Global warming and extreme weather events have been linked to a rise in cyanobacterial blooms, which threaten water quality and ecosystem services. However, during an extreme hot and dry summer, Microcystis was outcompeted by a dinoflagellate, Naiadinium polonicum, in a drinking water lake in southern Sweden. Surface water temperatures were particularly high in May and July, peaking at 18.7 and 24.3°C, respectively. A 3-year field study of the lake further revealed surface water temperature to be a strong predictor of N. polonicum biomass, but not Microcystis biomass. To investigate the mechanisms underlying the success of N. polonicum over Microcystis in 2018, we examined the direct effects of temperature on the recruitment and growth rates of both species. Recruitment experiments were conducted using lake sediments containing resting stages, while growth rate experiments used strains of both species isolated from the lake. Recruitment of N. polonicum was temperature dependent, declining at temperatures above 12°C, whereas its growth rate peaked at 20°C. In contrast, Microcystis recruitment was unaffected by temperature, with optimal growth at the highest temperature used in this study, 28°C. We conclude that the extreme heatwave acted as an "early spring," advancing the recruitment window for N. polonicum but not for Microcystis. This shift in timing gave the slower-growing dinoflagellate a crucial head start, allowing it to accumulate biomass and dominate the community before peak summer temperatures set in. These findings highlight how climate-induced shifts in temperature regimes can restructure phytoplankton communities, altering bloom dynamics in unpredictable ways.
The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes.
Mallomonas is among the most diverse genera of Chrysophyceae, yet many of its lineages remain taxonomically unresolved due to limited molecular sampling. Mallomonas series Peronoides, historically limited to four species, has posed persistent taxonomic difficulties, most notably the long-standing and problematic reliance on a rare hemispherical structure to distinguish M. bangladeshica from M. peroneides. Here, we present a comprehensive revision of Mallomonas section Peroneides stat. nov., formerly treated as ser. Peronoides, that integrates detailed morphological analyses with a five-gene phylogeny. Thirty-one strains isolated from 15 freshwater sites across five countries resolved into seven well-supported clades based on the nuclear ribosomal internal transcribed spacer (ITS) DNA region. Four corresponded to previously described species (M. bangladeshica, M. ceylanica, M. peroneides, M. stellata), whereas three represente novel taxa: M. cotyloides sp. nov., M. neotropica sp. nov., and M. palmata sp. nov. Morphological reassessment, including original iconotypes, identified reliable diagnostic characters in scale architecture; secondary layer distribution; and experimentally confirmed, temperature-dependent formation of the hemispherical structure. Phylogenetic analyses revealed two deeply divergent lineages within the section, reflecting distinct evolutionary trajectories in central depression morphology and scale diversification. Biogeographic and ecological data indicated a primary association with warm, humic freshwater habitats, although several taxa tolerate markedly cooler conditions. Together, these results refine species boundaries, resolve long-standing taxonomic ambiguities, and establish a robust framework for future taxonomic, phylogenetic, and ecological research on Mallomonas.
Nannochloropsis microalgae are widely recognized as sustainable cell factories for producing nutritional oils and biofuels due to their high-lipid content. However, a comprehensive understanding of the genetic basis of their oleaginous traits across diverse species has been limited. Here, we constructed a pan-genome of 17 Nannochloropsis species comprising 14,851 gene families. Our analysis defined a distinct genetic architecture for lipid metabolism: Gene families associated with vesicular transport formed a conserved core functional module, whereas the genetic collection for lipid metabolism showed greater plasticity and was primarily classified as part of the soft-core genome. This finding establishes a genetic blueprint for the coevolution between a stable cellular "logistics network" and an adaptable "biosynthetic factory." Evolutionary analysis further indicated that the DGAT and fatty acid desaturase families have species-specific expansions in Nannochloropsis, suggesting a potential role in enhancing lipid accumulation. By integrating 231 transcriptome datasets, we identified key genes (ACP2 and DGAT2) that were highly upregulated under nitrogen deprivation and pinpointed a set of core genes with high expression levels involved in vesicular transport. This "Infrastructure-Toolkit" model provides both genetic targets for strain improvement and a broader framework for understanding lipid accumulation in oleaginous microorganisms.
