The global dynamic of DNA methylation in response to heat stress revealed epigenetic mechanism of heat acclimation in Saccharina japonica

Saccharina japonica is an ecologically and economically important kelp in cold-temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica. We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non-coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho = 0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome-ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.     

Conserved and novel heat stress‐responsive microRNAs were identified by deep sequencing in Saccharina japonica (Laminariales,Phaeophyta)

As a temperate‐cold species, Saccharina japonica often suffers heat stress when it is transplanted to temperate and subtropical zones. Study the heat stress response and resistance mechanism of Saccharina is of great significance for understanding the acclimation to heat stress under domestication as well as for breeding new cultivars with heat stress resistance. In this study, we identified a set of heat stress‐responsive miRNAs and analysed their regulation during the heat stress response. CO (control) and heat stress (HS) sRNA libraries were constructed and sequenced. Forty‐nine known miRNAs and 75 novel miRNAs were identified, of which seven known and 25 novel miRNAs were expressed differentially under heat stress. Quantitative PCR of six selected miRNAs confirmed that these loci were responsive to heat stress. Thirty‐nine and 712 genes were predicted to be targeted by the seven known miRNAs and 25 novel miRNAs, respectively. Gene function and pathway analyses showed that these genes probably play important roles in S. japonica heat stress tolerance. The miRNAs identified represent the first set of heat‐responsive miRNAs identified from S. japonica, and their identification can help elucidate the heat stress response and resistance mechanisms in S. japonica.     

Identification of five small heat shock protein genes in Spodoptera frugiperda and expression analysis in response to different environmental stressors

Spodoptera frugiperda (J. E. Smith) is a highly adaptable polyphagous migratory pest in tropical and subtropical regions. Small heat shock proteins (sHsps) are molecular chaperones that play important roles in the adaptation to various environment stressors. The present study aimed to clarify the response mechanisms of S. frugiperda to various environmental stressors. We obtained five S. furcifera sHsp genes (SfsHsp21.3, SfsHsp20, SfsHsp20.1, SfsHsp19.3, and SfsHsp29) via cloning. The putative proteins encoded by these genes contained a typical α-crystallin domain. The expression patterns of these genes during different developmental stages, in various tissues of male and female adults, as well as in response to extreme temperatures and UV-A stress were studied via real-time quantitative polymerase chain reaction. The results showed that the expression levels of all five SfsHsp genes differed among the developmental stages as well as among the different tissues of male and female adults. The expression levels of most SfsHsp genes under extreme temperatures and UV-A-induced stress were significantly upregulated in both male and female adults. In contrast, those of SfsHsp20.1 and SfsHsp19.3 were significantly downregulated under cold stress in male adults. Therefore, the different SfsHsp genes of S. frugiperda play unique regulatory roles during development as well as in response to various environmental stressors.     

Impacts of environmental stress on resistance and resilience of algal‐associated bacterial communities

Algal‐associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa. The resistance and resilience of algal‐associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphological niches. Therefore, the level of response to various environmental perturbations may in fact be different for each niche‐specific community. Factorial in situ experiments were set up to investigate the effect of nutrient enrichment and temperature stress on the bacterial communities associated with Caulerpa cylindracea. Bacteria were characterized using the 16S rRNA gene, and the community compositions were compared between different parts of the algal thallus (endo‐, epi‐, and rhizomicrobiome). Resistance and resilience were calculated to further understand the changes of microbial composition in response to perturbations. The results of this study provide evidence that nutrient enrichment has a significant influence on the taxonomic and functional structure of the epimicrobiota, with a low community resistance index observed for both. Temperature and nutrient stress had a significant effect on the rhizomicrobiota taxonomic composition, exhibiting the lowest overall resistance to change. The functional performance of the rhizomicrobiota had low resilience to the combination of stressors, indicating potential additive effects. Interestingly, the endomicrobiota had the highest overall resistance, yet the lowest overall resilience to environmental stress. This further contributes to our understanding of algal microbiome dynamics in response to environmental changes.     

