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bioRxiv2024

Degradation of organic matter by ecologically distinct microbiomes uniformly promotes plant growth

In this study, we explore the relationship between ecologically distinct soil microbiomes and their role in plant growth promotion through organic matter (OM) decomposition. Using a controlled experimental system, we tested whether living microbiomes from geographically and ecologically distinct environments impact plant biomass when provided with OM in the form of dried, ground leaves. Results showed a consistent threefold increase in plant biomass when a living microbiome and organic matter were present, regardless of the microbiomes origin, which included agricultural fields, desert soil, and pine-oak forest soil, municipal compost, and the microbiome on unautoclaved organic matter. Bacterial community profiling based on 16S amplicon sequencing revealed genera, e.g. Massilia, that were significantly associated with decomposition and subsequent plant growth promotion. This suggests a conserved functional capacity for organic matter decomposition across diverse microbiomes, likely due to evolutionary pressures to efficiently break down plant material for nutrient acquisition. The study provides a framework for further investigation into microbial consortia that enhance plant growth via decomposition, offering a robust experimental system to identify microbes and microbial processes that could be harnessed to improve nutrient uptake from organic inputs like cover crops.

microbiology↗

bioRxiv2024

Comparative genomic insight into the myxobacterial carbohydrate-degrading potential and their ecological impact.

Myxobacteria are an intriguing group of social-behavior-depicting microbes with unique physiological characteristics such as fruiting body formation, gliding motility, and predation, encompassing the largest genomes (>9 Mb) within the Eubacteria kingdom. These soil-dwelling organisms are crucial for lignocellulosic biomass degradation, which has both ecological and industrial significance. While previous studies have demonstrated polysaccharide deconstruction abilities in a few myxobacterial species, we aim to elucidate the distribution of their Carbohydrate Active Enzymes (CAZymes) domains per organism, with a focus on proteins involved in the catabolism of critical polysaccharides such as cellulose, lignin, xylan, starch, pectin, fructan, chitin, and dextran, across 61 high-quality sequenced myxobacterial genomes. Our findings reveal that 3.5% of the total genes at the median level have domains related to CAZyme functions across different myxobacterial families. Notably, family Archangiaceae (4.4%) and Myxococcaceae (3.7%) members exhibit the most significant genomic diversity and potential for degrading multiple substrates within lignocellulosic biomass. These plentiful CAZymes probably enable these majorly soil-harboring myxobacteria to break down various carbohydrate substrates into simpler biological molecules, which not only allow these organisms to sustain in poor-nutrient environments but also enable them to be critical players in carbon cycling and organic matter decomposition. We conclude that myxobacteria have an unexplored genomic potential that may play an integral role in the degradation of recalcitrant plant biomass, potentially influencing soil health and composition. This study further suggests the critical ecological importance of these CAZymes in sustaining the balance of terrestrial ecosystems and diverse industrial applications. ImportancePolysaccharides are the most abundant polymers making up the Earths biomass. Polysaccharide degradation is well-known to be carried out by diverse microorganisms; however, there is more to be explored concerning the novel organisms that can degrade these biomolecules efficiently along with understanding the newer mechanisms and reactions carried out in this process. Soil-dwelling myxobacteria, model organisms for our study, are unique and under-studied social-behavior-depicting microbes. In this research, we investigated their genetic potential to encode carbohydrate-active enzymes involved in breaking down various substrates, including lignocellulosic biomass which is predominantly present in their habitat. We further emphasized their potential to be utilized in industrial applications amongst the paper-pulp, food-beverage, textile, and biofuel industries.

microbiology↗

bioRxiv2024

Joint consideration of selection and microbial generation count provides unique insights into evolutionary and ecological dynamics of holobionts