Sugar kelp (Saccharina latissima; order Laminariales) plays a vital role in kelp forest ecosystems, as well as an expanding kelp aquaculture industry, in the Gulf of Maine, United States. However, ocean warming is eroding the resilience of Maine's kelp forests and may be compromising their local genetic diversity, with impacts on population structure and gene flow. Here, we used genome-wide single nucleotide polymorphism (SNP) data to assess the genetic diversity, structure, and connectivity of S. latissima populations at 11 outer coastal sites spanning the historical range of kelp forests in Maine. Our analyses identified moderate genetic diversity and limited inbreeding within sites (average heterozygosity: 0.27). Further, they revealed that three clusters comprising four genetically distinct populations exist across the study region. Population structure was strongly associated with geographic distance and oceanographic features, as supported by principal coordinate analysis, FST calculations, Bayesian clustering, and spore dispersal modeling. Lastly, our outlier analysis identified genes potentially under selection. Thus, our findings highlight distinct, genetically unique kelp populations along Maine's coast and emphasize the need for regional management strategies that support both ecosystem resilience and sustainable aquaculture under climate change.
Recent studies sequencing algal type specimens, particularly in the green seaweed genus Ulva, have resolved longstanding nomenclatural uncertainties but have also triggered extensive name changes through the strict application of the principle of priority. Because the identity of a taxon name, for example, the name of a species, is ultimately determined by its nomenclatural type, sequencing type specimens can provide a powerful means to connect historical names with contemporary molecular species concepts. However, we argue that comprehensive type sequencing is unlikely to provide a practical or lasting route to nomenclatural stability across algae. The large backlog of historical names, the continuing description of new taxa, changing species concepts, and substantial technical and logistical challenges associated with sequencing historical material suggest that a complete sequence-based nomenclatural framework will remain difficult to achieve. In addition, repeated nomenclatural changes may reduce the accessibility and usability of accumulated biological knowledge for both specialists and non-specialists. Here, we invite the phycological community to reflect on the balance of taxonomic accuracy, scientific progress, and nomenclatural stability. We discuss the benefits and drawbacks of alternative mechanisms already available under the International Code of Nomenclature, including epitypification and conservation of names, and highlight the concept of protection, currently available for fungi, as potential approaches to promote nomenclatural stability in algae.
The availability of easy-to-measure and inexpensive biomarkers is a challenge for monitoring environmental stress in organisms. Although it has been proposed that non-directional deviations from a symmetrical pattern in morphological traits (called fluctuating asymmetry. FA) may be directly related to environmental stress, this postulate has been questioned. Self-similarity symmetry (fractal) is one possible approach to addressing FA analysis, but there are very few studies with this approach, and the results have been inconclusive. Here, we evaluate whether fractal descriptors of thallus morphology in the habitat-forming fucoid Fucus limitaneus reflect environmental stress across multiple contexts, including seasonal variation, vertical gradients in the intertidal zone, and the possible long-term impact of an invasive species. Our results show that fractal metrics did not vary consistently across these contrasting environmental conditions, suggesting that in this system, FA based on fractal geometry does not reliably track environmental stress. This is possibly because stress is expressed through alternative ecological and biomechanical processes rather than through modifications of thallus self-similarity.
