SEPALLATA­-like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs
Background The architecture of inflorescence and the development of floral organs can influence the yield of seeds and have a significant impact on plant propagation. E-class floral homeotic MADS-box genes exhibit important roles in regulation of floral transition and differentiation of floral organs. Woad (Isatis indigotica) possesses unique inflorescence, floral organs and fruit. However, very little research has been carried out to determine the function of MADS-box genes in this medicinal cruciferous plant species. Results SEPALLATA orthologs in I. indigotica were cloned by degenerate PCR. The sequence possessing the highest identity with SEP2 and SEP4 of Arabidopsis were named as IiSEP2 and IiSEP4, respectively. Constitutive expression of IiSEP2 in Columbia (Col-0) ecotype of Arabidopsis led to early flowering, and the number of the flowers and the lateral branches was reduced, indicating an alteration in architecture of the inflorescences. Moreover, the number of the floral organs was declined, the sepals were turned into carpelloid tissues bearing stigmatic papillae and ovules, and secondary flower could be produced in apetalous terminal flowers. In 35S::IiSEP4-GFP transgenic Arabidopsis plants in Landsberg erecta (Ler) genetic background, the number of the floral organs was decreased, sepals were converted into curly carpelloid structures, accompanied by generation of ovules. Simultaneously, the size of petals, stamens and siliques was diminished. In 35S::IiSEP4-GFP transgenic plants of apetalous ap1 cal double mutant in Ler genetic background, the cauliflower phenotype was attenuated significantly, and the petal formation could be rescued. Occasionally, chimeric organs composed of petaloid and sepaloid tissues, or petaloid and stamineous tissues, were produced in IiSEP4 transgenic plants of apl cal double mutant. It suggested that overexpression of IiSEP4 could restore the capacity in petal differentiation. Silencing of IiSEP4 by Virus-Induced Gene Silencing (VIGS) can delay the flowering time, and reduce the number and size of the floral organs in woad flowers. Conclusion All the results showed that SEPALLATA-like genes could influence the architecture of the inflorescence and the determinacy of the floral meristems, and was also related to development of the floral organs.
Ma et al. (2022) SEPALLATA­-like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs. PeerJ 10:e13034 https://doi.org/10.7717/peerj.13034
Alterations of gut fungal microbiota in patients with rheumatoid arthritis
Background Rheumatoid arthritis (RA) is a systemic autoimmune disease, in addition, gut microbiota plays an important role in the etiology of RA. However, our understanding of alterations to the gut fungal microbiota in Chinese population with RA is still limited. Methods Serum samples were obtained from 62 patients with RA, and 39 age- and gender-matched healthy controls (HCs). Fecal samples were obtained from 42 RA patients and 39 HCs. Fecal fungal microbiota targeting internal transcribed spacer region 2 (ITS2) rRNA genes was investigated using MiSeq sequencing, as well as their associations with some diagnostic biomarkers for RA. Results Our results showed that the fungal diversity did not alter in RA patients but taxonomic composition of the fecal fungal microbiota did. The gut mycobiota of RA patients was characterized by decreased abundance of Pholiota, Scedosporium, and Trichosporon. The linear discriminant analysis (LDA) effect size analysis (LEfSe) analysis identified several RA-enriched fungal genera, which were positively correlated with most RA biomarkers. Furthermore, since RA is an age- and gende-related disease, we classified RA patients into subgroups with age and gender and analyzed the sequencing results. Our data demonstrated that Wallemia and Irpex were the most discriminatory against RA patients over 60 years old, while Pseudeurotiaceae was the most discriminatory against female RA patients. Conclusions The case-control study presented here confirmed the alterations of gut fungal microbiota in Chinese patients with RA, and we speculated that the fungal dysbiosis may contribute to RA development.
Sun et al. (2022) Alterations of gut fungal microbiota in patients with rheumatoid arthritis. PeerJ 10:e13037 https://doi.org/10.7717/peerj.13037
Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
Gill et al. (2022) Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 10:e12835 https://doi.org/10.7717/peerj.12835
Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy
Iberian natural steppes have traditionally been used for extensive sheep grazing, which has been noted to be positively associated with steppe bird abundance and diversity. Sheep numbers in Spain, which harbors the largest European populations of many steppe bird species, decreased by 9.2 million (37.3%) between 1992 and 2020. Steppe birds in Spain have faced dramatic declines during the same period, but there is a lack of knowledge about the potential association between sheep and open-habitat bird declines. We used sheep data from the Spanish Ministry of Agriculture and bird data (1998–2018) from the Spanish Common Bird Monitoring Program to assess the association at the Spanish scale between sheep decline and the Farmland Bird Index (FBI) and the Natural Shrub-steppe Bird Index (SBI). We also used an independent dataset on population trends of the Dupont’s Lark (Chersophilus duponti) to assess the relationship between sheep numbers and the decline of this threatened steppe specialist passerine in Spain, whose European population is restricted to Iberian natural steppes. To test for a spurious relationship between temporal series, variables were tested for cointegration. After confirming cointegration, we found a strong positive relationship between sheep abundance and the trends of the FBI and SBI indices during the period 1998–2018. The association between sheep abundance and trends of the Dupont’s Lark (2004–2015) was positive although it was not statistically significant. Although the main causes of decline of farmland and steppe birds are mainly related to agricultural intensification and land use changes, the correlation found, using two independent cointegrated datasets, between the reduction in farmland and shrub-steppe birds and sheep numbers at the country scale suggests that the decline of steppe birds in Spain may be also associated with the decline in sheep numbers. This agrees with previous studies that found a positive relationship between intermediate levels of sheep grazing and steppe bird abundance in Iberian steppes. Further research (e.g. experimental studies) is needed to corroborate our study and identify the most appropriate level of grazing intensity for protecting the most farmland and shrub-steppe birds. Our results suggest that the promotion of extensive grazing should be considered as a key factor in future Common Agricultural Policy reforms and conservation programmes to protect steppe birds.