The relationship between, and joint selection on, a host and its microbes - the holobiont - can impact evolutionary and ecological outcomes of the host and its microbial community. Here we present a novel agent-based modelling framework for understanding the ecological dynamics of hosts and their microbiomes. Our model explicitly incorporates numerous microbial generations per host generation allowing for selection on both host and microbe. We apply our model to explore community fitness and diversity in the face of rapid environmental change. We demonstrate that multiple microbial generations can buffer changes experienced across host lifetimes by smoothing environmental transitions. Our simulations reveal that microbial fitness and host fitness may be at odds with each other when considering the impact of vertical inheritance of microbial communities from a host to its offspring - where high values favour microbial fitness, while low values favour host fitness - these tradeoffs are minimized when microbial generation count per host generation is high. We suggest that these results arise from cross-generational priority effects which maintain diversity within the community and can subsequently be acted upon by selection. Our model is readily extensible into new areas of holobiont research and provides novel insights into holobiont evolution under variable environmental conditions.

microbiology↗

bioRxiv2024

Spruce hybrids show superior cumulative growth and intermediate response to climate anomalies, as compared to their ecologically divergent parental species

Climate change brings new constraints to which trees will have to adapt, including more frequent weather extremes. Black spruce and red spruce are phylogenetically close but adapted to different ecological conditions, and they form a natural hybrid zone where their distributions come into contact. Thus, they represent an interesting model to study the effect of introgressive hybridization in the context of climate change, given that interspecific gene flow could affect their capacity to adapt where their natural distributions overlap. Using a common-garden field test gathering 20-year-old progeny trees resulting from rigorous controlled crosses including previously verified genetic identity of the parents, growth patterns and wood density differences could be observed between species and between them and their F1 hybrids. A dendroecological analytical approach relying on wood cores was used and revealed similar wood responses to climatic variations between species, both through lifetime climate sensitivity and through episodic stress response indexes. They were however differentially expressed in early- and latewood between black spruce and red spruce, differences likely driven by diverging cambial phenology adaptations to different growing season lengths. F1 hybrids exhibited hybrid vigor for cumulative growth under the test site conditions, but showed intermediate values for traits related to climate response. These results offer new perspectives for understanding the dynamics of adaptation in hybrid zones in the context of climate change, as well as for guiding conservation and genetic improvement efforts. HighlightsO_LIF1 cumulative growth is higher than their ecologically contrasted parents. C_LIO_LIHybrids had intermediate climate responses C_LIO_LIParental species responded similarly to climate anomalies, but in various intra-ring part. C_LIO_LICambial phenology likely drives divergences in wood reaction to climate anomalies C_LI

plant biology↗

bioRxiv2024

Global Biogeography of Prokaryotes in Mangrove Sediments: Spatial Patterns and Ecological Insights from 16S rDNA Metabarcoding

The global asymmetry in the floristic diversity distribution within mangrove ecosystems is well-documented. However, sediment microbial communities, which play crucial ecological roles, are often overlooked in mangrove biogeography studies. This study aimed to investigate the diversity, composition, and distribution of prokaryotic communities across distinct mangrove bioregions (12 countries and territories from the Caribbean bioregion, Southeast America, East Africa, Indo-Malaysia and Australasia). We conducted a meta-analysis by compiling 16S rDNA datasets from 17 previous studies (540 samples) over a six year period (2014-2020) and applied community ecology analyses combined with random forest models. Although no significant correlation was observed between tree richness and microbial diversity, a microbial hotspot was identified in the Indo-West Pacific region. Microbiota associated with different mangroves displayed opposite latitudinal diversity gradients and beta-dispersions. Distance-decay relationships were weak but statistically significant. Random forest models identified key microbial taxa, and the OTUs shared across all bioregions suggested the presence of a potential core mangrove microbiota. Taxonomic and statistical analyses underscored the great heterogeneity of microbiota composition, heavily influenced by the study (e.g., molecular and bioinformatic methodologies). Future research on mangrove microbiome would benefit from standardized sampling and sequencing methods. Despite current limitations, distance-decay relationship confirmed the influence of dispersal barriers for mangrove sediment microbiota. This study also suggests that environmental factors, rather than plant diversity alone, may play a prominent role in shaping the diversity, composition and distribution of prokaryotic communities in mangrove sediments.

