Environment-induced heritable variations are common in Arabidopsis thaliana.

Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.

Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals.

The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.

New genes helped acorn barnacles adapt to a sessile lifestyle.

Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.

The spatial correlation network structure and its formation mechanism of urban high-quality economic development: a comparative analysis from the Yangtze River Economic Belt and the Yellow River Basin in China.

In the context of regional integration, it is more than crucial to compare and analyze the spatial correlation network structure and formation mechanism of high-quality economic development in the Yangtze River Economic Belt and the Yellow River Basin urban cities as an attempt to strengthen collaborative work on high-quality economic development in both river basins. The paper measured high-quality economic development of the Yangtze River Economic Belt and the Yellow River Basin from 2010 to 2021. Then, it employed social network analysis and the QAP method to study the network structure's characteristics and formation mechanism. The conclusion of the research illustrates a few points clearly that first, the high-quality economic development of the two rivers presents a complex and multithreaded network structure. Although the network structure is hold at a comparatively stable state, the correlation degree needs improvement. Second, cities such as Chongqing, Wuhan, Hefei, Nanjing, Hangzhou, Shanghai, and Changsha and cities like Zhengzhou, Xi'an, Luoyang, Yulin, Hulunbuir, Ordos, and Nanyang are at the very central as well as central position of the network. The spatial correlation networks of the Yangtze River Economic Belt and the Yellow River Basin can be divided into four plates: "agent plate," "main outflow plate," "bidirectional spillover plate," and "main inflow plate." Third, reverse geographical distance and differences in the digital economy attach great significance to the spatial correlation networks of the two basins. The difference in urbanization level makes significant impacts only on the spatial correlation network of the Yangtze River Economic Belt, while the difference in environmental regulation and material capital accumulation only significantly influences the spatial correlation network of the Yellow River Basin.

Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests.

Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.

The effectiveness of artificial microbial community selection: a conceptual framework and a meta-analysis.

The potential for artificial selection at the community level to improve ecosystem functions has received much attention in applied microbiology. However, we do not yet understand what conditions in general allow for successful artificial community selection. Here we propose six hypotheses about factors that determine the effectiveness of artificial microbial community selection, based on previous studies in this field and those on multilevel selection. In particular, we emphasize selection strategies that increase the variance among communities. We then report a meta-analysis of published artificial microbial community selection experiments. The reported responses to community selection were highly variable among experiments; and the overall effect size was not significantly different from zero. The effectiveness of artificial community selection was greater when there was no migration among communities, and when the number of replicated communities subjected to selection was larger. The meta-analysis also suggests that the success of artificial community selection may be contingent on multiple necessary conditions. We argue that artificial community selection can be a promising approach, and suggest some strategies for improving the performance of artificial community selection programs.

Physiological and transcriptomic responses to cold waves of the most cold-tolerant mangrove, Kandelia obovata.

Mangrove forests inhabit tropical or subtropical intertidal zones and have remarkable abilities in coastline protection. Kandelia obovata is considered the most cold-tolerant mangrove species and has been widely transplanted to the north subtropical zone of China for ecological restoration. However, the physiological and molecular mechanisms of K. obovata under colder climate was still unclear. Here, we manipulated the typical climate of cold waves in the north subtropical zone with cycles of cold/recovery and analyzed the physiological and transcriptomic responses of seedlings. We found that both physiological traits and gene expression profiles differed between the first and later cold waves, indicating K. obovata seedlings were acclimated by the first cold experience and prepared for latter cold waves. 1,135 cold acclimation-related genes (CARGs) were revealed, related to calcium signaling, cell wall modification, and post-translational modifications of ubiquitination pathways. We identified the roles of CBFs and CBF-independent transcription factors (ZATs and CZF1s) in regulating the expression of CARGs, suggesting both CBF-dependent and CBF- independent pathways functioned in the cold acclimation of K. obovata. Finally, we proposed a molecular mechanism of K. obovata cold acclimation with several key CARGs and transcriptional factors involved. Our experiments reveal strategies of K. obovata coping with cold environments and provide prospects for mangrove rehabilitation and management.

Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana.

The phenotypes of plants can be influenced by the environmental conditions experienced by their parents. However, there is still much uncertainty about how common and how predictable such parental environmental effects really are. We carried out a comprehensive experimental test for parental effects, subjecting plants of multiple Arabidopsis thaliana genotypes to 24 different biotic or abiotic stresses, or combinations thereof, and comparing their offspring phenotypes in a common environment. The majority of environmental stresses caused significant parental effects, with -35% to +38% changes in offspring fitness. The expression of parental effects was strongly genotype-dependent, and multiple environmental stresses often acted nonadditively when combined. The direction and magnitude of parental effects were unrelated to the direct effects on the parents: Some environmental stresses did not affect the parents but caused substantial effects on offspring, while for others, the situation was reversed. Our study demonstrates that parental environmental effects are common and often strong in A. thaliana, but they are genotype-dependent, act nonadditively, and are difficult to predict. We should thus be cautious with generalizing from simple studies with single plant genotypes and/or only few individual environmental stresses. A thorough and general understanding of parental effects requires large multifactorial experiments.

