-Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

DNA methylation and histone modifications induced by abiotic stressors in plants

BACKGROUND

A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants.

DISCUSSION

Plant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications.

CONCLUSIONS

Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.

The LEA gene family in tomato and its wild relatives: genome-wide identification, structural characterization, expression profiling, and role of SlLEA6 in drought stress

BACKGROUND

Late embryogenesis abundant (LEA) proteins are widely distributed in higher plants and play crucial roles in regulating plant growth and development processes and resisting abiotic stress. Cultivated tomato (Solanum lycopersicum) is an important vegetable crop worldwide; however, its growth, development, yield, and quality are currently severely constrained by abiotic stressors. In contrast, wild tomato species are more tolerant to abiotic stress and can grow normally in extreme environments. The main objective of this study was to identify, characterize, and perform gene expression analysis of LEA protein families from cultivated and wild tomato species to mine candidate genes and determine their potential role in abiotic stress tolerance in tomatoes.

RESULTS

Total 60, 69, 65, and 60 LEA genes were identified in S. lycopersicum, Solanum pimpinellifolium, Solanum pennellii, and Solanum lycopersicoides, respectively. Characterization results showed that these genes could be divided into eight clusters, with the LEA_2 cluster having the most members. Most LEA genes had few introns and were non-randomly distributed on chromosomes; the promoter regions contained numerous cis-acting regulatory elements related to abiotic stress tolerance and phytohormone responses. Evolutionary analysis showed that LEA genes were highly conserved and that the segmental duplication event played an important role in evolution of the LEA gene family. Transcription and expression pattern analyses revealed different regulatory patterns of LEA genes between cultivated and wild tomato species under normal conditions. Certain S. lycopersicum LEA (SlLEA) genes showed similar expression patterns and played specific roles under different abiotic stress and phytohormone treatments. Gene ontology and protein interaction analyses showed that most LEA genes acted in response to abiotic stimuli and water deficit. Five SlLEA proteins were found to interact with 11 S. lycopersicum WRKY proteins involved in development or resistance to stress. Virus-induced gene silencing of SlLEA6 affected the antioxidant and reactive oxygen species defense systems, increased the degree of cellular damage, and reduced drought resistance in S. lycopersicum.

CONCLUSION

These findings provide comprehensive information on LEA proteins in cultivated and wild tomato species and their possible functions under different abiotic and phytohormone stresses. The study systematically broadens our current understanding of LEA proteins and candidate genes and provides a theoretical basis for future functional studies aimed at improving stress resistance in tomato.

The arbuscular mycorrhizal fungus Rhizophagus irregularis harmonizes nuclear dynamics in the presence of distinct abiotic factors

Arbuscular mycorrhizal fungi (AMF) are widespread obligate root symbionts that assist plants in obtaining nutrients and protection against environmental stresses. In the model species Rhizophagus irregularis, heterokaryotic strains (AMF dikaryons) carry thousands of nuclei originating from two parental strains whose frequency varies depending on strains and host identity. Here, using digital droplet PCR, we demonstrate that surrounding abiotic factors (temperature, phosphorus, and pH) also change the nuclear dynamics of such strains in root organ cultures. Furthermore, when spatially separated portions of the AMF mycelium grow under different abiotic conditions, all the produced spores carry highly similar nuclear ratios. Overall, these findings demonstrate that abiotic stressors impact the nuclear organization of a widespread group of multinucleate plant symbionts, and reveal remarkable mechanisms of nuclear ratio harmonization across the mycelium in these prominent symbionts.

A high solids field-to-fuel research pipeline to identify interactions between feedstocks and biofuel production

BACKGROUND

Environmental factors, such as weather extremes, have the potential to cause adverse effects on plant biomass quality and quantity. Beyond adversely affecting feedstock yield and composition, which have been extensively studied, environmental factors can have detrimental effects on saccharification and fermentation processes in biofuel production. Only a few studies have evaluated the effect of these factors on biomass deconstruction into biofuel and resulting fuel yields. This field-to-fuel evaluation of various feedstocks requires rigorous coordination of pretreatment, enzymatic hydrolysis, and fermentation experiments. A large number of biomass samples, often in limited quantity, are needed to thoroughly understand the effect of environmental conditions on biofuel production. This requires greater processing and analytical throughput of industrially relevant, high solids loading hydrolysates for fermentation, and led to the need for a laboratory-scale high solids experimentation platform.

RESULTS

A field-to-fuel platform was developed to provide sufficient volumes of high solids loading enzymatic hydrolysate for fermentation. AFEX pretreatment was conducted in custom pretreatment reactors, followed by high solids enzymatic hydrolysis. To accommodate enzymatic hydrolysis of multiple samples, roller bottles were used to overcome the bottlenecks of mixing and reduced sugar yields at high solids loading, while allowing greater sample throughput than possible in bioreactors. The roller bottle method provided 42-47% greater liquefaction compared to the batch shake flask method for the same solids loading. In fermentation experiments, hydrolysates from roller bottles were fermented more rapidly, with greater xylose consumption, but lower final ethanol yields and CO₂ production than hydrolysates generated with shake flasks. The entire platform was tested and was able to replicate patterns of fermentation inhibition previously observed for experiments conducted in larger-scale reactors and bioreactors, showing divergent fermentation patterns for drought and normal year switchgrass hydrolysates.

