shavonna Bent, Benjamin A. S. Van Mooy, …, Andreas Norlin, Jessica Turner, Arianna Krinos, Harriet Alexander, Mak Saito

Journal of Phycology  ·  07 Jul 2025  ·  doi:10.1111/JPY.70051

New niches for larger phytoplankton in a warmer, more resource-limited ocean

Suzana G. Leles, Lara Breithaupt, Arianna Krinos, Harriet Alexander, Holly V. Moeller, Lana Flanjak, Charlotte Laufkotter, Elena Litchman, María Aranguren-Gassis, Naomi M. Levine

openRxiv  ·  27 Jun 2025  ·  doi:10.1101/2025.06.22.660956

Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots

Miguel F. Romero-Gutiérrez, Arianna I. Krinos, Xyrus Maurer-Alcala, John A. Burns, Ramunas Stepanauskas, Tanja Woyke, Frederik Schulz

openRxiv  ·  26 Mar 2025  ·  doi:10.1101/2025.03.26.645542

Intraspecific Diversity in Thermal Performance Determines Phytoplankton Ecological Niche

Arianna I. Krinos, Sara K. Shapiro, Weixuan Li, Sheean T. Haley, Sonya T. Dyhrman, Stephanie Dutkiewicz, Michael J. Follows, Harriet Alexander

Ecology Letters  ·  01 Jan 2025  ·  doi:10.1111/ele.70055

2024

Missing microbial eukaryotes and misleading meta-omic conclusions

Arianna I. Krinos, Margaret Mars Brisbin, Sarah K. Hu, Natalie R. Cohen, Tatiana A. Rynearson, Michael J. Follows, Frederik Schulz, Harriet Alexander

Nature Communications  ·  14 Nov 2024  ·  doi:10.1038/s41467-024-52212-w

Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Natalie R. Cohen, Arianna I. Krinos, Riss M. Kell, Rebecca J. Chmiel, Dawn M. Moran, …, John A. Breier, Michael V. Jakuba, Rod Johnson, Harriet Alexander, Mak A. Saito

Nature Communications  ·  25 Aug 2024  ·  doi:10.1038/S41467-024-51583-4

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Arianna I. Krinos, Robert M. Bowers, Robin R. Rohwer, Katherine D. McMahon, Tanja Woyke, Frederik Schulz

Microbiome  ·  20 Jul 2024  ·  doi:10.1186/s40168-024-01831-y

Intraspecific diversity in thermal performance determines phytoplankton ecological niche

Arianna I. Krinos, Sara K. Shapiro, Weixuan Li, Sheean T. Haley, Sonya T. Dyhrman, Stephanie Dutkiewicz, Michael J. Follows, Harriet Alexander

openRxiv  ·  15 Feb 2024  ·  doi:10.1101/2024.02.14.580366

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Arianna I. Krinos, Robert M. Bowers, Robin R. Rohwer, Katherine D. McMahon, Tanja Woyke, Frederik Schulz

openRxiv  ·  12 Feb 2024  ·  doi:10.1101/2024.02.09.579653

2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

Harriet Alexander, Sarah K. Hu, Arianna I. Krinos, Maria Pachiadaki, Benjamin J. Tully, Christopher J. Neely, Taylor Reiter

mBio  ·  19 Dec 2023  ·  doi:10.1128/MBIO.01676-23

Protistan community composition and metabolism in the North Pacific Subtropical Gyre: Influences of mesoscale eddies and depth

Samantha J. Gleich, Sarah K. Hu, Arianna I. Krinos, David A. Caron

Environmental Microbiology  ·  11 Dec 2023  ·  doi:10.1111/1462-2920.16556

Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Natalie R. Cohen, Arianna I. Krinos, Riss M. Kell, Rebecca J. Chmiel, Dawn M. Moran, …, John A. Breier, Michael V. Jakuba, Rod Johnson, Harriet Alexander, Mak A. Saito

openRxiv  ·  21 Nov 2023  ·  doi:10.1101/2023.11.20.567900

Vitamin B12 conveys a protective advantage to phycosphere-associated bacteria at high temperatures

Margaret Mars Brisbin, Alese Schofield, Matthew R McIlvin, Arianna I Krinos, Harriet Alexander, Mak A Saito

ISME Communications  ·  25 Aug 2023  ·  doi:10.1038/s43705-023-00298-6

Vitamin B ₁₂ conveys a protective advantage to phycosphere-associated bacteria at high temperatures