microbiology↗

bioRxiv2025

Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy

Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids are poorly understood. To address this problem, we compared the fitness effects of chromosomal and plasmid genes in the plant symbiont Rhizobium leguminosarum. Here we show that plasmids are depleted in beneficial genes compared to the chromosome, and this effect is stronger for ancient plasmids compared to recently acquired plasmids. These findings support the hypothesis that evolution drives beneficial genes to become localized to the bacterial chromosome, resulting in a gradual decay in the ecological value of plasmids. These findings question the ecological importance of plasmids and highlight the challenge of understanding how plasmids persist over the long term.

evolutionary biology↗

bioRxiv2025

Comprehensive phylogenetic reconstructions support ancestral omnivory in the ecologically diverse bat family Phyllostomidae

Adaptive radiations often occur with an early burst of ecological diversification, which requires not only various available niches but also a generalist ancestor with wide ecological niche breadths. However, ancestral generalism remains hard to test in empirical cases. The New World leaf-nosed bats (family Phyllostomidae) represent an unparalleled mammalian adaptive radiation with diverse dietary niches including arthropods, blood, terrestrial vertebrates, nectar, and fruits. However, when and how often phyllostomid bats transitioned from insectivory to fruit or nectar feeding remains unclear. Here we tested the hypotheses of ancestral insectivory versus ancestral omnivory in Phyllostomidae (141 species) using improved trait reconstructions based on multi-response phylogenetic threshold models, while explicitly accounting for phylogenetic uncertainty. Our results indicate that complementary fruit feeding has fully evolved at the early burst of the phyllostomid radiation and started to evolve in the most recent common ancestor of the family, supporting the ancestral omnivory hypothesis. In addition, fruit feeding probably evolved before nectar eating in Phyllostomidae, in contrast to the claims of previous studies. Extending this analysis to all bat families (621 species) reveals independent evolution of ancestral fruit feeding in four families, namely the Pteropodidae (Old World fruit bats) and three families from the Noctilionoidea superfamily. Despite the ancestral omnivory of these fruit-eating families, only Phyllostomidae and Pteropodidae show high species diversity and evolved predominant and strict fruit feeding. Therefore, our results reveal that ancestral generalism (i.e., omnivory) may be a precondition of but does not necessarily lead to adaptive radiations which also require subsequent niche partitioning and speciation.

evolutionary biology↗

bioRxiv2025

Ecology and sexual conflict drive the macroevolutionary dynamics of female-limited colour polymorphisms

Sexual conflict over mating has been documented in many species, both in the field and in experimental studies. In pond damselflies (family Coenagrionidae), sexual conflict maintains female-limited colour poly-morphisms, with one female morph typically being a male mimic. However, it is not known whether sexual conflict can also explain the evolutionary origin of novel female morphs, and if so, what ecological factors play a role in this macroevolutionary transition, by modulating the strength of the conflict. Furthermore, the effects of sexual conflict on phylogenetic diversification remain controversial, with studies arguing that the evolution of alternative reproductive morphs, such as female-limited colour morphs, could either hinder or accelerate speciation. Here, we use phylogenetic comparative methods to show that female colour polymorphisms are more likely to evolve when population densities at breeding sites are high, and that these demographic conditions are more common at high latitudes and in open landscapes. We show that female-limited polymorphisms typically evolve from sexually dimorphic ancestors through the addition of a male-like female morph, consistent with the hypothesis of selection for male mimicry. Female polymorphic and sexually dimorphic lineages diversify at a higher rate than sexually monomorphic lineages, suggesting a broad diversity-promoting role of inter-sexual interactions based on visual signals. We conclude that female colour polymorphisms evolve in a predictable fashion, and are likely driven by ecological conditions that increase the rate of pre-mating interactions and thus the intensity of sexual conflict.

