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PubMed2025

Harnessing fern stress adaptations: From evolution and ecophysiology to molecular biology.

Ferns are the second most diverse vascular plant lineage after angiosperms and have been a key ecological component of Earth's biodiversity for more than 380 million years. Importantly, ferns are sister to seed plants, providing a critical outgroup for understanding the evolution of seed plant features. Ferns are remarkably resilient to abiotic and biotic stresses due to a long evolutionary history with adaptations to diverse habitats, stresses, and herbivores. As a result, ferns produce a multitude of secondary metabolites with unique bioactivities; these chemicals are potentially linked to the adaptation of ferns to herbivory, various abiotic and biotic stresses, and changing environments. Assembled reference genomes and the identification of key metabolic compounds of multiple ferns have already made significant contributions to human health and well-being. Here, we review the recent scientific advances in fern research, including evolution, stress resistance, metabolites and medicinal utilization, and comparative multi-omics applications. We propose that integrated investigations involving ecological, physiological, and molecular techniques will facilitate the future research translation of fern resources in diverse areas including soil remediation, biopesticides, and medicine. Advances in our understanding of fern molecular biology will provide new insights into the evolution of land plants and promote the utilization of ferns for heightened environmental restoration, crop protection and human health.

Ferns↗
PubMed2026

Marine Vibrio Biocatalysts as Unique Green Transformation (GX) Tools at the Time to Sustainable Development Goals (SDGs).

Vibrios have sustained various types of ocean ecosystems, being key players in marine mineral cycles and essential partners in specific groups of marine life. Observed genome plasticity and metabolic versatility are some of the unique biological features of vibrios, and these traits could contribute in expanding their ecological niche in marine environments. Vibrios are now recognized as ecophysiologically essential microbial species for our planet. At the time to "Sustainable Development Goals" (SDGs), their genome plasticity and metabolic versatility have also been studied with the aim of solving global issues such as energy production and plastic pollution by creating new microbial biocatalysts. Here, we introduce recent progress on the application of vibrios aiming towards green transformation (GX).

Vibrio↗
PubMed2025

Picocyanobacteria in the Chesapeake Bay: isolation, diversity, and adaptation.

Tiny unicellular cyanobacteria or picocyanobacteria (0.5-3 µm) are important due to their ecological significance. Chesapeake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria. Studies of Chesapeake Bay picocyanobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus. They laid the foundation for revealing the ecophysiology, biogeography, genomics, and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries. The Bay picocyanobacteria are known to better tolerate the changes in temperature, salinity, and heavy metals compared to their coastal and open-ocean counterparts. Many picocyanobacteria isolated from the Bay contain rich toxin-antitoxin (TA) genes, suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments. Distinct winter and summer picocyanobacteria are present in the Bay, suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary. While the Bay contains subcluster 5.2 Synechococcus, it also contains freshwater Synechococcus, Cyanobium, and marine Synechococcus due to river influx and the ocean's tidal influence. Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea, showing a link between the Bay and polar picocyanobacteria. Genomic sequences of estuarine picocyanobacteria provide new insight into the taxonomy and evolution of freshwater, estuarine, and marine unicellular cyanobacteria. Estuaries connect freshwater and marine ecosystems. This overview attempts to extend what we learned from Chesapeake Bay picocyanobacteria to picocyanobacteria in freshwater and marine waters.

Chesapeake Bay↗
PubMed2025

Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.

Lake ecosystems play a fundamental role in the global biogeochemical cycling of essential elements such as carbon, nitrogen, and phosphorus. Microorganisms within these ecosystems mediate key processes that regulate these cycles. Metagenomic analyses provide valuable insights into the taxonomic and functional diversity of microbial communities in various environments, including freshwater habitats. Here, we present a comprehensive metagenomic dataset derived from Lake Soyang, the largest freshwater reservoir in South Korea. A total of 28 metagenomes were generated from water samples collected across two distinct sampling periods: the first set (n = 8) was obtained between April 2014 and January 2015 from two depths (1 m and 50 m) in four different seasons, while the second set (n = 20) was collected between January 2019 and November 2019 from five depths (1, 10, 20, 40, and 90 m) over four seasons. Metagenomic sequencing yielded 9.3-21.8 Gbp per sample. This dataset provides a valuable resource for future studies exploring the ecophysiological characteristics of microbial communities in pelagic freshwater environments.

