Biology subjects

Krinos, A. I.

Publications and source records attributed to Krinos, A. I..

11 recordsLinked to original sources

bioRxiv2026

Nutrient response strategies drive coastal range shifts of phytoplankton taxa

Coastal phytoplankton blooms are important drivers of regional and global marine primary production. Recently documented increases in coastal phytoplankton blooms in the first quarter of the 21st century may be a consequence in part of changing environmental conditions and have important ecological implications. Here, we explore coastal phytoplankton dynamics in Cape Cod Bay, MA, USA. We use a 20-year phytoplankton ecology dataset to identify potential drivers of the increasing prevalence of two regionally-rare phytoplankton taxa: a coccolithophore thought to thrive in the global open ocean, and a dinoflagellate genus with potentially toxic members. Using metatranscriptomics, we show that these minor phytoplankton taxa leverage unique strategies to gain a competitive advantage under nutrient limitation compared to traditionally dominant taxa and compared to a diatom taxon that became modestly more abundant over the study period. Our results highlight the ecological dynamics arising from long-term shifts in temperature and nutrient status in coastal ecosystems.

ecology↗

bioRxiv2025

Global Metagenomics Reveals Hidden Protist Diversity

Protists, defined as eukaryotes distinct from animals, plants, and fungi, are a polyphyletic group that dominates the eukaryotic tree of life, exhibiting significant phylogenetic diversity and fulfilling critical ecological roles. Historically, research has prioritized protists associated with animals and plants, particularly those of medical significance, thereby overlooking the majority of protist diversity. Conventional molecular methods, such as 18S rRNA gene amplicon sequencing, frequently encounter limitations, including primer binding bias and PCR bias caused by gene length variations, resulting in a biased representation of protistan diversity. Further, most protist lineages are notoriously difficult to cultivate. Here, we apply a cultivation-independent approach in which we analyzed over 30,000 assembled metagenomes and protist single cell genomes and 21 long 18S rRNA gene amplicon data sets from various global ecosystems, including marine, freshwater, and soil environments. We recovered 157,956 18S rRNA gene sequences ([≥]800 bp), which clustered into 103,338 operational taxonomic units (OTUs) at 97% sequence identity and 24,438 OTUs at 85% identity. Notably, 81% of 9,543 non-singleton clusters at 85% identity classified as protists consisted exclusively of environmental sequences, uncovering a wealth of novel, uncultivated, and unclassified protist diversity. A comprehensive taxonomic framework of eukaryotes based on concatenated 18S and 28S rRNA genes that incorporated most novel lineages revealed substantial underrepresentation of Amoebozoa, Discoba, and Rhizaria in reference databases, with many lacking isolate or genome sequence representation. Further, we identified 13 eukaryotic lineages with novelty on higher taxonomic ranks, such as class and phylum-level, that lack representation in public databases. The corresponding 85% OTUs were primarily affiliated with Excavata, with some branching deeply in the eukaryotic tree. Comprehensive analysis of the global distribution of protists revealed uneven microbial diversity across supergroups and ecosystems, with notable novelty particularly in soil and marine environments. We then examined co-occurrence between protists and prokaryotes, predicting putative symbiotic or predator-prey relationships, particularly among understudied protist groups with bacteria such as Verrucomicrobia and Rickettsiales. Our results substantially enhance the understanding of protistan diversity and distribution, revealing taxonomic blind spots and laying groundwork for future studies of these organisms ecological roles.

microbiology↗

bioRxiv2024

Intraspecific diversity in thermal performance determines phytoplankton ecological niche