Cyanobacterial harmful algal blooms (cHABs) are increasingly frequent and severe globally. Recently, the St. Louis River Estuary (SLRE) has experienced numerous cHABs, but the locations, timing, and environmental conditions associated with them are unknown. We first investigated environmental predictors of cyanobacteria through a multifaceted approach, highlighting key relationships to understand past cHABs, and then performed a detailed spatiotemporal redundancy analysis of sampling data to optimize site selection and sampling frequency for future monitoring. We employed an oversampling approach over 2 years at eight spatially heterogeneous stations. Random forest analysis paired with constrained ordination indicated that warm, late-summer temperatures were an important predictor of cyanobacterial abundance (biovolume), and drought-mediated stoichiometric nitrogen limitation may have facilitated dominance by diazotrophic cyanobacteria in 2023. Temporal redundancy analysis revealed no ideal sampling frequency, but late summer, weekly sampling, and as-needed bloom response collections were deemed critical for tracking cHABs. A 30- to 40-day lag effect between water temperature and cyanobacterial abundance suggested temperature as an early warning predictor of summer bloom intensity. Water quality was more spatially heterogeneous than phytoplankton communities, informing future monitoring site selection designed to comprehensively capture water quality variability and minimize phytoplankton community redundancy while prioritizing sites with past blooms. Our findings inform an optimized monitoring program for the SLRE and demonstrate a feasible monitoring optimization approach that could be developed and applied elsewhere to track risks from cHABs and other stressors.
Genome size varies tremendously across eukaryotes, which often contain far more DNA than expected from their biological complexity. To explain this paradox, selection-based hypotheses propose that genome size evolves through selection acting on life-history traits correlated with the phenotypic effects, independent of its genic content. To test the association between genome size and resting cyst size-a structure with morphology that may reflect overall body size-we selected chrysophyte algae (Chrysophyceae) producing siliceous stomatocysts as a model. In this study, we obtained and identified 85 chrysophyte strains representing 31 Mallomonas species using nuclear ITS rDNA region barcoding and estimated their genome sizes using propidium iodide flow cytometry. Within this genus, we observed more than a 75-fold variation in genome size (0.15-11.25 pg) and frequent substantial intraspecific variation, in some cases consistent with whole-genome doubling (polyploidization). By summarizing the published genome size records, adding our new measurements and combining them with published cyst sizes, we assembled a data set for 54 chrysophyte species to examine the relationship between genome size and cyst volume. Linear regression on log-transformed data revealed a strong positive correlation ( R adj 2 = 0.626, p < 0.001), showing that species with larger genomes tend to produce larger stomatocysts. In chrysophytes, this relationship is considerably stronger than the widely documented genome size-cell size correlation observed across eukaryotes. Our findings suggest that stomatocyst size is a more informative predictor of genome size in this group and highlight the potential for using stomatocyst sizes to infer ancestral genome sizes from the fossil record.
Organelle genomes offer a powerful tool for red algal evolutionary studies. Although the number of Rhodophyta genomes has increased substantially over the past 2 decades, only two mitochondrial genomes have been reported for the red algal order Thoreales. In this study, we generated 10 new complete mitochondrial genomes of Thoreales, representing the order's two genera and eight species, which, combined with additional mitogenomes of related orders of the subclass Nemaliophycidae, resulted in a comprehensive dataset of 20 mitogenomes. Thoreales mitogenomes exhibited little variation, ranging in length from 25,022 bp to 26,369 bp, with GC content from 25.6% to 28.3%, gene numbers from 46 to 54, and protein-coding genes from 21 to 25. Four genes were missing in one or more species (atp4, rpl20, sdh2, and sdh4), and no introns were detected. Synteny among members of Thoreales was highly conserved and similar to other orders of Nemaliophycidae. Phylogenomic analyses strongly supported the monophyly of Thoreales within Nemaliophycidae. Within the order, Nemalionopsis and Thorea as well as the relationship among the species received full support. Nemalionopsis shawii and N. parkeri formed an early-diverging clade that was sister to Thorea, which had species that resolved into two distinct lineages lacking evident geographic or morphological differentiation. By expanding the available dataset from two to 10 mitogenomes, this study provides a broad organellar perspective on Thoreales evolution, contributing to new insights into the systematics and diversification of freshwater red algae and, potentially, for clarifying inter-ordinal relationships within Nemaliophycidae.
