Exploring the molecular mechanism of coloration differences in two Meconopsis wilsonii subspecies: australis and orientalis.

Flower color diversity is a key taxonomic trait in Meconopsis species, enhancing their appeal as ornamental flowers. However, knowledge of the molecular mechanisms of flower color formation in Meconopsis species is still limited. M. wilsonii subsp. australis (Australis) and M. wilsonii subsp. orientalis (Orientalis) have a developmental stage presenting red-purple flowers, while Orientalis also presents blue coloration at the full-bloom period, making them an important model for exploring the mechanism of blue flower formation in M. wilsonii. In this study, we collected petals from Australis and Orientalis at different developmental stages to compare the coloration differences between the two species and detect the molecular mechanisms of blue color in Orientalis. We identified that cyanidin was the main anthocyanin in the flowers of both species, and the blue color in Orientalis primarily arises from anthocyanins (Cyanidin-3-O-sambubioside). RNA sequencing analysis was performed to detect the gene expression in the anthocyanin biosynthesis pathway, and the results suggested that gene regulation for anthocyanin biosynthesis may not be the direct reason for blue color formation in Orientalis. In addition, the growth solid of Orientalis was rich in Fe and Mg ions, and a large amount of Fe and Mg ions accumulated in the petals of Orientalis. Combined with the gene functional enrichment results, we found that the purple and red-purple colors of these two species were presented by different glycosylation levels of cyanidin, while the violet color of Orientalis might be the results of metalloanthocyanins by Fe and Mg ions, which also relieved the toxicity caused by the high content of Fe and Mg ions in its cells. The environmental adaptation-related genes were highly expressed of in both species, such as adaptation to desiccation, water deprivation, freezing, etc. Our results revealed the coloration differences between Australis and Orientalis and described the molecular mechanisms of blue coloration in Orientalis. The data in our analysis could enrich the genetic resources for M. wilsonii for further studies.

Global change and physiological challenges for fish of the Amazon today and in the near future.

Amazonia is home to 15% (>2700, in 18 orders) of all the freshwater fish species of the world, many endemic to the region, has 65 million years of evolutionary history and accounts for 20% of all freshwater discharge to the oceans. These characteristics make Amazonia a unique region in the world. We review the geological history of the environment, its current biogeochemistry and the evolutionary forces that led to the present endemic fish species that are distributed amongst three very different water types: black waters [acidic, ion-poor, rich in dissolved organic carbon (DOC)], white waters (circumneutral, particle-rich) and clear waters (circumneutral, ion-poor, DOC-poor). The annual flood pulse is the major ecological driver for fish, providing feeding, breeding and migration opportunities, and profoundly affecting O2, CO2 and DOC regimes. Owing to climate change and other anthropogenic pressures such as deforestation, pollution and governmental mismanagement, Amazonia is now in crisis. The environment is becoming hotter and drier, and more intense and frequent flood pulses are now occurring, with greater variation between high and low water levels. Current projections are that Amazon waters of the near future will be even hotter, more acidic, darker (i.e. more DOC, more suspended particles), higher in ions, higher in CO2 and lower in O2, with many synergistic effects. We review current physiological information on Amazon fish, focusing on temperature tolerance and ionoregulatory strategies for dealing with acidic and ion-poor environments. We also discuss the influences of DOC and particles on gill function, the effects of high dissolved CO2 and low dissolved O2, with emphasis on water- versus air-breathing mechanisms, and strategies for pH compensation. We conclude that future elevations in water temperature will be the most critical factor, eliminating many species. Climate change will likely favour predominantly water-breathing species with low routine metabolic rates, low temperature sensitivity of routine metabolic rates, high anaerobic capacity, high hypoxia tolerance and high thermal tolerance.

Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution.

DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.

Direction Selective Neurons Responsive to Horizontal Motion in a Crab Reflect an Adaptation to Prevailing Movements in Flat Environments.

All animals need information about the direction of motion to be able to track the trajectory of a target (prey, predator, cospecific) or to control the course of navigation. This information is provided by direction selective (DS) neurons, which respond to images moving in a unique direction. DS neurons have been described in numerous species including many arthropods. In these animals, the majority of the studies have focused on DS neurons dedicated to processing the optic flow generated during navigation. In contrast, only a few studies were performed on DS neurons related to object motion processing. The crab Neohelice is an established experimental model for the study of neurons involved in visually-guided behaviors. Here, we describe in male crabs of this species a new group of DS neurons that are highly directionally selective to moving objects. The neurons were physiologically and morphologically characterized by intracellular recording and staining in the optic lobe of intact animals. Because of their arborization in the lobula complex, we called these cells lobula complex directional cells (LCDCs). LCDCs also arborize in a previously undescribed small neuropil of the lateral protocerebrum. LCDCs are responsive only to horizontal motion. This nicely fits in the behavioral adaptations of a crab inhabiting a flat, densely crowded environment, where most object motions are generated by neighboring crabs moving along the horizontal plane.SIGNIFICANCE STATEMENT Direction selective (DS) neurons are key to a variety of visual behaviors including, target tracking (preys, predators, cospecifics) and course control. Here, we describe the physiology and morphology of a new group of remarkably directional neurons exclusively responsive to horizontal motion in crabs. These neurons arborize in the lobula complex and in a previously undescribed small neuropil of the lateral protocerebrum. The strong sensitivity of these cells for horizontal motion represents a clear example of functional neuronal adaptation to the lifestyle of an animal inhabiting a flat environment.