Temperature has a primary influence on phytoplankton physiology and affects biodiversity and ecology. To examine how intraspecific diversity and temperature shape plankton populations, we grew 12 strains of the ecologically-important coccolithophore Gephyrocapsa huxleyi isolated from regions of different temperature for [~]45 generations (2 months), each at 6-8 temperatures, and characterized the acclimated thermal response curve of each strain. Even with virtually identical temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day-1. While some thermal curves were effectively symmetrical, others had more slowly declining growth rates above the "thermal optimum," and thermal niche widths varied between 16.7 and 24.8 {degrees}C. This suggests that different strains use distinct thermal response mechanisms. We investigated the ecological implications of such intraspecific diversity on thermal response using an ocean ecosystem simulation resolving distinct phytoplankton thermal phenotypes. Resolving model analogs of thermal "generalists" and "specialists" (similar to those observed in G. huxleyi) resulted in a distinctive global biogeography of preferred thermal niche widths with a nonlinear latitudinal pattern. We leveraged the model output to predict the ranges of the 12 strains we studied in the laboratory and demonstrated how this approach could refine predictions of phytoplankton thermal geographic range in situ. Our combination of observed thermal traits and modeled biogeography highlights the capacity of diverse groups to persist through temperature shifts. Significance StatementIntraspecific diversity in the phytoplankton may underpin their distribution. We show that within a single coccolithophore species, thermal response curves have diverse trait parameters. For example, many strains had a variable range of temperatures at which they could survive (thermal niche width). Adding this thermal niche width diversity to an ecosystem model simulation impacted phytoplankton coexistence and overall biomass. These observations show that thermal niche width is a gap in phytoplankton representation in ecosystem models that impacts modeled phytoplankton biogeography and concomitant carbon cycle dynamics. Including thermal tolerance is crucial to predictive modeling as ocean temperature dynamics change.

ecology↗

bioRxiv2024

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

BackgroundProtists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the worlds best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last twenty years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community, and to hypothesize about their interactions with bacteria. ResultsBased on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Further, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g. ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. ConclusionsWe demonstrate that metagenomic sequence-based community analysis can complement existing eorts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes, and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

ecology↗

bioRxiv2023

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

Protists (microeukaryotes) are key contributors to marine carbon cycling, influencing the transfer of energy to higher trophic levels and the vertical movement of carbon to the ocean interior. Their physiology, ecology, and interactions with the chemical environment are still poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle (AUV) Clio, the microbial community along a 1,050 km transect in the western North Atlantic Ocean was surveyed at 10-200 m vertical depth increments to capture metabolic microeukaryote signatures spanning a gradient of oligotrophic, continental margin, and productive coastal ecosystems. Plankton biomass was collected along the surface of this transect and across depth features, and taxonomy and metabolic function were examined using a paired metatranscriptomic and metaproteomic approach. A shift in the microeukaryote community composition was observed from the euphotic zone through the mesopelagic and into the bathypelagic ocean. A diverse surface assemblage consisting of haptophytes, stramenopiles, dinoflagellates and ciliates was represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m depth, and fungal proteins emerging in waters >3,000 m depth. In the broad microeukaryote community, nitrogen stress biomarkers were found in productive coastal sites, with phosphorus stress biomarkers in offshore waters where Saharan dust input is thought to supply iron and nitrogen. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, macronutrients, and trace metals.

ecology↗

bioRxiv2023

Missing microbial eukaryotes and misleading meta-omic conclusions

Meta-omics has become commonplace in the study of microbial eukaryotes. The explosion of available data has inspired large-scale analyses, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. However, genome and transcriptome databases are prone to misannotation biases, and meta-omic inventories may have no recoverable taxonomic annotation for more than half of assembled contigs or predicted proteins. Direct mapping solely to organisms of interest might introduce a problematic misattribution bias, while full databases can annotate any cataloged organism but may be imbalanced between taxa. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We argue that ongoing curation of genetic resources is critical in accurately annotating protists in situ in meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem. We show that taxonomic membership of sequence clusters demonstrates more accurate estimated community composition than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and database selection and evaluation is a critical part of correctly annotating protistan taxonomy in environmental datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the critical importance of both database completeness and curation in enabling accurate environmental interpretation.

microbiology↗

bioRxiv2023

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

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{o}C for R. pomeroyi, 40{o}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.

microbiology↗

bioRxiv2022

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

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 communities of multiple species. Metatranscriptomics in particular offers an understanding of real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. However, these approaches are rarely validated. A systematic validation of metatranscriptome assembly and annotation methods is necessary to appropriately assess (1) the fidelity of our community composition measurements and (2) the confidence of novel taxonomic and functional content discovered with metatranscriptomics. Here, we present euk rhythmic, an automated and customizable multi-assembler workflow for eukaryotic metatranscriptome assembly, annotation, and analysis, and validate the ability of the pipeline to recapitulate simulated eukaryotic community-level expression data treated as a gold standard. Finally, we apply this pipeline to two previously published metatranscriptomic datasets, showing both recapitulation of previous results as well as enhanced taxonomic and functional gene discovery.