Threats to Terrestrial Plants from Emerging Nanoplastics.

Nanoplastics are ubiquitous in ecosystems and impact planetary health. However, our current understanding on the impacts of nanoplastics upon terrestrial plants is fragmented. The lack of systematic approaches to evaluating these impacts limits our ability to generalize from existing studies and perpetuates regulatory barriers. Here, we undertook a meta-analysis to quantify the overall strength of nanoplastic impacts upon terrestrial plants and developed a machine learning approach to predict adverse impacts and identify contributing features. We show that adverse impacts are primarily associated with toxicity metrics, followed by plant species, nanoplastic mass concentration and size, and exposure time and medium. These results highlight that the threats of nanoplastics depend on a diversity of reactions across molecular to ecosystem scales. These reactions are rooted in both the spatial and functional complexities of nanoplastics and, as such, are specific to both the plastic characteristics and environmental conditions. These findings demonstrate the utility of interrogating the diversity of toxicity data in the literature to update both risk assessments and evidence-based policy actions.

Plant-defense mimicry facilitates rapid dispersal of short-lived seeds by hornets.

Rates of seed dispersal have rarely been considered important. Here, we demonstrate through field observations and experiments that rapid dispersal is essential for the unusually short-lived seeds of Aquilaria sinensis (agarwood; Thymelaeaceae), which desiccate and die within hours of exposure by fruit dehiscence in the hot, dry forest canopy in tropical southwest China. We show that three species of Vespa hornets remove most seeds within minutes of exposure. The hornets consume only the fleshy elaiosomes and deposit most seeds in damp shade, where they can germinate, a mean of 166 m from the parent tree. Electrophysiological assays and field experiments demonstrate that the hornets are attracted by highly volatile short-carbon-chain (C5-C9) compounds, including aldehydes, ketones, alcohols, and acids, emitted from the dehiscent fruit capsule. These attractive fruit volatiles share 14 of 17 major electrophysiologically active compounds with those emitted from herbivore-damaged leaves, which attract predators, including hornets. Rapid seed dispersal thus appears to have been achieved in this species by the re-purposing of a rapid indirect defense mechanism. We predict that rapid seed dispersal by various mechanisms will be more widespread than currently documented and suggest that volatile attractants are more effective in facilitating this than visual signals, which are blocked by vegetation.

Asymmetric character displacement in mixed oak stands.

Ecological character displacement (ECD) refers to a pattern of increased divergence at sites where species ranges overlap caused by competition for resources. Although ECD is believed to be common, there are few in-depth studies that clearly establish its existence, especially in plants. Thus, we have compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks: Quercus dentata and Quercus aliena. In contrast to previous studies, we define sympatry and allopatry at a local scale, thereby comparing populations that can or cannot directly interact. Using genetic markers, we found greater genetic divergence between the two oak species growing in mixed stands and inferred that long-term gene flow has predominantly occurred asymmetrically from the cold-tolerant species (Q. dentata) to the warm-demanding later colonizing species (Q. aliena). Analysis of leaf traits revealed greater divergence in mixed than in pure oak stands. This was mostly due to the later colonizing species being characterized by more resource-conservative traits in the presence of the other species. Controlling for relevant environmental differences did not alter these conclusions. These results suggest that asymmetric trait divergence can take place where species coexist, possibly due to the imbalance in demographic history of species resulting in asymmetric inter-specific selection pressures.

Waterborne Polyurethane Acrylates Preparation towards 3D Printing for Sewage Treatment.

Conventional immobilized nitrifying bacteria technologies are limited to fixed beds with regular shapes such as spheres and cubes. To achieve a higher mass transfer capacity, a complex-structured cultivate bed with larger specific surface areas is usually expected. Direct ink writing (DIW) 3D printing technology is capable of preparing fixed beds where nitrifying bacteria are embedded in without geometry limitations. Nevertheless, conventional bacterial carrier materials for sewage treatment tend to easily collapse during printing procedures. Here, we developed a novel biocompatible waterborne polyurethane acrylate (WPUA) with favorable mechanical properties synthesized by introducing amino acids. End-capped by hydroxyethyl acrylate and mixed with sodium alginate (SA), a dual stimuli-responsive ink for DIW 3D printers was prepared. A robust and insoluble crosslinking network was formed by UV-curing and ion-exchange curing. This dual-cured network with a higher crosslinking density provides better recyclability and protection for cryogenic preservation. The corresponding results show that the nitrification efficiency for printed bioreactors reached 99.9% in 72 h, which is faster than unprinted samples and unmodified WPUA samples. This work provides an innovative immobilization method for 3D printing bacterial active structures and has high potential for future sewage treatment.

Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions.

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.

Biodiversity at disequilibrium: updating conservation strategies in cities.

Greenspaces represent an ark for urban biodiversity, but understanding their carrying capacity to sustain species remains challenging. Old greenspaces that were fragmented from natural habitats are now overcrowded, while revegetated new greenspaces remain vacant. This is because they have different processes leading towards biodiversity equilibrium, and conservation management needs to differentiate between fragmented and revegetated greenspaces.

Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations.

