bims-pisump 2018-05-27 papers

Issue of 2018–05–27
five papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Plant Physiol Biochem. 2018 Apr 13. pii: S0981-9428(18)30167-0. [Epub ahead of print]128 134-141

Co-evolutionary associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties.

Lei Tian, Shaohua Shi, Lina Ma, Fahad Nasir, Xiujun Li, Lam-Son Phan Tran, Chunjie Tian.

The plants and root-associated microbiomes are closely related. Plant metabolic substances can serve as a nutrient source for the microbiome, and in return, the microbiome can regulate the production of plant metabolic substances. Wild rice (Oryza rufipogon), as the ancestor of cultivated rice (Oryza sativa), has changed several metabolic pathways and root-associated microbiome during evolution. Thus, the study of the different associations between metabolic pathways and root-associated microbiomes in wild and cultivated rice varieties is important for rice breeding. In this article, the co-evolutionary association between metabolic pathways, which are based on transcriptome data, and root-associated microbiomes, which are based on 16S rRNA and internal transcribed spacer (ITS) amplicon data, in wild and cultivated rice was studied. The results showed that the enriched pathways were differentially correlated with the enriched microbiomes in wild and cultivated rice varieties. Pathways for 'Glutathione metabolism', 'Plant-pathogen interaction', 'Protein processing in endoplasmic reticulum' and 'Tyrosine metabolism' were positively associated with the improved relative abundance of bacterial and fungal operational taxonomic units (OTUs) in wild rice. On the other hand, 'Glycolysis/Gluconeogenesis', 'Brassinosteroid biosynthesis', 'Carbon metabolism', 'Phenylpropanoid biosynthesis' and 'Caffeine metabolism' were positively correlated with the improved relative abundance of bacterial and fungal OTUs in cultivated rice. Redundancy analysis showed that certain bacterial and fungal species could positively and significantly affect plant gene expression; for instance, Streptomyces, with 8.7% relative abundance in bacterial community, significantly affected plant gene expression in wild rice. This study can provide the theoretical basis for recognizing the associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties, and can provide practical significance for developing useful bacterial and fungal resources in wild rice.

Keywords: Cultivated rice; Microbiome; Pathway analysis; Transcriptome; Wild rice

DOI: https://doi.org/10.1016/j.plaphy.2018.04.009

Plant Biol (Stuttg). 2018 May 20.

Germination niche breadth varies inconsistently among three Asclepias congeners along a latitudinal gradient.

Jessamine Finch, Jeffrey L Walck, Siti N Hidayati, Andrea T Kramer, Victoria Lason, Kayri Havens.

Species responses to climate change will be primarily driven by their environmental tolerance range, or niche breadth, with the expectation that broad niches will increase resilience. Niche breadth is expected to be greater in more heterogeneous environments and moderated by life history. Niche breadth also varies across life stage. Therefore, the life stage with the narrowest niche may serve as the best predictor of climatic vulnerability. To investigate the relationship between niche breadth, climate, and life stage we identify germination niche breadth for dormant and nondormant seeds in multiple populations of three milkweed (Asclepias) species. Complementary trials evaluated germination under conditions simulating historic and predicted future climate by varying cold-moist stratification temperature, length, and incubation temperature. Germination niche breadth was derived from germination evenness across treatments (Levins Bn ), with stratified seeds considered less dormant than non-stratified seeds. Germination response varies significantly among species, populations, and treatments. Cold-moist stratification ≥ 4 weeks (1-3°C) followed by incubation at 25/15°C+ achieves peak germination for most populations. Germination niche breadth significantly expands following stratification and interacts significantly with latitude of origin. Interestingly, two species display a positive relationship between niche breadth and latitude, while the third presents a concave quadratic relationship. Germination niche breadth significantly varies by species, latitude, and population, suggesting an interaction between source climate, life history, and site-specific factors. Results contribute to our understanding of inter- and intraspecific variation in germination, underscore the role of dormancy in germination niche breadth, and have implications for prioritizing and conserving species under climate change. This article is protected by copyright. All rights reserved.