bioinformatics↗

bioRxiv2021

Estimating the maximal growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns

Microbial eukaryotes are ubiquitous in the environment and play important roles in key ecosystem processes, including accounting for a significant portion of global primary production. Yet, our tools for assessing the functional capabilities of eukaryotic microbes in the environment are quite limited because many microbes have yet to be grown in culture. Maximum growth rate is a fundamental parameter of microbial lifestyle that reveals important information about an organisms functional role in a community. We developed and validated a genomic estimator of maximum growth rate for eukaryotic microbes, enabling the assessment of growth potential for organisms and communities directly in the environment. We produced a database of over 700 maximum growth rate predictions from genomes, transcriptomes, and metagenome-assembled genomes. By comparing the maximal growth rates of existing culture collections with environmentally-derived genomes we found that, unlike for prokaryotes, culture collections of microbial eukaryotes are only minimally biased in terms of growth potential. We then extended our tool to make community-wide estimates of growth potential from over 500 marine metagenomes, mapping growth potential across the global oceans. We found that prokaryotic and eukaryotic communities have highly correlated growth potentials near the ocean surface, but there is no correlation in their genomic potentials deeper in the water column. This suggests that fast growing eukaryotes and prokaryotes thrive under similar conditions at the ocean surface, but that there is a decoupling of these communities as resources become scarce deeper in the water column.

microbiology↗

bioRxiv2021

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

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 not 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 datasets. 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 (0.8-2000{micro}m) 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 the known marine phylogenetic diversity through the increase in coverage of likely particle- and host-associated taxa. We also demonstrate an approach to infer the putative functional mode of the recovered eukaryotic MAGs. A global survey of the TOPAZ MAGs enabled the identification of ecological cohorts, driven by specific environmental factors, and putative host-microbe associations. ImportanceDespite the ecological importance of single-celled eukaryotic organisms in marine environments, the majority are difficult to cultivate in the lab. Sequencing genetic material extracted from environmental samples enables researchers to document naturally-occurring protistan communities. However, conventional sequencing methodologies cannot separate out the genomes of individual organisms. To more completely capture the entire genomic content of mixed protistan community, we can create bins of sequences that represent the same organism. We developed a pipeline that enables scientists to bin individual organisms out of metagenomic reads, and show results that provide exciting insights into what protistan communities are present in the ocean and what roles they play in the ecosystem. Here, a global survey of both eukaryotic and prokaryotic MAGs enabled the identification of ecological cohorts, driven by specific environmental factors, and putative host-microbe associations. Accessible and scalable computational tools, such as EukHeist, are likely to accelerate the identification of meaningful genetic signatures from large datasets, ultimately expanding the eukaryotic tree of life.

microbiology↗

bioRxiv2019

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

Despite growing evidence that climate change will increase temperature variability and the frequency of temperature extremes, many modeling studies that analyze the effects of warming scenarios on cyanobacteria in lakes examine uniform warming temperature scenarios without including any variability. Here, we used the one-dimensional hydrodynamic General Lake Model coupled to Aquatic EcoDynamics modules (GLM-AED) to simulate 11 years of nitrogen-fixing and non-nitrogen-fixing cyanobacterial biomass in Lake Mendota (Madison, WI, USA). We developed climate scenarios with either uniform (constant) warming or variable warming based on random sampling of daily air temperatures from either a normal or Poisson probability distribution. We found that while the median cyanobacterial biomass among repeated simulations for each of the years was similar regardless of whether or not air temperature variability was included in the climate scenarios, the randomly-sampled air temperature distribution scenarios exhibited much greater variability in the year-to-year cyanobacterial biomass estimates. Our results suggest that including temperature variability in climate scenarios may substantially change our understanding of how climate warming may alter cyanobacterial blooms over yearly to decadal time scales. To more effectively predict the range of possible future cyanobacterial dynamics, both the magnitude and variability of warming must be considered when developing climate scenarios for lake modeling studies.

ecology↗