Dispersal biophysics and adaptive significance of dimorphic diaspores in the annual Aethionema arabicum (Brassicaceae).

Heteromorphic diaspores (fruits and seeds) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments, particularly fluctuations in favourable temperatures and unpredictable precipitation regimes in arid climates. We conducted comparative analyses of the biophysical and ecophysiological properties of the two distinct diaspores (mucilaginous seed (M+ ) vs indehiscent (IND) fruit) in the dimorphic annual Aethionema arabicum (Brassicaceae), linking fruit biomechanics, dispersal aerodynamics, pericarp-imposed dormancy, diaspore abscisic acid (ABA) concentration, and phenotypic plasticity of dimorphic diaspore production to its natural habitat and climate. Two very contrasting dispersal mechanisms of the A. arabicum dimorphic diaspores were revealed. Dehiscence of large fruits leads to the release of M+ seed diaspores, which adhere to substrata via seed coat mucilage, thereby preventing dispersal (antitelechory). IND fruit diaspores (containing nonmucilaginous seeds) disperse by wind or water currents, promoting dispersal (telechory) over a longer range. The pericarp properties confer enhanced dispersal ability and degree of dormancy on the IND fruit morph to support telechory, while the M+ seed morph supports antitelechory. Combined with the phenotypic plasticity to produce more IND fruit diaspores in colder temperatures, this constitutes a bet-hedging survival strategy to magnify the prevalence in response to selection pressures acting over hilly terrain.

Environmental Adaptations Improve Everyday Action in Schizophrenia.

Cognitive functioning, particularly executive functioning, is a strong predictor of functional outcomes in people with schizophrenia. Cognitive remediation has been shown to improve specific cognitive processes, but adjunctive interventions are required for meaningful gains in adaptive functioning, particularly in people with chronic illness. This study examined whether (and how) environmental adaptations, used without training, may circumvent cognitive difficulties and facilitate everyday task performance in individuals with chronic schizophrenia. Forty-two individuals with chronic schizophrenia/schizoaffective disorder were administered cognitive measures and two versions of the Naturalistic Action Test (NAT)-a standard version (ST-NAT), and a user-centered version (UC-NAT) that incorporated environmental adaptations designed to facilitate task performance. The NAT conditions were counterbalanced across participants. Analyses compared performance between the NAT versions and examined the cognitive correlates of each NAT condition. Individuals with schizophrenia made fewer errors on the UC-NAT as compared to the ST-NAT; this between-group difference was significant for all error types. Compared to the ST-NAT, the UC-NAT performance was not significantly associated with an executive function measure of planning. Environmental adaptations may be implemented without extensive training to improve everyday action in individuals with chronic schizophrenia. Environmental adaptations that reduce planning demands may be most effective in this population.

Smart Aqueous Zinc Ion Battery: Operation Principles and Design Strategy.

The zinc ion battery (ZIB) as a promising energy storage device has attracted great attention due to its high safety, low cost, high capacity, and the integrated smart functions. Herein, the working principles of smart responses, smart self-charging, smart electrochromic as well as smart integration of the battery are summarized. Thus, this review enables to inspire researchers to design the novel functional battery devices for extending their application prospects. In addition, the critical factors associated with the performance of the smart ZIBs are comprehensively collected and discussed from the viewpoint of the intellectualized design. A profound understanding for correlating the design philosophy in cathode materials and electrolytes with the electrode interface is provided. To address the current challenging issues and the development of smart ZIB systems, a wide variety of emerging strategies regarding the integrated battery system is finally prospected.

The Effect of Sexes and Seasons on the Morphological Structures of the Ruminant Digestive System of Blue Sheep (Pseudois nayaur).