Abstract Morphological identification of macroalgae can be time‐consuming and species may be difficult to observe, collect, or identify, preventing detailed study on the distribution and ecology of many species. The use of eDNA in species surveillance and biodiversity assessments has gained considerable traction in studying macroalgae, as it provides an opportunity for increased sampling efficiency and a reduced reliance on taxonomic expertise for morphological identification. However, it is crucial to understand how eDNA tools may bias results of species diversity and detection and how these biases differ from traditional morphological surveys. The present study compared species composition and detection rates of dive quadrat collections with a combination of morphological identification and DNA barcoding (i.e., traditional survey methods) to two types of eDNA tools: quantitative polymerase chain reaction (qPCR) using four species‐specific qPCR assays and metabarcoding using two metabarcoding markers. Metabarcoding detected nearly two times more species than traditional surveys; however, species overlap was as low as 19.2%, and some large conspicuous and ecologically important macroalgae were not detected by metabarcoding. This result suggests that metabarcoding uncovers a host of taxa largely distinct from dive surveys. Metabarcoding and qPCR proved capable of detecting target species even at very low abundances, but both showed a high incidence of false negatives. Results presented here support a combined approach leveraging the considerable strengths of eDNA in concert with species validation and abundance metrics provided by tradtional surveys.
The cyanobacterial genus Lyngbya was once thought to be a cosmopolitan genus, inhabiting nearly every biome across the globe. However, utilization of genetic, and more recently genomic, sequencing has revealed that this morphologically homogenous taxon in fact comprises distinct evolutionary clades, leading to the plethora of newly described Cyanobacterial genera split from Lyngbya. Despite this, no comparisons can be made to L. confervoides, and thus begging the question: who is Lyngbya? To answer this, we collected cyanobacterial tufts from intertidal pools in Cádiz, Spain, in line with the original descriptions of L. confervoides from Agardh and Gomont. Morphological and genetic characterization were conducted on two Lyngbya-like strains isolated from the type location. We identified strain BLCC-M349 to match the original description and iconograph, thereby designating it as the epitype of L. confervoides with BLCC-M349 serving as the reference strain. The descriptions of both Lyngbya and L. confervoides are emended and sequences of the 16S rRNA gene, the 16S-23S ITS rRNA region, and the genome are provided. Additionally, we describe a novel species of Okeania as well as synonymize select species of Capilliphycus to Lyngbya.
Neoporphyra haitanensis and Neopyropia yezoensis are two economically important seaweeds in Asia, yet their germplasm identification is often hindered by high phenotypic plasticity and limited molecular resources. To address this, we utilized a genome skimming strategy on five No. haitanensis and two Ny. yezoensis cultivars to retrieve their plastome information (including whole plastome sequences, plastome-divergent hotspots, and plastome-derived SSRs) and to identify genome-wide polymorphic nuclear SSRs. The plastomes of No. haitanensis (201,110-201,310 bp) were markedly larger than those of Ny. yezoensis (191,974 bp), a difference largely driven by expansions in intergenic regions. Gene annotation identified 253 genes in No. haitanensis and 256 in Ny. yezoensis, with the latter uniquely containing two additional hypothetical ORFs (ORF33 and ORF35) and an extra rRNA gene (rrfB). Further comparative analysis revealed seven hypervariable regions (π > 0.1), five of which-apcE-tatC, psbW-trnR, psbX-accD, trnW-rpl11, and ycf32-rpl32-are intergenic spacers with strong potential as species-discriminatory barcodes. We also characterized 26-30 chloroplast-derived SSRs and identified notable interspecific variations in their repeat-type profiles. Importantly, we developed 230 and 505 high-quality polymorphic nuclear SSRs for No. haitanensis and Ny. yezoensis, respectively, predominantly trinucleotide repeats, offering a robust toolset for fine-scale genetic analyses. Phylogenetic reconstruction using 201 shared plastid protein-coding genes clearly separated the two species into distinct clades, supporting their independent evolutionary trajectories, and further revealed intraspecific genetic differentiation, particularly with the cultivar ZD-1 forming a distinct branch within No. haitanensis. This study provides comprehensive genomic resources-including complete plastomes, hypervariable regions, and polymorphic SSR markers-that will facilitate germplasm identification, phylogenetic studies, and molecular breeding in Porphyra sensu lato.