Republic of Korea↗
PubMed2026

Bacterial extracellular vesicles exhibit distinct functional potential across biogeographic provinces of the South Pacific Ocean.

Bacterial extracellular vesicles (BEVs) are nanoscale membranous structures released by diverse types of bacteria, and are capable of transporting and delivering biological compounds between cells. Experimental investigation of BEVs in laboratory model systems indicates that these nanoparticles may play a number of roles in the ecophysiology of marine bacterial communities, but their functional potential in the environment remains unclear. Here we describe the proteomic composition of BEV populations over more than 5000 nautical miles of surface waters in the South Pacific, linking BEV cargoes to the bacterial communities producing them. The presence of marine BEVs was consistently observed across a range of biogeochemical conditions, with an overall abundance comparable to that of bacterial cells (up to 108 BEVs L-1). The protein cargo of marine BEVs, however, differed significantly among ocean regions. The BEV populations were enriched in carbohydrate transporters under phytoplankton bloom conditions, and contained iron uptake-related proteins in nutrient-limited waters. These data suggest that BEVs could enable cells to perform key extracellular functions in the marine environment. Our observations highlight the ubiquity of marine BEVs and biogeographic patterns in their ecological potential across oceanic scales.

Extracellular Vesicles↗
PubMed2025

Climatic data sources and limitations of ecological niche models impact the estimations of historical ranges and niche overlaps in distantly related Korean salamanders.

BACKGROUND: Ecological niche models (ENMs) and analyses of niche overlap/divergence have become popular methods in ecology and evolutionary biology. These analyses rely on environmental data available from several databases. However, the influence of data sources on these analyses is rarely tested. Here, we test the impact of climatic data choice on the prediction of current and Plio-Pleistocene suitable habitats for two distantly related, but broadly sympatric, salamanders endemic to the Korean Peninsula. We ran MaxEnt separately on WorldClim and CHELSA climate data. We then hindcasted ENMs to five time periods of the Plio-Pleistocene, bracketing the estimated intraspecific divergence times for these species. We then quantified the differences in predictions between WorldClim- and CHELSA-based models. Also, given the sympatry and similar habitat requirements of the two species, we tested for niche overlaps using niche identity and background tests and tested the sensitivity of the results to climatic data choice. RESULTS: The ENMs successfully predicted contemporary suitable habitats for the two species. However, the predictions were highly sensitive to climatic data choice as well as variable combinations. The hindcasted ENMs produced contrasting predictions depending on the choice of climatic dataset and failed to predict suitable habitats for some Pleistocene time periods regardless of the climatic data choice. The niche analyses were also sensitive to climatic data choice, with results suggesting either niche overlaps or divergence depending on the climatic dataset used for the analyses. CONCLUSIONS: Our study highlights the influence of climatic data choice on the outcomes of ENMs and niche analyses. Our results also underscore the limitations of macroclimate-based ENMs, especially when the species is likely buffered from macroclimatic changes by microhabitat. We argue for the need for additional ecological, ecophysiological, and population genomic studies to better understand the range formation of these enigmatic species.

Animals↗
PubMed2026

Quantifying the Evolutionary Potential for Delta Smelt Persistence in a Warming Habitat.

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature. Using a pedigree and whole genome sequencing data, we characterized the genetic basis of CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size and degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait. We observed modest heritability for CTMax at rearing temperatures of 15°C and 18°C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (i.e., many loci detected with a GxE effect). This temperature-dependent genomic architecture is consistent with our finding that additive genetic variation for CTMax was reduced under warmer rearing conditions, indicating a potential constraint on adaptive evolutionary change. The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for captive management and may inform supplementation of fish to the wild in an ever-warming environment.

conservation physiology↗
PubMed2026

Quantifying the evolutionary potential for Delta Smelt persistence in a warming habitat.

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature, which will be important to maintain for their persistence in a rapidly warming future. Using a pedigree and whole genome sequencing data, we characterized the genetic variation and genomic architecture for CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size, degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait, which could constrain adaptation under thermal stress. We found that larger fish had reduced CTMax, although this effect was diminished at elevated temperatures. We observed modest heritability for CTMax at rearing temperatures of 15°C and 18°C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (many loci detected with a GxE effect). The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for refuge management and may inform supplementation in an ever-warming environment.

conservation physiology↗