evolutionary biology↗

bioRxiv2025

Ecological relationships between human gut bacteria predicted from analysis of dense microbiome time series data from US travelers in Bangladesh

Gut microbiomes provide critical host homeostatic functions, resulting from a complex web of ecological interactions among community members. We studied these interactions using a time-lagged correlational strategy of dense longitudinal sequence data from Western individuals traveling abroad to Bangladesh who experienced diarrhea. We identified both negative (140) and positive (78) relationships between bacterial pairs. Positive relationships occurred in pairs that were significantly more phylogenetically distant, such as inter-order associations between Clostridiales and Bacteroidales, while negative relationships were more between more phylogenetically related pairs. Further analysis of computationally predicted genome content and metabolic pathways revealed that cooperative bacterial pairs overlapped less in function and offered each other metabolic support, while competitive pairs were more likely to compete for the same resources. Predicted levels of B vitamins (B5 and B3), enoyl acyl- carrier protein (acp) reductase II (FabK) and its metabolites, and nucleotide/nucleoside derivatives were able to differentiate negatively and positively associated microbe pairs. Ultimately, our findings show that combining time-series analysis with metabolic/genomic network analysis can identify relationships between bacteria with plausible causal mechanisms that are consistent with existing ecological and biochemical observations. IMPORTANCEUnderstanding how microbes in the gut interact with each other is important for devising strategies to target the human gut microbiome therapeutically. For instance, understanding competitive relationships, where a shared need of similar limited resources limits the degree to which two microbes can co-exist, can inform strategies for limiting colonization of undesirable microbes. Understanding cooperative relationships, where one microbe provides the other with substrates needed for growth, can inform strategies to promote desirable microbes. By evaluating dense time-series gut microbiome data from individuals who experienced diarrhea while traveling, we were able to predict both cooperative and competitive relationships among human gut microbes as those whose abundances were significantly related within an individual over time. Strikingly, in subsequent analyses performed using inferred genomic information, pairs with negative associations from the time series analysis were predicted to compete over more metabolic substrates, and pairs with positive associations had significantly more metabolic complementarity. These predictions regarding the underlying molecular bases of interactions could inform how nutritional environment will impact interactions between gut microbiome community members.

microbiology↗

bioRxiv2025

The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions

Genome size is known to reflect aspects of the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to microbial prevalence, relative abundance and co-occurrence in the environment. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems, including 80,561 medium-to-high quality genomes. We identified 9,028 species (defined by ANI >95%) across a manually curated dataset of 636 freshwater metagenomes and calculated their relative abundance. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, and a greater prevalence than expected based on their mean abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, our network analysis revealed that prokaryotes with reduced genomes are found in co-occurrent groups comprising up to 295 species. The species in these groups potentially possess a diminished capacity for synthesizing essential metabolites such as vitamins, amino acids and nucleotides, which may foster complex metabolic interdependencies within the community. Moreover, the fitness advantage of losing biosynthetic functions appears to be frequency dependent: while nucleotide biosynthesis is the most retained biosynthetic function, amino acid and then vitamin biosynthesis are more frequently lost. Our study finds that genome size is linked to microbial community structure and ecological adaptation to freshwaters. Our results underscore genome streamlining as a central ecological and evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.

microbiology↗

bioRxiv2025

Cultural and Ecological Dimensions of Spice Diversity: Indigenous Knowledge and Practices in Hadiya and Kambata-Tembaro, Central Ethiopia