Constant adaptation to environmental changes is required by ruminants to allow them to adapt to different ecological niches and feeding habits. In addition, the morphology and function of ruminant digestive systems reveal some adaptive evolutionary characteristics. Blue sheep (Pseudois nayaur) display a variety of morpho-physiological adaptations that are typical of grazers. In this study, we collected 64 adult blue sheep samples (whole animal carcasses) from the Helan Mountains, China, during different seasons. The external morphological parameters, digestive system morphological indexes, and rumen surface enlargement factors were determined. Our results reveal that the rumen and reticulum weights were positively correlated with the body weight (p = 0.004), while the food channel aperture, intestinal length, and weight of the blue sheep digestive tract presented no significant differences between different seasons (p > 0.05) and sexes (p > 0.05). There were significant differences (p < 0.001) in the density, length, and width of mastoids, and the rumen surface enlargement factor was 2.85 ± 1.37, which is typical of roughage feeders. The nutritional and ecological characteristics of blue sheep represent obvious morphological and physiological adaptations to an herbivorous diet. Adopting a quick foraging strategy allows blue sheep to rapidly consume and excrete large amounts of feed, thus obtaining the required energy for their activities and facilitating better adaption to environmental changes.

Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review.

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.

Investigating the Ability of Edwardsiella ictaluri and Flavobacterium covae to Persist within Commercial Catfish Pond Sediments under Laboratory Conditions.

Two prevalent bacterial diseases in catfish aquaculture are enteric septicemia of catfish and columnaris disease caused by Edwardsiella ictaluri and Flavobacterium covae, respectively. Chronic and recurring outbreaks of these bacterial pathogens result in significant economic losses for producers annually. Determining if these pathogens can persist within sediments of commercial ponds is paramount. Experimental persistence trials (PT) were conducted to evaluate the persistence of E. ictaluri and F. covae in pond sediments. Twelve test chambers containing 120 g of sterilized sediment from four commercial catfish ponds were inoculated with either E. ictaluri (S97-773) or F. covae (ALG-00-530) and filled with 8 L of disinfected water. At 1, 2, 4-, 6-, 8-, and 15-days post-inoculation, 1 g of sediment was removed, and colony-forming units (CFU) were enumerated on selective media using 6 × 6 drop plate methods. E. ictaluri population peaked on Day 3 at 6.4 ± 0.5 log10 CFU g-1. Correlation analysis revealed no correlation between the sediment physicochemical parameters and E. ictaluri log10 CFU g-1. However, no viable F. covae colonies were recovered after two PT attempts. Future studies to improve understanding of E. ictaluri pathogenesis and persistence, and potential F. covae persistence in pond bottom sediments are needed.

Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.

BACKGROUND: Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments. RESULTS: Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages. CONCLUSIONS: This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.

Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments.

Recent genome-resolved metagenomic analyses of microbial communities from diverse environments have led to the discovery of many novel lineages that significantly expand the phylogenetic breadth of Archaea. Here, we report the genomic characterization of a new archaeal family based on five metagenome-assembled genomes retrieved from acid mine drainage sediments. Phylogenomic analyses placed these uncultivated archaea at the root of the candidate phylum Parvarchaeota, which expand this lesser-known phylum into two family levels. Genes involved in environmental adaptation and carbohydrate and protein utilization were identified in the ultra-small genomes (estimated size 0.53-0.76 Mb), indicating a survival strategy in this harsh environment (low pH and high heavy metal content). The detection of genes with homology to sulfocyanin suggested a potential involvement in iron cycling. Nevertheless, the absence of the ability to synthesize amino acids and nucleotides implies that these archaea may acquire these biomolecules from the environment or other community members. Applying evolutionary history analysis to Parvarchaeota suggested that members of the two families could broaden their niches by acquiring the potentials of utilizing different substrates. This study expands our knowledge of the diversity, metabolic capacity, and evolutionary history of the Parvarchaeota.

Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus.

The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/ Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1,173 genes, with the accessory genome containing 4,941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.

Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence.

Candidatus Methylospira mobilis is a recently described spiral-shaped, micro-aerobic methanotroph, which inhabits northern freshwater wetlands and sediments. Due to difficulties of cultivation, it could not be obtained in a pure culture for a long time. Here, we report on the successful isolation of strain Shm1, the first axenic culture of this unique methanotroph. The complete genome sequence obtained for strain Shm1 was 4.7 Mb in size and contained over 4800 potential protein-coding genes. The array of genes encoding C1 metabolic capabilities in strain Shm1 was highly similar to that in the closely related non-motile, moderately thermophilic methanotroph Methylococcus capsulatus Bath. The genomes of both methanotrophs encoded both low- and high-affinity oxidases, which allow their survival in a wide range of oxygen concentrations. The repertoire of signal transduction systems encoded in the genome of strain Shm1, however, by far exceeded that in Methylococcus capsulatus Bath but was comparable to those in other motile gammaproteobacterial methanotrophs. The complete set of motility genes, the presence of both the molybdenum-iron and vanadium-iron nitrogenases, as well as a large number of insertion sequences were also among the features, which define environmental adaptation of Methylospira mobilis to water-saturated, micro-oxic, heterogeneous habitats depleted in available nitrogen.

Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.