Margaret Mars Brisbin, Alese Schofield, Matthew McIlvin, Arianna I. Krinos, Harriet Alexander, Mak Saito

openRxiv  ·  30 Jul 2023  ·  doi:10.1101/2023.07.30.551168

Missing microbial eukaryotes and misleading meta-omic conclusions

Arianna I. Krinos, Margaret Mars Brisbin, Sarah K. Hu, Natalie R. Cohen, Tatiana A. Rynearson, Michael J. Follows, Frederik Schulz, Harriet Alexander

openRxiv  ·  30 Jul 2023  ·  doi:10.1101/2023.07.30.551153

Correction: Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander

BMC Bioinformatics  ·  05 May 2023  ·  doi:10.1186/S12859-023-05313-0

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander

BMC Bioinformatics  ·  03 Mar 2023  ·  doi:10.1186/S12859-022-05121-Y

2022

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

Natalie R. Cohen, Harriet Alexander, Arianna I. Krinos, Sarah K. Hu, Robert H. Lampe

Frontiers in Marine Science  ·  28 Jun 2022  ·  doi:10.3389/FMARS.2022.867007

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander

openRxiv  ·  26 Apr 2022  ·  doi:10.1101/2022.04.25.489326

2021

Estimating global variation in the maximum growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns

JL Weissman, Edward-Robert O. Dimbo, Arianna I. Krinos, Christopher Neely, Yuniba Yagües, …, Sarah Laperriere, David A. Caron, Benjamin Tully, Harriet Alexander, Jed A. Fuhrman

openRxiv  ·  16 Oct 2021  ·  doi:10.1101/2021.10.15.464604

The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning Environment

Benjamin J. Tully, Joy Buongiorno, Ashley B. Cohen, Jacob A. Cram, Arkadiy I. Garber, …, Daan R. Speth, Elizabeth A Suter, Christopher B. Trivedi, Luis E. Valentin-Alvarado, JL Weissman

Frontiers in Education  ·  14 Oct 2021  ·  doi:10.3389/FEDUC.2021.711618

Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton

Harriet Alexander, Sarah K. Hu, Arianna I. Krinos, Maria Pachiadaki, Benjamin J. Tully, Christopher J. Neely, Taylor Reiter

openRxiv  ·  25 Jul 2021  ·  doi:10.1101/2021.07.25.453713

EUKulele: Taxonomic annotation of the unsung eukaryotic microbes

Arianna Krinos, Sarah Hu, Natalie Cohen, Harriet Alexander

Journal of Open Source Software  ·  08 Jan 2021  ·  doi:10.21105/joss.02817

2020

Seasonal changes and the unexpected impact of environmental disturbance on skin bacteria of individual amphibians in a natural habitat

Jenifer B Walke, Matthew H Becker, Arianna Krinos, Elizabeth A B Chang, Celina Santiago, Thomas P Umile, Kevin P C Minbiole, Lisa K Belden

FEMS Microbiology Ecology  ·  05 Dec 2020  ·  doi:10.1093/FEMSEC/FIAA248

Ecosystem-scale nutrient cycling responses to increasing air temperatures vary with lake trophic state

Kaitlin J. Farrell, Nicole K. Ward, Arianna I. Krinos, Paul C. Hanson, Vahid Daneshmand, Renato J. Figueiredo, Cayelan C. Carey

Ecological Modelling  ·  01 Aug 2020  ·  doi:10.1016/J.ECOLMODEL.2020.109134

2019

Including variability in air temperature warming scenarios in a lake simulation model highlights uncertainty in predictions of cyanobacteria

Arianna I. Krinos, Kaitlin J. Farrell, Vahid Daneshmand, Kensworth C. Subratie, Renato J. Figueiredo, Cayelan C. Carey

openRxiv  ·  15 Aug 2019  ·  doi:10.1101/734285

Enhancing collaboration between ecologists and computer scientists: lessons learned and recommendations forward

Cayelan C. Carey, Nicole K. Ward, Kaitlin J. Farrell, Mary E. Lofton, Arianna I. Krinos, …, Renato J. Figueiredo, Jonathan P. Doubek, Paul C. Hanson, Philip Papadopoulos, Peter Arzberger

Ecosphere  ·  01 May 2019  ·  doi:10.1002/ECS2.2753

2018

Ocean acidification: effects of pH on 45Ca uptake by lobster branchiostegites

Lilian Nagle, Skye Brown, Arianna Krinos, Gregory A. Ahearn

Journal of Comparative Physiology B  ·  14 Jul 2018  ·  doi:10.1007/S00360-018-1173-2

Decoding divergence in marine protistan communities: from strain diversity to basin biogeography

Arianna I. Krinos Quinn

MBLWHOI Library  ·  [no date info]  ·  doi:10.1575/1912/70395