Traba et al. (2022) Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy. PeerJ 10:e12870 https://doi.org/10.7717/peerj.12870
Analysis and comparison of protein secondary structures in the rachis of avian flight feathers
Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.
Lin et al. (2022) Analysis and comparison of protein secondary structures in the rachis of avian flight feathers. PeerJ 10:e12919 https://doi.org/10.7717/peerj.12919
Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)
Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to decipher the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found high abundance proteins related to nitrate and amino acids metabolismsin the salt-tolerant cultivars. The significant increase in abundance of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. Moreover, the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including sterol side chain reductase, gamma aminobutyrate transaminase and starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future.
Wang et al. (2022) Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium). PeerJ 10:e12955 https://doi.org/10.7717/peerj.12955
Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)
Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful information for the understanding of the complex mechanisms of plant hormones in controlling pod size by regulating the cell size in peanuts and will facilitate the improvement of peanut breeding.
Wang et al. (2022) Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.). PeerJ 10:e12965 https://doi.org/10.7717/peerj.12965
Response of bacterial community structure to different ecological niches and their functions in Korean pine forests
A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.
Ji et al. (2022) Response of bacterial community structure to different ecological niches and their functions in Korean pine forests. PeerJ 10:e12978 https://doi.org/10.7717/peerj.12978
Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China
Background With the exacerbating effects of the global climate change and the more and more attention to the study of plant carbon sink, an increasing number of researches on plant carbon sinks has grown. Although many studies exist on shrub vegetation, soil and litters, most studies focus on the community structure, biomass, surface soil of single plant and shrub layer vegetation, and lack the studies which included the potential relationships between climate change and ecological stoichiometric elements, comprehensive research on main species, even herb and litter layer. In order to provide relevant theoretical basis and data support, it is necessary to take the main terrestrial shrub ecosystem in Central Yunnan as the starting point to analyze and explore its carbon sink distribution characteristics, formation causes, the correlation between climatic factors (temperature and precipitation) and stoichiometric elements, which from community and species levels. Methods Plants which originated from 12 main shrub species, litter and soil samples which collected in 69 plots were from 23 plots (Q1–Q23) of 11 cities (countries) in the central Yunnan, China. The biomass and carbon density distribution pattern of each shrub ecosystem and the potential correlations with main climate factors was explored and identified. Some indexes were analyzed such as biomass and carbon density of each part of the shrub ecosystem distribution pattern, correlation, significant changes, formation reasons with the mean value (±standard deviation: SD). Through the redundancy analysis(RDA) of carbon (c), nitrogen (n), phosphorus (P) and main climate factors (precipitation and temperature), the distribution pattern of stoichiometric elements in shrub ecosystem can be judged. Results (1) The above-ground biomass (AGB), under-ground biomass (UGB) and root-shoot ratio (R/S) were between 1.13–2.03 t/hm2, 0.62–1.49 t/hm2, and 0.38–0.84, the carbon element was distributed in herb layer under-ground part and rhizomes of the shrub layer mostly. (2) The fitting slope of AGB and UGB of shrub communities and species was in accordance with the allometric distribution growth relationship, the R/S of shrubs was smaller than other vegetation types. Mean annual temperature (MAT) and mean annual precipitation (MAP) are not the main factors which affect the biomass and R/S. (3) The contents of C, N and P elements in leaves were significantly higher than other parts in shrub layer. P in shrub layer above-ground part is much higher than under-ground part. The surface soil layer has the highest C content, and decreased with the depth, so as the impact of vegetation and litter on the content of soil elements. Both of the correlation of MAT with N content of leaf, C/N of stem, the correlation of MAP with C content, C/N of soil is the greatest.
Guo et al. (2022) Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China. PeerJ 10:e13005 https://doi.org/10.7717/peerj.13005
Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants
Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.
Li et al. (2022) Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants. PeerJ 10:e13012 https://doi.org/10.7717/peerj.13012