Exploring salt tolerance and indicator traits across four temperate lineages of the common wetland plant, Phragmites australis.

Common reed (Phragmites australis) is a widely utilized plant for wetland restoration and construction, facing challenges posed by high salinity as a stressor. Among the diverse P. australis lineages, functional traits variation provides a valuable genetic resource for identifying salt-tolerant individuals. However, previous investigations on P. australis salt tolerance have been restricted to regional scales, hindering the identification of key functional traits associated with salt tolerance in natural habitats. To address this gap, we conducted a greenhouse experiment to assess and compare the salt tolerance of four major temperate P. australis lineages worldwide. We utilized the maximum quantum yield of photosystem II (Fv/Fm) as a health indicator, while final biomass and wilt status served as indicators of salt tolerance across lineages. Our findings revealed significant differentiation in plant functional traits among different lineages, but no significant effect of interaction between salinity and lineage on most traits. Correlation analyses between salt-tolerance indicators and functional traits in the control group indicated that biomass, leaf width, and relative leaf water content are potential predictors of salt tolerance. However, ecological strategies, physiological traits, and latitudinal origin did not exhibit significant correlations with salt tolerance. Our study provides valuable indicator traits for effectively screening salinity-tolerant genotypes of P. australis in field settings, and holds significant potential for enhancing wetland construction and biomass production in marginal lands.

Soil salinity, not plant genotype or geographical distance, shapes soil microbial community of a reed wetland at a fine scale in the Yellow River Delta.

Soil salinization is one of the most severe environmental problems restricting biodiversity maintenance and ecosystem functioning in a coastal wetland. Recent studies have well documented how salinization affects soil microbial communities along vegetation succession of coastal wetlands. However, the salinity effect is rarely assessed in the context of plant intraspecific variation. Here, we analyzed the soil bacterial and fungal communities of Phragmites australis wetland using amplicon high-throughput sequencing at a fine scale (within 1000 m) in the Yellow River Delta. Our results revealed that microbial diversity is significantly correlated to soil salinity (assessed as electrical conductivity, EC) but not to soil nutrients (N and P content) or plant intraspecific traits (leaf length, shoot height, and neutral genetic variation). Specifically, the microbial diversity tended to decrease with increased EC, and the bacterial community was more sensitive to EC change than the fungal community. The dominant bacterial phyla were Proteobacteria, Actinobacteria, and Chloroflexi, and the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The relative abundance of Actinobacteria was significantly negatively correlated to EC, while Proteobacteria were positively correlated to EC. In high salinity (> 1 mS/cm), the role of the stochastic processes became more important in community assembly according to habitat niche breadth estimation, neutral community model, C-score metric, and normalized stochasticity ratio. Additional common garden and microcosm experiments provided evidence that the genotype effect of P. australis on soil microbiome might only occur between lineages from different regions but not from the same region like the Yellow River Delta. Our findings provide new insights into soil microbial community assembly processes with the intraspecific variation of host plants in the wetland ecosystem and offer a scientific reference for salinity mitigation and vegetation management of coastal wetlands under future global changes.

In silico identification and verification of ferroptosis-related genes in type 2 diabetic islets.

Type 2 diabetes (T2D) is a major global public health burden, with ß-cell dysfunction a key component in its pathogenesis. However, the exact pathogenesis of ß-cell dysfunction in T2D is yet to be fully elucidated. Ferroptosis, a recently discovered regulated form of non-apoptotic cell death, plays a vital role in the development of diabetes and its complications. The current study aimed to identify the key molecules involved in ß-cell ferroptosis3 in patients with T2D using the mRNA expression profile data of GSE25724 by bioinformatic approaches. The differentially expressed mRNAs (DE-mRNAs) in human islets of patients with T2D were screened using the islet mRNA expression profiling data from the Gene Expression Omnibus and their intersection with ferroptosis genes was then obtained. Ferroptosis-related DE-mRNA functional and pathway enrichment analysis in T2D islet were performed. Using a protein-protein interaction (PPI) network constructed from the STRING database, Cytoscape software identified ferroptosis-related hub genes in the T2D islet with a Degree algorithm. We constructed a miRNA-hub gene network using the miRWalk database. We generated a rat model of T2D to assess the expression of hub genes. A total of 1,316 DE-mRNAs were identified in the islet of patients between T2D and non-T2D (NT2D), including 221 and 1,095 up- and down-regulated genes. Gene set enrichment analysis revealed that the ferroptosis-related gene set was significantly different in islets between T2D and NT2D at an overall level. A total of 33 ferroptosis-related DE-mRNAs were identified, most of which were significantly enriched in pathways including ferroptosis. The established PPI network with ferroptosis-related DE-mRNAs identified five hub genes (JUN, NFE2L2, ATG5, KRAS, and HSPA5), and the area under the ROC curve of these five hub genes was 0.929 in the Logistic regression model. We constructed a regulatory network of hub genes and miRNAs, and the results showed that suggesting that hsa-miR-6855-5p, hsa-miR-9985, and hsa-miR-584-5p could regulate most hub genes. In rat model of T2D, the protein expression levels of JUN and NFE2L2 in pancreatic tissues were upregulated and downregulated, respectively. These results contribute to further elucidation of ferroptosis-related molecular mechanisms in the pathogenesis of ß-cell dysfunction of T2D.

Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis).

Polyploidization in plants is thought to have occurred as coping mechanism with environmental stresses. Polyploidization-driven adaptation is often achieved through interplay of gene networks involved in differentially expressed genes, which triggers the plant to evolve special phenotypic traits for survival. Phragmites australis is a cosmopolitan species with highly variable phenotypic traits and high adaptation capacity to various habitats. The species' ploidy level varies from 3x to 12x, thus it is an ideal organism to investigate the molecular evolution of polyploidy and gene regulation mediated by different numbers of chromosome copies. In this study, we used high-throughput RNAseq data as a tool, to analyze the gene expression profiles in tetraploid and octoploid P. australis. The estimated divergence time between tetraploid and octoploid P. australis was dated to the border between Pliocene and Pleistocene. This study identified 439 up- and 956 down-regulated transcripts in tetraploids compared to octoploids. Gene ontology and pathway analysis revealed that tetraploids tended to express genes responsible for reproduction and seed germination to complete the reproduction cycle early, and expressed genes related to defense against UV-B light and fungi, whereas octoploids expressed mainly genes related to thermotolerance. Most differentially expressed genes were enriched in chaperones, folding catalysts and protein processing in endoplasmic reticulum pathways. Multiple biased isoform usage of the same gene was detected in differentially expressed genes, and the ones upregulated in octoploids were related to reduced DNA methylation. Our study provides new insights into the role of polyploidization on environmental responses and potential stress tolerance in grass species.

The river shapes the genetic diversity of common reed in the Yellow River Delta via hydrochory dispersal and habitat selection.

Understanding the driving mechanisms of local genetic diversity is a fundamental challenge under the global environmental changes. Rivers provide an excellent study system to demonstrate the effects of hydrochory dispersal and habitat selection on genetic diversity of riparian flora. In this study, we focused on the genetic variation of common reed (Phragmites australis) in the Yellow River Delta, China. Firstly, samples were collected in the Yellow River Delta, its neighboring wetland and its upstream plain. The genetic variation of P. australis was investigated using two chloroplast DNA fragments and eleven nuclear microsatellites. The findings showed that the genetic variation of P. australis in the Yellow River Delta belonged to two distinct lineages (haplotype O and haplotype P), which were similar to the upstream, and to the neighboring populations, respectively. Moreover, the genetic results suggested the potential dispersal of haplotype O from upstream to downstream. Secondly, we surveyed the plant functional traits of common reed from the Yellow River Delta in the field and in the common garden. The results showed significant differences between riverine and non-riverine populations in plant functional traits (e.g. specific leaf area and leaf length), haplotype composition and genetic clustering, which implied natural selection by habitat conditions. Lastly, we re-analyzed the plant performance data from a salt manipulation experiment with different haplotypes, and the results supported that salinity is a significant selective stressor on P. australis lineages in the Yellow River Delta. Our study highlights the significance of hydrochory dispersal and habitat selection in the river effects on genetic diversity of riparian flora, and provides important information for biodiversity conservation and wetland management in the Yellow River Delta.

Insight into the effect of nitrogen-rich substrates on the community structure and the co-occurrence network of thermophiles during lignocellulose-based composting.