Keywords: environmental heterogeneity; intraspecific variability; latitude-niche breadth hypothesis; milkweed; physiological dormancy; population variation; seed germination

DOI: https://doi.org/10.1111/plb.12843

Plant Biol (Stuttg). 2018 May 20.

Analysis of intraspecific seeds diversity in Astragalus aquilanus (Fabaceae) endemic species of Central Apennine.

V Di Cecco, M Di Musciano, A A D'Archivio, A R Frattaroli, L Di Martino.

This work aims to study the seeds of the endemic species Astragalus aquilanus from four different populations of Central Italy. We investigated the seed morpho-colorimetric features (shape and size) and chemical differences (through infrared spectroscopy) among populations and between dark and light seeds. Seed morpho-colorimetric quantitative variables, describing shape, size and colour seed traits, were measured using image analysis techniques. Fourier transform infrared (FT-IR) spectroscopy was used to attempt seed chemical characterization. The measured data were analysed by step-wise linear discriminant analysis (LDA). Moreover, we analysed the correlation between the four most important traits and six climatic variables extracted from WorldClim 2.0. LDA on seeds traits shows a clear differentiation of the four populations, which can be attributed to a different chemical composition, as confirmed by Wilk's lambda test (p<0.001). A strong correlation between morphometric traits and temperature (annual mean temperature, mean temperature of the warmest and coolest quarter), colorimetric traits and precipitation (annual precipitation, and precipitation of wettest and driest quarter) was observed. The characterization of Astragalus aquilanus seeds has shown a large intraspecific plasticity both in morpho-colorimetric and chemical composition. These results confirm the strong relationship between the type of seed produced and the climatic variables. This article is protected by copyright. All rights reserved.

Keywords: IR spectrum; Intraspecific diversity; interpopulation variability; morpho-colorimetric analysis; seed image analysis; trait-environment relationship

DOI: https://doi.org/10.1111/plb.12844

Plant Biol (Stuttg). 2018 May 20.

Linking seed germination and plant height: a case study of a wetland community on the eastern Tibet Plateau.

Kun Liu, Suzhen Cao, Guozhen Du, Jerry M Baskin, Carol C Baskin, Haiyan Bu, Wei Qi, Ting Liang.

Seed germination is the earliest trait expressed in a plant's life history, and it can directly affect the expression of post germination traits. Plant height is central to plant ecological strategies, because it is a major determinant of the ability of a species to compete for light. Thus, linking seed germination and plant height at the community level is very important to understanding plant fitness and community structure. Here, we tested storage condition and temperature requirements for germination of 31 species from a wetland plant community on the eastern Tibet Plateau, and analyzed correlation of germination traits with plant height in relation to storage condition. Germination percentage was positively related to plant height, and this relationship disappeared when seeds were incubated at a low temperature (i.e. 5°C) or after they were stored under wet-cold conditions. The response of seeds to dry+wet-cold storage was negatively related to plant height. Based on the scores of each species on the first two principal components derived from PCA, species were classified into two categories by Hierarchical Clustering, and there was a significant difference between germination and plant height of species in these two categories. These results suggest that the requirements for seed germination together with seasonal change in environmental conditions determine the window for germination and in turn plant growth season and resource utilization and ultimately plant height. This article is protected by copyright. All rights reserved.

Keywords: Tibet Plateau; plant traits; storage condition; temperature requirement; wetland

DOI: https://doi.org/10.1111/plb.12845

Plant Mol Biol. 2018 May 19.

Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology.

Beate Thal, Hans-Peter Braun, Holger Eubel.

KEY MESSAGE: Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins. Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.

Keywords: Cellular metabolism; Nodulation; Rhizobium leguminosarum; Shotgun mass spectrometry; Symbiotic nitrogen fixation; Vicia faba

DOI: https://doi.org/10.1007/s11103-018-0736-7