Inferring the genetic responses to acute drought stress across an ecological gradient

Background How do xerophytic species thrive in environments that experience extreme annual drought? Although critical to the survival of many species, the genetic responses to drought stress in many non-model organisms has yet to be explored. We investigated this question in Mentzelia section Bartonia (Loasaceae), which occurs throughout western North America, including arid lands. To better understand the genetic responses to drought stress among species that occur in different habitats, the gene expression levels of three species from Mentzelia were compared across a precipitation gradient. Two de novo reference transcriptomes were generated and annotated. Leaf and root tissues were collected from control and drought shocked plants and compared to one another for differential expression. A target-gene approach was also implemented to better understand how drought-related genes from model and crop species function in non-model systems. Results When comparing the drought-shock treatment plants to their respective control plants, we identified 165 differentially expressed clusters across all three species. Differentially expressed genes including those associated with water movement, photosynthesis, and delayed senescence. The transcriptome profiling approach was coupled with a target genes approach that measured expression of 90 genes associated with drought tolerance in model organisms. Comparing differentially expressed genes with a ≥ 2 log-fold value between species and tissue types showed significant differences in drought response. In pairwise comparisons, species that occurred in drier environments differentially expressed greater genes in leaves when drought shocked than those from wetter environments, but expression in the roots mostly produced opposite results. Conclusions Arid-adapted species mount greater genetic responses compared to the mesophytic species, which has likely evolved in response to consistent annual drought exposure across generations. Drought responses also depended on organ type. Xerophytes, for example, mounted a larger response in leaves to downregulate photosynthesis and senescence, while mobilizing carbon and regulating water in the roots. The complexity of drought responses in Mentzelia suggest that whole organism responses need to be considered when studying drought and, in particular, the physiological mechanisms in which plants regulate water, carbon, cell death, metabolism, and secondary metabolites.

Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria

Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO3 or NH4Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH4Cl medium than in NaNO3 medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH4Cl medium than NaNO3 medium. 15N turnover rate analysis revealed that the nitrogen assimilation rate in NH4Cl medium was higher than in NaNO3 medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO3 and NH4Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.

Competition alters species’ plastic and genetic response to environmental change

Species react to environmental change via plastic and evolutionary responses. While both of them determine species’ survival, most studies quantify these responses individually. As species occur in communities, competing species may further influence their respective response to environmental change. Yet, how environmental change and competing species combined shape plastic and genetic responses to environmental change remains unclear. Quantifying how competition alters plastic and genetic responses of species to environmental change requires a trait-based, community and evolutionary ecological approach. We exposed unicellular aquatic organisms to long-term selection of increasing salinity—representing a common and relevant environmental change. We assessed plastic and genetic contributions to phenotypic change in biomass, cell shape, and dispersal ability along increasing levels of salinity in the presence and absence of competition. Trait changes in response to salinity were mainly due to mean trait evolution, and differed whether species evolved in the presence or absence of competition. Our results show that species’ evolutionary and plastic responses to environmental change depended both on competition and the magnitude of environmental change, ultimately determining species persistence. Our results suggest that understanding plastic and genetic responses to environmental change within a community will improve predictions of species’ persistence to environmental change.

Genetic Responses and Aflatoxin Inhibition during Co-Culture of Aflatoxigenic and Non-Aflatoxigenic Aspergillus flavus

Aflatoxin is a carcinogenic mycotoxin produced by Aspergillus flavus. Non-aflatoxigenic (Non-tox) A. flavus isolates are deployed in corn fields as biocontrol because they substantially reduce aflatoxin contamination via direct replacement and additionally via direct contact or touch with toxigenic (Tox) isolates and secretion of inhibitory/degradative chemicals. To understand touch inhibition, HPLC analysis and RNA sequencing examined aflatoxin production and gene expression of Non-tox isolate 17 and Tox isolate 53 mono-cultures and during their interaction in co-culture. Aflatoxin production was reduced by 99.7% in 72 h co-cultures. Fewer than expected unique reads were assigned to Tox 53 during co-culture, indicating its growth and/or gene expression was inhibited in response to Non-tox 17. Predicted secreted proteins and genes involved in oxidation/reduction were enriched in Non-tox 17 and co-cultures compared to Tox 53. Five secondary metabolite (SM) gene clusters and kojic acid synthesis genes were upregulated in Non-tox 17 compared to Tox 53 and a few were further upregulated in co-cultures in response to touch. These results suggest Non-tox strains can inhibit growth and aflatoxin gene cluster expression in Tox strains through touch. Additionally, upregulation of other SM genes and redox genes during the biocontrol interaction demonstrates a potential role of inhibitory SMs and antioxidants as additional biocontrol mechanisms and deserves further exploration to improve biocontrol formulations.