This study presents a comprehensive ethnobotanical investigation into the diversity and cultural significance of spices in the Hadiya and Kambata-Tembaro zones of Central Ethiopia. Through semi-structured interviews, focus group discussions, and participatory observations with local communities, including a strong representation of women were applied. Thirty five spice species, primarily herbaceous, with Lamiaceae emerging as the most dominant family documents. The findings underscore the centrality of homegardens as reservoirs of agrobiodiversity and hubs of traditional knowledge transmission. Spices were found to serve diverse roles culinary, medicinal, and ritual positioning them as biocultural keystone species intricately linked to local health systems, cultural identity, and daily life. Community preference rankings and culinary preparation methods revealed nuanced valuations based not only on taste but also cultural symbolism and perceived health benefits. Moreover, the study highlights gendered and socioeconomic dimensions of spice use and management, revealing persistent inequalities in resource access, decision-making, and benefit-sharing, despite womens key roles in preserving and utilizing these resources. The research emphasizes the need for inclusive, gender-sensitive policies that recognize and protect indigenous ecological knowledge systems. It calls for participatory, community-led conservation strategies and further interdisciplinary studies on sustainable harvesting and the ecological dynamics of spice species across land-use systems. Overall, this study contributes to the growing body of knowledge advocating for the integration of traditional knowledge into national biodiversity and food security agendas, highlighting the importance of empowering local communities especially women to ensure the resilience of cultural and biological heritage amid environmental and socioeconomic change.

plant biology↗

bioRxiv2025

Cryptic and Ecologically Relevant Locomotor Activity Patterns in Lake Malawi Cichlids Revealed Through Computer Vision Pipeline

Cichlid fishes have long been a popular model for ecology and evolutionary biology. Not only do they exhibit nearly unparalleled taxonomic diversity, but their community structures are both complex and extremely dense. Niche partitioning along dietary axes has been credited in maintaining cichlid biodiversity in a broad sense; however, it is common for cichlid species with overlapping diets to co-exist, leading to the search for other mechanisms to explain the maintenance of cichlid biodiversity. Behavioral variation has the potential to lead to fine-scale (i.e., micro-) habitat partitioning, but analyzing complex animal behavior poses several challenges, including time, cost and reproducibility. Modern tools, such as Machine Learning (ML), ease the burden of behavioral analyses, and are increasingly used in the field. Here, we present the application of tools from a well-developed sub-field of ML, Computer Vision (CV), to extract locomotor behavioral data from four Lake Malawi cichlid species. Our dataset consisted of low-resolution (320x240), twenty-four-hour infrared videos of activity in 4 cichlid species. We first analyzed a pair of species with divergent behaviors, diets and habitats (i.e., Abactochromis labrosus versus Tropheops kumwera), representing a proof-of-concept comparison. Next we analyzed activity in two closely related species with broadly similar behaviors and overlapping diets and habitats (i.e., Maylandia sp. Daktari versus Maylandia faiaziberi). In both comparisons, our analysis involved the quantification of tank usage patterns and stop/rest activity. Not only did our data align with the known ecologies and behaviors of the species in our proof-of-concept comparison, but they revealed novel behavioral differences between all species, especially as related to variation in tank usage from day to night. Our approach provides a window into potential cryptic behavioral niche partitioning, as well as a foundation for future, high-throughput analyses to study the genetic basis and evolution of behavior.

animal behavior and cognition↗

bioRxiv2025

Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats

From its earliest beginnings, lifes expansion into new habitats has been profoundly shaped by its reciprocal interactions with Earths changing environments. Understanding how ancient metabolisms co-evolved with their environments requires uncovering the ecological and evolutionary processes that structured the functionally linked genes and networks underlying these metabolisms. Here, we focus on nitrogen (N2) fixation, one of lifes most critical metabolisms, and investigate the drivers of complexity in its associated gene machinery today. We used a large-scale comparative genomics framework to construct a comprehensive catalog of extant N2 fixation-associated genes and assessed their distribution across diverse microbial genomes and environmental backgrounds. Genomes enriched in N2 fixation genes generally have larger genome sizes, broader metabolic capabilities, wider habitat ranges, and are predominantly associated with mesophilic and aerobic lifestyles. Evolutionary reconstructions reveal a pattern of early gene gains in ancestral diazotrophs followed by lineage-specific gene losses in later diverging taxa, suggesting evolutionary trade-offs shaped by changing environments. These findings demonstrate that the evolution of N2 fixation has been intertwined with the composition and organization of the genes supporting the overarching N2 metabolism, driven by feedback between genome evolution and shifting environmental and ecological conditions.

