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Abstract: Periphyton exists ubiquitously in paddy ecosystems of coastal mudflat area, playing significant roles in salt and nutrient cycling between the water and soil interface. However, the definition, composition, influenced factors, and potential function of paddy periphyton are still unclear. We attempt to define paddy periphyton as an integrated and independent microcosm, which is dominated by phototrophic communities, containing both biotic components, such as algal, fungal, bacterial, protozoan, and metazoan, and abiotic components, such as soil, extracellular polymeric substance, and detritus. They interact with each other such as predation and competition, co‐inhabiting in a common microhabitat. The development of paddy periphyton mainly includes three processes: growth stage, mature stage, and fading stage. Paddy periphyton has a significant influence on the salt migration in paddy ecosystem that was reclaimed from coastal mudflat by improving the soil structure, assimilating and adsorbing the salt like sodium chloride, and inhibiting the salt accumulation near the soil surface. As for nutrient management, the roles of paddy periphyton can be summarized as a slow‐released bio‐fertilizer, a nutrient‐removal agent, a nutrient mediator, and a nutrient indicator in mudflat‐reclaimed paddy ecosystem. All these imply that paddy periphyton may be a new and promising biotechnological tool for better salt and nutrient management in paddy ecosystems that degraded from mudflat land, which has a vast potential in the amelioration and fertility improvement of salt‐affected soils, as well as control of nonpoint agricultural pollution in coastal areas. [ABSTRACT FROM AUTHOR]

The mitochondrion is the energy-producing factory of eukaryotic cells, in which oxidative phosphorylation (OXPHOS) is the main pathway for the production of adenosine triphosphate (ATP) by cellular respiration. Because of their vital role in metabolism, mitochondrial proteins are predicted to evolve primarily under constant purifying selection. However, all mitochondrial coding genes of malacostraca had a significantly higher synonymous nt divergence (Ks) in this study. Complex I (NADH dehydrogenase) and complex V (ATP synthase) had a much higher ratio of non-synonymous to synonymous nt divergence (Ka/Ks) and non-synonymous diversity (πNS), whereas complex III (cytochrome bc1 complex) and complex IV (cytochrome c oxidase) had a significantly lower Ka/Ks and non-synonymous diversity (πNS). The Ka/Ks, πNS, πS, and Ka results revealed that two types of mitochondrial genes, NADH dehydrogenase and ATP synthase, in malacostraca were consistent with accelerated evolution. Furthermore, two other types of mitochondrial genes, cytochrome bc1 complex and cytochrome c oxidase, were consistent with purifying selection. Generally, the evolutionary pattern of all mitochondrial proteins of the OXPHOS pathway in malacostraca was not entirely consistent with purifying selection. [ABSTRACT FROM AUTHOR]

There has been a recent emphasis on production of large-sized Eriocheir sinensis broodstock. In China, aquaculturists generally prefer wild-caught (WC) crabs from the Yangtze River as broodstock because offspring performance is superior to that of pond-reared (PR) broodstock. Currently, however, there is a ban on fishing in the Yangtze River, and effects on E. sinensis breeding have not been ascertained. There was comparison in the present study of reproductive performance and semen characteristics of male broodstock of PR and WC groups. After copulation, sperm quantity in the vas deferens of crabs in specimens of both groups was large, although there was a consistent decrease in vaso-somatic index. Although sperm density of PR crabs was less, that of WC specimens remained relatively constant. Specimens of neither group, however, had changes in the hepatopancreas index or condition factor, and sperm survival was close to 100%. Although the acrosome reaction was detected in response to cold-temperature induction, there were differences in extent of reaction to cold temperatures. Importantly, in as many as 98% of sperm from female spermathecae, the reaction was completed, which was considerably greater than 15% for sperm of males post-mating. It is concluded there was no difference between PR and WC crabs with respect to reproductive performance or semen characteristics, and, notably, sperm from PR crabs were of sufficient quality for use in E. sinensis aquaculture enterprises. Accordingly, it is predicted the Yangtze River fishing ban would only have a limited effect on supply of male E. sinensis broodstock. [ABSTRACT FROM AUTHOR]