BACKGROUND: Restoration through planting is the dominant strategy to conserve mangrove ecosystems. However, many of the plantations fail to survive. Site and seeding selection matters for planting. The process of afforestation, where individuals were planted in a novel environment, is essentially human-controlled transplanting events. Trying to deepen and expand the understanding of the effects of transplanting on plants, we have performed a seven-year-long reciprocal transplant experiment on Kandelia obovata along a latitudinal gradient. RESULTS: Combined phenotypic analyses and next-generation sequencing, we found phenotypic discrepancies among individuals from different populations in the common garden and genetic differentiation among populations. The central population with abundant genetic diversity and high phenotypic plasticity had a wide plantable range. But its biomass was reduced after being transferred to other latitudes. The suppressed expression of lignin biosynthesis genes revealed by RNA-seq was responsible for the biomass reduction. Moreover, using whole-genome bisulfite sequencing, we observed modification of DNA methylation in MADS-box genes that involved in the regulation of flowering time, which might contribute to the adaptation to new environments. CONCLUSIONS: Taking advantage of classical ecological experiments as well as multi-omics analyses, our work observed morphology differences and genetic differentiation among different populations of K. obovata, offering scientific advice for the development of restoration strategy with long-term efficacy, also explored phenotypic, transcript, and epigenetic responses of plants to transplanting events between latitudes.

Fine-tuning Flowering Time via Genome Editing of Upstream Open Reading Frames of Heading Date 2 in Rice.

Flowering time of rice (Oryza sativa L.) is among the most important agronomic traits for region adaptation and grain yield. In the process of rice breeding, efficient and slightly modulating the flowering time of an elite cultivar would be more popular with breeder. Hence, we are interested in slightly increasing the expression of flowering repressors by CRISPR/Cas9 genome editing system. It was predicated there were three uORFs in 5' leader sequence of Hd2. In this study, through editing Hd2 uORFs, we got four homozygous mutant lines. Phenotypic analysis showed that the hd2 urf edited lines flowered later by 4.6-11.2 days relative to wild type SJ2. Supporting the later flowering phenotype, the expression of Ehd1, Hd3a, and RFT1 is significantly decreased in hd2 urf than that in wild type. Moreover, we found that the transcription level of Hd2 is not affected, whereas the Hd2 protein level was increased in hd2 urf compared with wild type, which indicated that Hd2 uORFs indeed affect the translation of a downstream Hd2 pORF. In summary, we developed a efficient approach for delaying rice heading date based on editing uORF region of flowering repressor, which is time and labor saving compared to traditional breeding. In future, uORF of other flowering time related genes, including flowering promoter and flowering repressor genes, can also be used as targets to fine-tune the flowering time of varieties.

Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association.

Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. pumila, and its specific pollinating wasp, Wiebesia pumilae. We combine multi-omics with validation experiments to reveal molecular mechanisms underlying this specialized interaction. In the plant, we identify the specific compound attracting pollinators and validate the function of several key genes regulating its biosynthesis. In the pollinator, we find a highly reduced number of odorant-binding protein genes and an odorant-binding protein mainly binding the attractant. During antagonistic interaction, we find similar chemical profiles and turnovers throughout the development of galled ovules and seeds, and a significant contraction of detoxification-related gene families in the pollinator. Our study identifies some key genes bridging coevolved mutualists, establishing expectations for more diffuse insect-pollinator systems.

Differentiation of Cold Tolerance in an Artificial Population of a Mangrove Species, Kandelia obovata, Is Associated With Geographic Origins.

Temperature is one of the climatic factors that shape the geographic distribution of plant populations. Mangroves are temperature-sensitive plants, and their distributions are severely limited by low temperatures. It is unknown, however, to what extent temperature contributes to their population differentiation and evolution. Kandelia obovata (Rhizophoraceae) is a mangrove species with high cold tolerance in the Northern Hemisphere. We investigated the phenotypic responses of an artificial population of K. obovata, with plants transplanted from different source populations, to extremely low temperatures during winter of 2015-2016 in Yueqing County (28°20'N), Zhejiang Province of China. Using two binary traits, "with/without leaves alive on the branches" and "with/without alive buds on the tips of branches," we classified plants in this artificial population into strong, moderate and poor cold resistance groups. We further assessed the genetic diversity, structure and differentiation of these three groups, as well as five natural populations along a latitudinal gradient using ten nuclear and six plastid microsatellite markers. Microsatellite data revealed genetic differentiation among the natural populations along the latitudinal gradient. Molecular data indicated that the cold tolerance of three groups in the artificial population was associated with their geographic origins, and that the most cold-tolerant group came from the northernmost natural population. Our study thus indicates that natural populations of K. obovata may have evolved divergent capacity of cold tolerance.

Adaptive transgenerational effects remain significant.

The comment by Sánchez-Tójar et al. (2020, Ecol Lett) questioned the methodology, transparency and conclusion of our study (Ecol Lett, 22, 2019, 1976). The comment has overlooked important evolutionary assumptions in their reanalysis, and the issues raised were in fact dealt with through the peer-review process. Far from being biased, the key conclusion of our meta-analysis still stands; transgenerational effects are largely adaptive.