microbiology↗

bioRxiv2025

Domain gain or loss in fungal chitinases drives ecological specialization toward antagonism or immune suppression

The evolutionary origins of fungal effector proteins remain poorly understood, particularly how structural changes reprogram antimicrobial enzymes into host-adapted immune suppressors. Here, we show that domain modularity drives ecological specialization in chitinase effectors of the beneficial root endophyte Serendipita indica. The GH18 chitinase SiCHIT, which carries a C-terminal carbohydrate-binding module (CBM5), is expressed during fungal competition and antagonizes the fungal pathogen Bipolaris sorokiniana in the rhizosphere, thereby protecting plant roots. Deletion of the CBM5 abolishes this antifungal activity, while fusion of CBM5 to the CBM5-lacking paralog SiCHIT2 restores pathogen inhibition. In contrast, SiCHIT2 is induced during root colonization and suppresses chitin-triggered reactive oxygen species production, promoting immune evasion and host compatibility. These results identify CBM5 as a modular determinant of effector function, switching chitinase activity between microbial antagonism and host immune suppression. Our findings support an evolutionary scenario in which effector function in planta arises through domain loss and transcriptional divergence from an antimicrobial precursor, consistent with transitions along the saprotrophy-to-symbiosis continuum. Significance StatementEffector proteins play key roles in shaping fungal interactions with both plant hosts and microbial competitors, yet how these functions evolve remains unclear. Here, we show that structural domain modularity enables ecological specialization of two paralogous chitinases arising from gene duplication in the root endophyte Serendipita indica. Through domain deletion and fusion, we demonstrate that a carbohydrate-binding module (CBM5) determines whether a chitinase functions in microbial antagonism or immune evasion. Our findings provide mechanistic evidence for effector diversification via domain loss and transcriptional divergence, supporting an evolutionary trajectory from antimicrobial activity to host adaptation. This work advances our understanding of how modular architecture drives effector evolution and niche specialization in symbiotic fungi. HighlightsO_LIGain or loss of a CBM5 binding domain drives effector specialization between fungal antagonism and immune suppression C_LIO_LICBM5 acts as a modular determinant enabling antifungal activity in the GH18 chitinase SiCHIT C_LIO_LIThe CBM5-lacking paralog SiCHIT2 suppresses host immunity and promotes root colonization C_LIO_LIFunctional divergence following gene duplication illustrates evolutionary repurposing of an antimicrobial enzyme into an immune-suppressive effector C_LI

plant biology↗

bioRxiv2025

Ecological Factors Affecting Prosociality in Marmoset Monkeys

Prosocial behaviors, such as cooperation and food sharing, are critical for maintaining group cohesion in social species, yet the influence of transient physiological states on these behaviors remains poorly understood. This study investigates how short-term ecological factors impact social behavior in common marmosets (Callithrix jacchus), a highly prosocial nonhuman primate species. Specifically, we tested how food divisibility (small vs. large food items) and time since food access (TSFA; 0 hours, 1 hour, and 3 hours) influenced food sharing behavior. Results revealed that larger food portions consistently promoted prosocial interactions, while longer durations since food access shifted behavior toward individualism. A significant interaction between TSFA and food size indicates that the effect of food size on prosocial behavior varies with hunger state: increasing TSFA weakens the prosocial impact of large food portions. These findings suggest that marmoset prosociality is sensitive to immediate ecological conditions, reflecting flexible, context-dependent social decision-making.