• Poplar-Agricultural compound management is an efficient ecological management mode. • Soil moisture of Poplar-Agriculture compound management was 1.06–1.17 times with 5–21 % higher soil organic matter. • Poplar compound plantation improves soil and forest environment. • Sustainable management of agroforestry model in costal mudflat reclaimed lands is created. The coastal area of northern Jiangsu is rich in land resources. Meanwhile, Poplar-Agricultural compound management is an efficient and ecological management mode. Thus, it is of great significance to explore the application of agroforestry in different specific soil types in the coastal areas of northern Jiangsu. This study was conducted to investigate the dynamics changes of soil quality and crop growth physiology in eight Poplar-Agricultural complex management mode (Poplar pure forest (CY), Populus L. + Arachis hypogaea (YH), Populus L.+Glycine max (YD), Populus L.+Ipomoea batatas (YS) under coastal silt soil and CY*, YH* YD*.YS* under desalted soil after initial fresh water treatment). The results indicate that under the same soil conditions, compared with pure forests, the effects of Poplar-Agricultural compound management on soil physical and chemical properties were more significant. The growth status of trees was generally better under the condition of desalted soil and the survival rate was 35%–40% higher than that of saline soil. However, the survival rate of trees under the combined management of forestry and agriculture was 5%–10% higher than that of pure forest under the same soil condition. The microenvironment and crop photosynthesis were significantly affected by site conditions. Specifically, microenvironment was more stable under the condition of desalted soil and the photosynthetic effect of crops was better than that of silt soil. Overall, desalinized soil was more suitable for the growth of poplar plantation than silt soil, and Poplar-Agricultural compound management improved soil and forest environment which was better than pure poplar plantation. The study demonstrates that Poplar-Agricultural compound management plays an important role in improving soil quality and crop photosynthesis, and the selection of suitable specific soil conditionals can provide fundamental information for the sustainable development and management of agroforestry model in costal mudflat reclaimed lands. [ABSTRACT FROM AUTHOR]

The exotic species smooth cordgrass (Spartina alterniflora) is recognized as an important invasive species in China, introduced about 40 years ago. The consistent smooth cordgrass invasion significantly modified the coastal ecosystem. Understanding the ecological succession and mechanisms of wetland soil ecosystems is essential for biological conservation after the landscape change resulting from the smooth cordgrass invasion. In this study, five different invasion stages of a 16-year smooth cordgrass invasion sequence were identified in a coastal wetland as no invasion, initial invasion, young invasion, mature invasion, and senescing invasion. The succession of macrofaunal communities and environments were investigated along the gradient of invasion stages. The infauna decreased, and the epifauna increased along the invasion sequence. The significant differences of the communities were detected among the mud flats experiencing different invasion stages. The initial and young invasion stages of smooth cordgrass possibly promote the macrofaunal biodiversity, but biodiversity decreased at mature and senescing invasion stages. The ecological effect of smooth cordgrass invasion on macrofauna depended on the species' traits and the invasion stage. The environmental properties co-varied with invasion stages, and varied significantly among selected habitats. Total organic carbon (TOC), total nitrogen, and the carbon-nitrogen ratio (C/N) strongly related to the smooth cordgrass coverage, stem density, and height. C/N was identified as the key factor for shaping the environment by principal components analysis, and TOC for regulating the macrofaunal community by canonical correspondence analysis. The succession of macrofaunal communities should be considered as a comprehensive response to the variations on environmental properties co-varying with smooth cordgrass invasion in coastal wetlands. Image 1 • Soil macrofaunal communities vary through Spartina alterniflora invasion stages. • Effects of S. alterniflora invasion on soil macrofauna depended on species traits. • S. alterniflora vegetation development significantly influenced soil nutrient conditions. • Early S. alterniflora invasion stages promote soil macrofaunal biodiversity. [ABSTRACT FROM AUTHOR]

How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte., (© 2024. The Author(s).)

Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

The light-dark cycle significantly impacts the growth and development of animals. Mantis shrimps (Oratosquilla oratoria) receive light through their complex photoreceptors. To reveal the adaptive expression mechanism of the mantis shrimp induced in a dark environment, we performed comparative transcriptome analysis with O. oratoria cultured in a light environment (Oo-L) as the control group and O. oratoria cultured in a dark environment (Oo-D) as the experimental group. In the screening of differentially expressed genes (DEGs) between the Oo-L and Oo-D groups, a total of 88 DEGs with |log2FC| > 1 and FDR < 0.05 were identified, of which 78 were upregulated and 10 were downregulated. Then, FBP1 and Pepck were downregulated in the gluconeogenesis pathway, and MKNK2 was upregulated in the MAPK classical pathway, which promoted cell proliferation and differentiation, indicating that the activity of mantis shrimp was slowed and the metabolic rate decreases in the dark environment. As a result, the energy was saved for its growth and development. At the same time, we performed gene set enrichment analysis (GSEA) on all DEGs. In the KEGG pathway analysis, each metabolic pathway in the dark environment showed a slowing trend. GO was enriched in biological processes such as eye development, sensory perception and sensory organ development. The study showed that mantis shrimp slowed down metabolism in the dark, while the role of sensory organs prominent. It provides important information for further understanding the energy metabolism and has great significance to study the physiology of mantis shrimp in dark environment., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Ectomycorrhizal (ECM) fungi play fundamental roles in host plant growth and terrestrial ecosystems. Cedrus deodara is cultivated in several regions in China, has high ecological, economic and medicinal value, for its afforestation and providing timber and wood oil. Here, we investigated ECM colonization status of four urban C. deodara forests in Nantong, East China. We also characterized soil spore banks by conducting bioassay experiments using soils collected from these forests. In total, we identified 19 ECM fungal species, of which 13 species were found in mature forests and 9 species were identified in bioassay experiments, with only 3 species shared. Soil pH and available P content had significant effects on species occurrence in both mature trees and bioassay seedlings on local scales. ECM communities clearly (A = 0.391, p = 0.006) separated mature forests from spore banks. Thelephoracae was the richest family we detected associated with C. deodara , while Trichophaea sp . was the most dominant in mature forests, and Wilcoxina sp . was dominant in spore banks. ECM richness affected the growth of bioassay seedlings, especially after inoculation with 2 ECM species, promoting root growth, significantly (F = 3.028, p = 0.050), but it had no effects on shoots (F = 1.778, p = 0.177). No effect of inoculation rate was found on seedlings growth. To conserve this important tree species, the ECM fungi that are associated with it should be considered., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wen, Lin, Xu, Ma, Peng, Sun, Tang and Shi.)

Background: As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind., Methods and Results: A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria., Conclusion: This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

With the wide use of copper nanoparticles (CuNPs) in various industrial and commercial applications, they inevitably enter the aquatic environment. However, their behavior in the aquatic environment and potential toxicity to aquatic organisms remain little known. In this study, we investigated the behavior of CuNPs in freshwater, as well as the toxicity and bioaccumulation of CuNPs and copper sulfate (CuSO 4 ), used as a positive control for copper ions toxicity, in red swamp crayfish (Procambarus clarkii). The results showed that CuNPs released copper ions into freshwater and aggregated rapidly in freshwater, and their release of copper ions and aggregation slowed down at a higher concentration of CuNPs. The calculated 72-h LC 50 values for crayfish were 1.18 and 0.54 mg/L for CuNPs and CuSO 4 , respectively. Cu accumulation in the gill and hepatopancreas from CuSO 4 treatments was significantly higher than that from CuNPs, and the highest Cu bioaccumulation level in crayfish was found in the gill, followed by hepatopancreas and muscle with the exposure of copper. The activities of the antioxidative enzymes in the crayfish significantly decreased after exposure to CuNPs for 48 h, compared to the control (without CuNPs or CuSO 4 ). Histological examination revealed that there was no significant alteration of hepatopancreas in the crayfish exposed to CuNPs. Meanwhile, the growth of crayfish was not significantly inhibited by CuNPs. These results suggested that CuNPs exposure can induce oxidative stress in the crayfish, gill is the main tissue for their accumulation, and their toxicity is mainly caused by the released copper ions., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Copper (Cu 2+ ), which represents a major physiological challenge for crab culture, is ubiquitous in the aquatic culture environment, and gills are the first organs that come into direct contact with the environment. However, the molecular basis of the response of crabs to Cu 2+ stress remains unclear. Here, we conducted a transcriptome and differential expression analysis on the gills from Chinese mitten crab unexposed and exposed to Cu 2+ for 24 h. The comparative transcriptome analysis identified 2486 differentially expressed genes (DEGs). GO functional analysis and KEGG pathway analysis revealed some DEGs, which were mostly related to immunity, metabolism, osmotic regulation, Cu 2+ homeostasis regulation, antioxidant activity, and detoxification process. Some pathways related to humoral and cellular immunity, such as phagosome, peroxisome, lysosome, mTOR signaling pathway, PI3K-Akt signaling pathway, Toll-like receptor signaling pathway, and T cell receptor signaling pathway were enhanced under Cu 2+ stress. In addition, Cu 2+ stress altered the expression patterns of key phagocytosis and apoptosis genes (lectin, cathepsin L, Rab7, and HSP70), confirming that Cu 2+ can induce oxidative stress and eventually even apoptosis. Histological analysis revealed that the copper can induce damage at the cellular level. This comparative transcriptome analysis provides valuable molecular information to aid future study of the immune mechanism of Chinese mitten crab in response to Cu 2+ stress and provides a foundation for further understanding of the effects of metal toxicity.