Thermophilic microorganisms play vital roles in the composting process. To elucidate how raw materials affect thermophilic microbial community composition and their interactions, the succession of thermophilic bacterial and fungal communities were monitored in reed straw co-composting with four common nitrogen-rich substrates. The results of high-throughput sequencing showed that raw materials and composting process significantly changed bacterial and fungal community composition. Firmicutes and Actinobacteria drove the assembly of bacterial communities, while Ascomycetes drove the assembly of fungal communities. Network analysis indicated that during the composting process, the addition of nitrogen-rich sources abundant in easily degradable substances promoted the complexity of thermophilic microbial network. Moreover, microorganisms mainly exhibited synergistic effects, and inter-kingdom competition was more intense than intra-kingdom competition. Notably, rare species play essential roles in maintaining the network construction. Our findings provided novel insights into thermophilic microbial community assembly and their co-occurrence networks during the composting process.

Alteration of Intestinal Microbiota in 3-Deoxyglucosone-Induced Prediabetic Rats.

Our previous research suggests that 3-deoxyglucosone (3DG), formed in the caramelization course and Maillard reactions in food, is an independent factor for the development of prediabetes. Since the relationship between type 2 diabetes (T2D) and intestinal microbiota is moving from correlation to causality, we investigated the alterations in the composition and function of the intestinal microbiota in 3DG-induced prediabetic rats. Rats were given 50 mg/kg 3DG by intragastric administration for two weeks. Microbial profiling in faeces samples was determined through the 16S rRNA gene sequence. The glucagon-like peptide 2 (GLP-2) and lipopolysaccharide (LPS) levels in plasma and intestinal tissues were measured by ELISA and Limulus test, respectively. 3DG treatment did not significantly change the richness and evenness but affected the composition of intestinal microbiota. At the phylum level, 3DG treatment increased the abundance of nondominant bacteria Proteobacteria but did not cause the change of the dominant bacteria. Meanwhile, the abundance of the Prevotellaceae family and Parasutterela genus and the Alcaligencaeae family and Burkholderiales order and its attachment to the Betaproteobacteria class were overrepresented in the 3DG group. The bacteria of Candidatus Soleaferrea genus, Gelria genus, and Thermoanaerobacteraceae family and its attachment to Thermoanaerobacterales order were apparently more abundant in the control group. In addition, 45 KEGG pathways were altered after two-week intragastric administration of 3DG. Among these KEGG pathways, 13 KEGG pathways were involved in host metabolic function related to amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and metabolism of terpenoids and polyketides. Moreover, the increased LPS levels and the decreased GLP-2 concentration in plasma and intestinal tissues were observed in 3DG-treated rats, together with the impaired fasting glucose and oral glucose tolerance. The alterations in composition and function of the intestinal microbiota were observed in 3DG-treated rats, which provides a possible mechanism linking exogenous 3DG intake to the development of prediabetes.

Development and characterization of EST-SSR markers for Vitex negundo var. heterophylla (Lamiaceae).

PREMISE OF THE STUDY: Vitex negundo var. heterophylla (Lamiaceae) is a dominant shrub in the warm temperate zone of northern China. Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed to investigate its genetic diversity and structure. METHODS AND RESULTS: We detected 12,075 SSRs in V. negundo var. heterophylla using transcriptome sequencing. Primer pairs for 100 SSR loci were designed and amplified in three populations of V. negundo var. heterophylla. Sixty loci were amplified, of which 14 were polymorphic. The number of alleles per locus ranged from two to 15, and levels of observed and expected heterozygosity ranged from 0.241 to 0.828 and from 0.426 to 0.873, respectively. All primer pairs amplified PCR products from V. rotundifolia but only four of them amplified products from Leonurus japonicus. CONCLUSIONS: The identified EST-SSR markers will be useful for future molecular and reproductive ecology studies of V. negundo var. heterophylla and V. rotundifolia.

Identification of novel miRNAs and miRNA expression profiling in wheat hybrid necrosis.

MicroRNAs (miRNAs) play essential roles in a vast array of biological processes, including growth and development, defense against viral infection, and responses to environmental changes in plant. Wheat hybrid necrosis is an interesting genetic phenomenon observed frequency and it is lethal or semi lethal, resulting in gradual death or loss of productivity. However, the molecular basis and mechanisms associated with hybrid necrosis in wheat are still not well understood. Here, we report the population and expression profiles of miRNAs in wheat hybrid necrosis. We identified a total of 57 conserved miRNA families as well as 182 putative novel miRNAs. Expression profiling revealed that expression of 49 known miRNAs and 165 novel miRNAs was changed in hybrid necrosis. And the expression levels of some miRNAs and their predicated targets have been confirmed by qRT-PCR. These results indicate that these miRNAs, especially miR159, miR166, miR167 and miR5072 could be involved in the extensive regulation of gene expression in response to hybrid necrosis.