animal behavior and cognition↗

bioRxiv2025

Computational simulation of ecological drift for generating functional minimal microbiomes identifies key experimental and biotic factors influencing success

We describe a top-down engineering approach that leverages ecological drift to generate Minimal Microbiomes; microbial consortia that are relatively simple, cohesive, and functionally complete. This process can be applied to any microbial ecosystem, provided that the target microbiome can be experimentally mimicked. Empirical support for this approach has emerged from multiple independent studies. Here, we use simulations across diverse scenarios, significantly varying niche structures and biotic interactions, to explore the experimental conditions and source microbiome characteristics that favor successful outcomes. Our results indicate that the effectiveness of this approach is constrained by several factors, and that perfect outcomes should not be routinely expected. Nevertheless, despite its drawbacks, this strategy remains a powerful tool for simplifying microbiomes and isolating key co-adapted populations, enabling the construction of low-diversity consortia that retain community function and present ecological cohesion.

microbiology↗

bioRxiv2025

Study on physiological and ecological responses of alfalfa during the germination stage under drought, bicarbonate, and combined stress conditions

Alfalfa (Medicago sativa L.) is frequently constrained by drought and salinity during cultivation and production. This study aimed to investigate the differential response characteristics and underlying physiological and ecological mechanisms of alfalfa during the germination stage under drought stress, bicarbonate stress, and their combined effects. Twelve alfalfa varieties were subjected to germination tests using PEG-6000 to simulate drought stress (0-20%) and NaHCO{square} to simulate bicarbonate stress (0-30 mM). Based on the semi-inhibitory concentrations and phenotypic indices observed under single-stress conditions, a combined stress treatment was designed. The subordinate function method was employed to comprehensively evaluate the variations in stress responses among the twelve alfalfa varieties during the germination stage. Additionally, this study explored the physiological and ecological response mechanisms of drought-tolerant, salt-tolerant, and drought-salt-sensitive varieties. Among the 12 alfalfa varieties, WL363HQ has the strongest drought and salt tolerance, while WL319HQ is the most sensitive to drought and salt stress. Based on this, the varieties can be classified into drought-tolerant, salt-tolerant, and sensitive categories. At low concentrations, the drought-salt combination shows antagonism (salt alleviates drought inhibition); at high concentrations, it turns into synergy, and the inhibitory effect is amplified.WL363HQ adapts to the combined stress by maintaining stable SOD activity and gradually accumulating soluble sugar; WL319HQ shows sensitivity due to fluctuating SOD, membrane lipid peroxidation, and uncontrolled soluble sugar.

plant biology↗

bioRxiv2025

Novel insights into the chemodiversity and chemical ecology of the extremophile black yeast Hortaea werneckii, unlocking its potential for compound discovery

Hortaea werneckii is a halotolerant yeast, found in various habitats and which specialized metabolism remains largely unexplored. Moreover, its chemical response to high salinities has not been thoroughly investigated. To address this gap, a large-scale metabolomic study based on HPLC-HRMS/MS was conducted on 64 strains, collected from different habitats worldwide, and cultivated both on saline and non-saline media. The culture media salinity significantly modulated the strains metabolomes, suggesting the yeast exhibits a specific chemical response to high salt concentrations, potentially linked to halotolerance mechanisms. Additionally, the metabolomes were influenced by the ecological origin of the strains, with opportunistic pathogenic isolates producing distinct metabolites. Molecular networking revealed that H. werneckii synthesizes various chemical classes, including potential cytotoxic compounds, making this yeast a potentially interesting source of bioactive compounds. Hortein was detected as dominant and ubiquitous, emerging as a potential chemical marker for the species. This study highlights several compounds of interest, related to the chemical ecology and pathogenicity of H. werneckii. As most of them remain unidentified, future research should prioritize their isolation and identification, to improve our understanding of this extremophile organism and harness its potential in natural product discovery.

microbiology↗