Background: Olfaction plays a central role in mating, spawning, obtaining food and escaping predators, which is essential for survival and reproduction of animals. The nature of the olfactory perception in crabs, which is a major group of crustaceans, has remained elusive., Objective: This project aims to explore the molecular mechanism of olfaction in crabs and further improve our understanding of olfactory perception in crustaceans., Methods: The olfactory receptors and ingestion-related gene expression in Eriocheir japonica sinensis were studied by transcriptomic techniques. The de novo assembly, annotation and functional evaluation were performed with bioinformatics tools., Results: A series of chemosensory receptors associated with olfaction were identified including 33 EsIRs, 24 EsIGluRs, 58 EsVIGluRs, 1 EsOR and 1 EsGC-D. We found IRs were key odorant receptors demonstrating a specific species evolutionary trend in crustaceans. Furthermore, we identified ORs in E. j. sinensis and Litopenaeus vannamei. The incomplete EsOR and LvOR1 structures implied that ORs exist in crustaceans, and may have been degenerated or even lost in the olfactory evolutionary process. In addition, comparative transcriptome analysises demonstrated two possible olfactory transduction pathways of E. j. sinensis: the cGMP-mediated olfactory pathway related to vegetable odor molecules and the cAMP-mediated olfactory pathway related to meat odor molecules. The above results were consistent with its omnivorous ingestion of E. j. sinensis., Conclusions: Our study revealed the unique olfactory molecular mechanism of omnivorous crabs and provided valuable information for further functional research on the chemoreception mechanisms in crustaceans.

Tanshinones and phenolic acids are two important metabolites synthesized by the traditional Chinese medicinal plant Salvia miltiorrhiza. There is increasing market demand for these compounds. Here, we isolated and functionally characterized SmERF1L1, a novel JA (Jasmonic acid)-responsive gene encoding AP2/ERF transcription factor, from Salvia miltiorrhiza. SmERF1L1 was responsive to methyl jasmonate (MJ), yeast extraction (YE), salicylic acid (SA) and ethylene treatments. Subcellular localization assay indicated that SmERF1L1 located in the nucleus. Overexpression of SmERF1L1 significantly increased tanshinones production in transgenic S. miltiorrhiza hairy roots by comprehensively upregulating tanshinone biosynthetic pathway genes, especially SmDXR. Yeast one-hybrid (Y1H) and electrophoretic mobility shift assay (EMSA) showed that SmERF1L1 binds to the GCC-box of SmDXR promoter while dual luciferase (Dual-LUC) assay showed that SmERF1L1 positively regulated the expression of SmDXR. Our study suggested that the SmERF1L1 may be a good potential target for further metabolic engineering of bioactive component biosynthesis in S. miltiorrhiza., (Copyright © 2018 Elsevier Ltd. All rights reserved.)