CONCLUSION

A pipeline of small-scale AFEX pretreatment and roller bottle enzymatic hydrolysis was able to provide adequate quantities of hydrolysate for respirometer fermentation experiments and was able to overcome hydrolysis bottlenecks at high solids loading by obtaining greater liquefaction compared to batch shake flask hydrolysis. Thus, the roller bottle method can be effectively utilized to compare divergent feedstocks and diverse process conditions.

Phenotypic changes in microalgae at acidic pH mediate their tolerance to higher concentrations of transition metals

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Acid-tolerant microalgae were grown at pH 3.5 and 6.7 in presence of heavy metals (HMs).

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HMs-induced phenotypic changes in microalgae were evaluated by ATR-FTIR spectroscopy.

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Higher HMs bioavailability affected microalgae more at pH 6.7 than pH 3.5.

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Acclimation of microalgal strains to acidic pH significantly alleviates HMs toxicity.

Acclimatory phenotypic response is a common phenomenon in microalgae, particularly during heavy metal stress. It is not clear so far whether acclimating to one abiotic stressor can alleviate the stress imposed by another abiotic factor. The intent of the present study was to demonstrate the implication of acidic pH in effecting phenotypic changes that facilitate microalgal tolerance to biologically excess concentrations of heavy metals. Two microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were exposed to biologically excess concentrations of Cu (0.50 and 1.0 mg L^‒1), Fe (5 and 10 mg L^‒1), Mn (5 and 10 mg L^‒1) and Zn (2, 5 and 10 mg L^‒1) supplemented to the culture medium at pH 3.5 and 6.7. Chlorophyll autofluorescence and biochemical fingerprinting using FTIR-spectroscopy were used to assess the microalgal strains for phenotypic changes that mediate tolerance to metals. Both the strains responded to acidic pH by effecting differential changes in biochemicals such as carbohydrates, proteins, and lipids. Both the microalgal strains, when acclimated to low pH of 3.5, exhibited an increase in protein (< 2-fold) and lipid (> 1.5-fold). Strain MAS1 grown at pH 3.5 showed a reduction (1.5-fold) in carbohydrates while strain MAS3 exhibited a 17-fold increase in carbohydrates as compared to their growth at pH 6.7. However, lower levels of biologically excess concentrations of the selected transition metals at pH 6.7 unveiled positive or no effect on physiology and biochemistry in microalgal strains, whereas growth with higher metal concentrations at this pH resulted in decreased chlorophyll content. Although the bioavailability of free-metal ions is higher at pH 3.5, as revealed by Visual MINTEQ model, no adverse effect was observed on chlorophyll content in cells grown at pH 3.5 than at pH 6.7. Furthermore, increasing concentrations of Fe, Mn and Zn significantly upregulated the carbohydrate metabolism, but not protein and lipid synthesis, in both strains at pH 3.5 as compared to their growth at pH 6.7. Overall, the impact of pH 3.5 on growth response suggested that acclimation of microalgal strains to acidic pH alleviates metal toxicity by triggering physiological and biochemical changes in microalgae for their survival.

The interplay between temperature and an insecticide mixture modulates the stimulatory response of sublethally exposed Myzus persicae

Temperature can interact with chemical pesticides and modulate their toxicity. Sublethal exposure to pesticides is known to trigger hormetic responses in pests. However, the simultaneous effects of temperature and sublethal exposure to single or mixture-based insecticides on the insects' stimulatory responses are not frequently considered in toxicological studies. Here we investigated the combined effects of temperature on the lethal and sublethal responses of the green peach aphid Myzus persicae after exposure to commercial formulations of a neonicotinoid (thiamethoxam) and a pyrethroid (lambda-cyhalothrin) and their mixture. Firstly, the concentration-response curves of the insecticides were determined under four temperatures (15 °C, 20 °C, 25 °C, and 28 °C) by the leaf dipping method. Subsequently, the sublethal concentrations C0, CL1, CL5, CL10, CL15, CL20, and CL30 were selected to assess sublethal effects on aphids' longevity and reproduction under the same temperatures. The results showed that the mixture of thiamethoxam + lambda-cyhalothrin caused greater toxicity to aphids compared to the formulations with each active ingredient alone and that the toxicity was higher at elevated temperatures. Furthermore, the exposure to low concentrations of the mixture (thiamethoxam + lambda-cyhalothrin) and the separated insecticides induced stimulatory responses in the longevity and fecundity of exposed aphid females, but the occurrence of such hormetic responses depended on the insecticide type, its sublethal concentration, and the temperature as well as their interactions.