Individual-based eco-evolutionary models for understanding adaptation in changing seas

As climate change threatens species' persistence, predicting the potential for species to adapt to rapidly changing environments is imperative for the development of effective conservation strategies. Eco-evolutionary individual-based models (IBMs) can be useful tools for achieving this objective. We performed a literature review to identify studies that apply these tools in marine systems. Our survey suggested that this is an emerging area of research fuelled in part by developments in modelling frameworks that allow simulation of increasingly complex ecological, genetic and demographic processes. The studies we identified illustrate the promise of this approach and advance our understanding of the capacity for adaptation to outpace climate change. These studies also identify limitations of current models and opportunities for further development. We discuss three main topics that emerged across studies: (i) effects of genetic architecture and non-genetic responses on adaptive potential; (ii) capacity for gene flow to facilitate rapid adaptation; and (iii) impacts of multiple stressors on persistence. Finally, we demonstrate the approach using simple simulations and provide a framework for users to explore eco-evolutionary IBMs as tools for understanding adaptation in changing seas.

Selection of the reference genes for quantitative gene expression by RT-qPCR in the desert plant Stipagrostis pennata

The desert pioneer plant Stipagrostis pennata plays an important role in sand fixation, wind prevention, and desert ecosystem recovery. An absence of reference genes greatly limits investigations into the regulatory mechanism by which S. pennata adapts to adverse desert environments at the molecular and genetic levels. In this study, eight candidate reference genes were identified from rhizosheath development transcriptome data from S. pennata, and their expression stability in the rhizosheaths at different development stages, in a variety of plant tissues, and under drought stress was evaluated using four procedures, including geNorm, NormFinder, BestKeeper, and RefFinder. The results showed that GAPDH and elF were the most stable reference genes under drought stress and in rhizosheath development, and ARP6 and ALDH were relatively stable in all plant tissues. In addition, elF was the most suitable reference gene for all treatments. Analysis of the consistency between the reverse transcription-quantitative PCR (RT-qPCR) and RNA sequencing data showed that the identified elF and GAPDH reference genes were stable during rhizosheath development. These results provide reliable reference genes for assuring the accuracy of RT-qPCR and offer a foundation for further investigations into the genetic responses of S. pennata to abiotic stress.

Transcriptomic Effects of Acute Ultraviolet Radiation Exposure on Two Syntrichia Mosses

Ultraviolet radiation (UVR) is a major environmental stressor for terrestrial plants. Here we investigated genetic responses to acute broadband UVR exposure in the highly desiccation-tolerant mosses Syntrichia caninervis and Syntrichia ruralis, using a comparative transcriptomics approach. We explored whether UVR protection is physiologically plastic and induced by UVR exposure, addressing the following questions: (1) What is the timeline of changes in the transcriptome with acute UVR exposure in these two species? (2) What genes are involved in the UVR response? and (3) How do the two species differ in their transcriptomic response to UVR? There were remarkable differences between the two species after 10 and 30 min of UVR exposure, including no overlap in significantly differentially abundant transcripts (DATs) after 10 min of UVR exposure and more than twice as many DATs for S. caninervis as there were for S. ruralis. Photosynthesis-related transcripts were involved in the response of S. ruralis to UVR, while membrane-related transcripts were indicated in the response of S. caninervis. In both species, transcripts involved in oxidative stress and those important for desiccation tolerance (such as late embryogenesis abundant genes and early light-inducible protein genes) were involved in response to UVR, suggesting possible roles in UVR tolerance and cross-talk with desiccation tolerance in these species. The results of this study suggest potential UVR-induced responses that may have roles outside of UVR tolerance, and that the response to URV is different in these two species, perhaps a reflection of adaptation to different environmental conditions.