In the open ocean, extremely low iron (Fe) concentrations limit the growth of marine phytoplankton. To cope with Fe scarcity and its diverse chemical forms in seawater, phytoplankton have evolved distinct uptake strategies. Here, we compared two low-Fe-adapted diatoms, Thalassiosira oceanica and Phaeodactylum tricornutum, to assess the bioavailability of unchelated Fe and siderophore-bound forms, as well as their underlying Fe-uptake strategies. Growth inhibition assays with bathophenanthroline disulfonic acid (BPDS) indicated that both species acquired unchelated Fe at environmentally relevant concentrations by reductive pathways in which Fe(III) was reduced to Fe(II) prior to internalization. In contrast, their responses to hydroxamate siderophores, desferrioxamine B (DFB) and ferrichrome (FCH), diverged: P. tricornutum maintained substantial growth and Fe-uptake rates when reductive pathways were inhibited, consistent with a receptor-mediated non-reductive Fe-uptake pathway, whereas T. oceanica relied predominantly on reductive processes and transported FeDFB and FeFCH at much lower rates. These differences suggest that P. tricornutum may gain a competitive advantage in hydroxamate siderophore-rich waters. Overall, the diverse Fe-acquisition strategies among marine phytoplankton may determine their ecological success and spatial distribution in the ocean.
The genus Cladophora (Cladophorales, Ulvophyceae) has a long history of taxonomic challenges due to morphological plasticity and incongruence between traditional classifications and molecular phylogenies. Here, we propose Mysticladia gen. nov. to accommodate species previously assigned to Cladophora but phylogenetically placed within the Siphonocladus clade. Analyses of concatenated SSU + LSU rDNA gene sequences from specimens collected along the Brazilian coast revealed that populations morphologically identified as C. prolifera and C. aokii form a distinct and phylogenetically distant clade from Cladophora sensu stricto. Genetic divergence and morphological comparisons supported the recognition of two new cryptic species: Mysticladia nigra sp. nov. and M. edisonii sp. nov. Both seemingly restricted to the southwestern Atlantic. These species are morphologically indistinguishable from their closest relatives but distinguishable by DNA sequences. Additionally, we transfer C. prolifera, C. aokii, and C. coelothrix to Mysticladia. Our findings broaden the widespread cryptic diversity within the Cladophorales and emphasize the critical need for molecular analyses across populations in this group, including those already and correctly identified based on morphology alone. Such efforts are essential for elucidating cryptic lineages and species boundaries in simple filamentous green algae, where phenotypic plasticity often disguises true evolutionary relationships.
Non-geniculate coralline genus Harveylithon includes 12 species worldwide. In this study, we propose three new species, Ha. koreanum sp. nov., Ha. longiforme sp. nov., and Ha. planiforme sp. nov., based on integrative molecular and morphological analyses. These three new species share the diagnostic morphological characters of Harveylithon, including a monomerous, non-coaxial thallus construction with perithallial cells oriented perpendicularly to the surface; a hypothallial layer composed of rectangular cells aligned parallel to the substratum; and the presence of trichocytes occurring singly, in pairs, or in clusters. Our phylogenetic analyses of a concatenated four-gene data set (COI + rbcL + psbA + SSU rRNA) clearly resolved the three new species within Harveylithon, each forming a well-supported and distinct lineage. The topologies of the individual-gene phylogenies based on the psbA and the SSU rRNA genes were largely congruent and supported these relationships, whereas phylogenetic trees based on the rbcL and COI genes did not recover Harveylithon as monophyletic, with Dawsoniolithon species nested within the Harveylithon clade. Interspecific sequence divergences between new species and their congeners were 6.3%-13.7% for the COI gene, 0.8%-9.8% for the psbA gene, and 1.8%-14.6% for the rbcL gene. Harveylithon koreanum sp. nov. and Ha. planiforme sp. nov. are currently known from only Jeju Island in Korea, whereas Ha. longiforme sp. nov. was identified from both Jeju Island, Korea, and India, indicating that it may have a broad Indo-Pacific distribution. In addition, we newly generated the psbA gene sequence from the generitype, Ha. rupestre (TRH A3-149) and incorporated it into our molecular data set to stabilize the phylogenetic circumscription of the genus.