Functional genomic analysis of corals from natural CO2‐seeps reveals core molecular responses involved in acclimatization to ocean acidification

Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here, we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long‐term acclimatization to natural variation in pCO₂. In the coral host, only 61 genes were differentially expressed in response to pCO₂ environment, but the pattern of change was highly consistent between replicate populations, likely reflecting the core expression homeostasis response to ocean acidification. Functional annotations highlight lipid metabolism and a change in the stress response capacity of corals as key parts of this process. Specifically, constitutive downregulation of molecular chaperones was observed, which may impact response to combined climate change‐related stressors. Elevated CO₂ has been hypothesized to benefit photosynthetic organisms but expression changes of in hospite Symbiodinium in response to acidification were greater and less consistent among reef populations. This population‐specific response suggests hosts may need to adapt not only to an acidified environment, but also to changes in their Symbiodinium populations that may not be consistent among environments, adding another challenging dimension to the physiological process of coping with climate change.     

Effect of salinity on seed germination and seedling growth of the halophyte Suaeda japonica Makino

Seed germination and seedling growth of the annual halophyte species Suaeda japonica Makino were investigated in response to variable salinity of sediment pore water. The germination percentage of S. japonica’s soft brown seeds, which are dominant among dimorphic seeds, decreased with an increase in salinity, although germination was still observed at 1200‐mM NaCl concentration. The germination percentage and germination speed observed in April were higher than those observed in December when treated with sediment water with 400–1200 mM of NaCl concentrations. These data suggest that S. japonica seedlings could be established on sediments that experience high temperatures. Germination recovery of S. japonica seeds transferred from 600‐mM NaCl containing sediment (seawater equivalent) was lowest among 0–1200‐mM NaCl treatments, implying the low tolerance of seawater conditions of S. japonica seeds. Seeds germinated in 900‐ to 1200‐mM NaCl medium showed poor growth, but survived, in hypersaline conditions, and exhibited improvement in growth upon transfer to lower salinity.     

Effect of blue light on indoor seedling culture of <Emphasis Type="Italic">Saccharina japonica</Emphasis> (Phaeophyta)

Saccharina japonica is a brown alga that has been commercially cultured on a large scale in China. Integrating the light condition under seawater and the adaptation of Saccharina to this condition, it is expected that blue light would be beneficial to Saccharina culture system. Consequently, the detailed effect of blue light on the key stages during indoor seedling culture of S. japonica was investigated in this study. Irradiances and light qualities had little effect on zoospore attachment and germination. Egg formation occurred sooner under blue light than white light. Under optimum irradiances, 95 ± 4% female gametophytes gave rise to eggs in 6 d under blue light, while it took 12 d for over 90% formation of eggs under white light. Over a culture period of 3 weeks, mean sporeling length and width under blue light was 1.39 and 1.56 times of that under white light, respectively, while the mean sporeling size obtained under red light was only 25% of that under white light. The higher growth rate under blue light was largely due to higher photosynthetic efficiency, as indicated by chlorophyll fluorescence of photosystem II. In addition, the mean ratio of sporeling width to length under blue light was significantly higher than that under white light. These results suggest that blue light would be superior to white light for indoor seedling culture of S. japonica. Based on these findings, an improved S. japonica seedling culture system is discussed.     

Chromosome‐level genome assembly of the predator Propylea japonica to understand its tolerance to insecticides and high temperatures

The ladybird beetle Propylea japonica is an important natural enemy in agro‐ecological systems. Studies on the strong tolerance of P. japonica to high temperatures and insecticides, and its population and phenotype diversity have recently increased. However, abundant genome resources for obtaining insights into stress‐resistance mechanisms and genetic intra‐species diversity for P. japonica are lacking. Here, we constructed the P. japonica genome maps using Pacific Bioscience (PacBio) and Illumina sequencing technologies. The genome size was 850.90 Mb with a contig N50 of 813.13 kb. The Hi‐C sequence data were used to upgrade draft genome assemblies; 4,777 contigs were assembled to 10 chromosomes; and the final draft genome assembly was 803.93 Mb with a contig N50 of 813.98 kb and a scaffold N50 of 100.34 Mb. Approximately 495.38 Mb of repeated sequences was annotated. The 18,018 protein‐coding genes were predicted, of which 95.78% were functionally annotated, and 1,407 genes were species‐specific. The phylogenetic analysis showed that P. japonica diverged from the ancestor of Anoplophora glabripennis and Tribolium castaneum ~ 236.21 million years ago. We detected that some important gene families involved in detoxification of pesticides and tolerance to heat stress were expanded in P. japonica, especially cytochrome P450 and Hsp70 genes. Overall, the high‐quality draft genome sequence of P. japonica will provide invaluable resource for understanding the molecular mechanisms of stress resistance and will facilitate the research on population genetics, evolution and phylogeny of Coccinellidae. This genome will also provide new avenues for conserving the diversity of predator insects.