Ambient ultraviolet-B exposure brings quantum changes in phenotypic and molecular signatures of the embryo of a high-altitude fish, Tor putitora

Effects of environmentally relevant ultraviolet B (UVB) light on the embryonic development of a high-altitude dwelling endangered fish, Tor putitora (golden mahseer), were investigated for the first time. For that, three sets of embryos (in triplicates) were exposed to various ambient UVB light doses (1, 2 and 3 W/m2, corresponding to 3.6, 7.2 and 10.8 kJ/m2/day) for 1 h at two different embryonic stages (1 hpf-hours post fertilization and 32 hpf). Another set of embryos was exposed to visible light for the same duration and served as the light control (LC), and the last set was kept under ideal dark conditions for incubation (the dark control, DC). The results showed that the higher levels of UVB light (> 2 W/m2) decreased the hatching rate and survival of embryos and hatchlings, extended the hatching window or hatching time and caused embryonic and hatching deformities. The qPCR analysis revealed upregulation of genes such as nf-kb2, il-1β, tnfα, tlr5, nrf2, bcl2, caspase9, p53, ddb2, mmp13a, mc1r and hsp70 in a dose-dependent manner upon UVB exposure. Overall, the high ambient level of UVB exposure (3 W/m2, equivalent to 10.8 kJ/m2/day) in golden mahseer embryos proved to be lethal or sub-lethal, which were mediated by (or related to) immunological changes, oxidative stress, apoptosis, DNA damage and aberrant development. Further, harmful effects of UVB were found to be stage-dependent and were more significant at 32 hpf. The study is the first preliminary report, at the molecular level, on the impact of environmentally occurring UVB on the embryonic development of an endangered fish species, the golden mahseer.

Differential manifestation of RONS and antioxidant enzymes in response to singular versus combinatorial stress in Chironomus ramosus

In nature, organisms face multiple abiotic stress concurrently. Our previous study has indicated how threshold level of lethality depends on the type and combination of stressors. Many mechanisms exist by which organisms respond to stressors and maintain homeostasis. We examined the homeostatic pliability in an extremophilic oriental midge Chironomus ramosus larvae under various combinatorial stress conditions of desiccation (DS), heat (HS) and starvation (SS). Exposure to these stressors led to activation of a common response pathway of oxidative stress. Abundance of antioxidant enzymes like superoxide dismutase, catalase, glutathione reductase and glutathione peroxidase along with selective as well as stressor specific increase in total antioxidant capacity were reflected from the corresponding level of reactive oxygen and nitrogen species (RONS) in larvae exposed to various combinatorial stress. Additionally, we found stressor specific increment in lipid peroxidation level, protein carbonyl content and advanced oxidative protein products during the stress regime. Further investigation revealed a sharp decline in the activity of mitochondrial aconitase enzyme activity in response to abiotic stress induced oxidative stress. The combinatorial stressor specific comparative study based on biochemical and fluorescence based redox-endpoint assays confirmed that the generation of oxidative stress is the consequential convergent pathway of DS, HS and SS, but the quantum of RONS decides the redox potential of homeostatic response and survival rate.

Abiotic factors impact on oak forest decline in Lorestan Province, Western Iran

The Zagros oak forests in Iran are facing a concerning decline due to prolonged and severe drought conditions over several decades, compounded by the simultaneous impact of temperature on oak populations. This study in oak woodlands of central Zagros forests in Lorestan province analyzed abiotic factors such as climate properties, topographic features, land use, and soil properties from 1958 to 2022. We found that higher elevation areas with steeper slopes and diverse topography show significant potential for enhancing oak tree resilience in the face of climate change. Additionally, traditional land use practices like livestock keeping and dryland farming contribute to a widespread decline in oak populations. Preserving forest biodiversity and ensuring ecological sustainability requires immediate attention. Implementing effective land-use management strategies, such as protecting and regulating human-forest interaction, and considering meteorological factors to address this issue is crucial. Collaborative efforts from stakeholders, policymakers, and local communities are essential to oppose destructive suburban sprawl and other developments. Sustainable forestry practices should be implemented to improve the living standards of local communities that rely on forests and traditional livestock keeping, offer forestry-related jobs, and ensure social security. Such efforts are necessary to promote conservation awareness and sustainable practices, safeguarding this unique and vital ecosystem for future generations.

Insights from single-strain and mixed culture experiments on the effects of heatwaves on freshwater flagellates

The increasing frequency and intensity of heatwaves driven by climate change significantly impact microbial communities in freshwater habitats, particularly eukaryotic microorganisms. Heterotrophic nanoflagellates are important bacterivorous grazers and play a crucial role in aquatic food webs, influencing the morphological and taxonomic structure of bacterial communities. This study investigates the responses of three flagellate taxa to heatwave conditions through single-strain and mixed culture experiments, highlighting the impact of both biotic and abiotic factors on functional redundancy between morphologically similar protist species under thermal stress. Our results indicate that temperature can significantly impact growth and community composition. However, density-dependent factors also had a significant impact. In sum, stabilizing effects due to functional redundancy may be pronounced as long as density-dependent factors play a minor role and can be overshadowed when flagellate abundances increase.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.