Protists are the main consumers of phytoplankton in the marine environment, playing pivotal roles in the carbon cycle and nutrient regeneration. Heterotrophic dinoflagellates, which have been extensively studied, are the linking hubs for microbial food loops and classical food chains. In particular, Oxyrrhis marina has been used as a model predator in laboratory studies. Designed experiments were conducted to explore the effects of biological factors (prey type, particle size) and abiotic factors (temperature, nutrient limitation) on its growth and ingestion. Oxyrrhis marina had the ability to consume various algae, including Chromalveolata, Haptophyta, Chlorophyta, Bacillariophyta, and Ochrophyta. When prey had diameters ranging from 7.4 to 13 μm, O. marina exhibited the highest ingestion rates, growth rates, and cell volume. With increases in temperature, the ingestion rate, growth rate, and productivity of O. marina increased significantly, but the cell volume decreased dramatically. Compared to ingesting phosphorus-restricted prey, ingesting nitrogen-restricted prey significantly increased the ingestion rate, growth rate, and cell volume of O. marina. Nitrogen-restricted (phosphorus-restricted) O. marina preferred to select prey that contained more nitrogen (phosphorus) elements to regulate nutritional imbalance. The purpose of this study is to provide a theoretical foundation for understanding the selective ingestion of the heterotrophic dinoflagellate O. marina and its impact on the community structure of plankton.
The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.
The kelp populations of two cryptic species of Lessonia inhabiting the intertidal zone of the southeastern Pacific are vulnerable to local extinction and range contraction by being exposed to large-scale thermal extremes and strong harvesting by artisanal fisheries. Our study explored the effect of variable ocean temperature conditions on the germination of spores, a critical stage for post-disturbance persistence of local populations, including harvesting. Over a 15-month experimental period, we collected reproductive tissues from 10 tagged sporophytes of a wild local population of L. spicata in Central Chile (~33.5° S) and measured germination success. Reproductive activity closely tracked the presence of low (<14°C) ocean temperatures at the study site. Mean spore germination was over 80% from late Austral fall to late spring and sharply declined and became more variable under the warmer ocean conditions of summer and early fall. Unexpectedly, a mid-summer mesoscale upwelling event cooled seawater below 14°C, and spore germination success increased from <50% to up to 90%. Across the study period, germination showed a significant negative correlation with seawater temperature, down to a lag of 4 days prior to the collection of reproductive tissue. These results suggest both a temperature threshold and a temporal scale for spore priming in L. spicata, providing support to earlier hypotheses positing spatial heterogeneity in the upwelling regime as the leading driver of speciation in the Lessonia complex. Together, our results provide an important evolutionary insight for the conservation, restocking, and management of the Lessonia complex.
The division Rhodophyta (red algae) includes an inconspicuous and often overlooked component of benthic freshwater biota. In many cases, freshwater red algae are considered indicators of good ecological status, yet their environmental preferences remain poorly understood. Species richness is low globally, and the distribution of many taxa remains poorly known. Here, we report the occurrence of 12 taxa of benthic red algae in 272 Estonian streams, based on 734 sampling sites and 1263 sampling occasions. The aim of this study is to identify the key environmental drivers of freshwater red algae occurrence and to evaluate their potential as indicators of water quality. Red algae were recorded in 20% of the samples. The influence of 37 environmental variables on the occurrence of red algae was assessed using machine-learning algorithms (random forest and gradient boosting trees). Hydrological and hydrochemical variables were by far the most important variable groups, followed by bottom substrate, watershed land cover and land use, and geological bedrock type. Among the hydrochemical variables, biological oxygen demand was the single most important predictor, indicating a high sensitivity of freshwater red algae to labile organic pollution. In contrast, the effect sizes of mineral and total nutrients were lower and more nuanced, suggesting that freshwater red algae are not particularly sensitive indicators of eutrophication. Some division-level responses may have been obscured by contrasting species-specific patterns. Species-level effects were often difficult to verify using machine-learning approaches due to low occurrence frequencies.
