Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research showed that Arabidopsis memorizes a first cold stress (priming) and improves its primed freezing ...tolerance further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic and transcriptomic changes during early cold priming or triggering after 3 days at 4°C interrupted by a memory phase. DREB1 family transcription factors DREB1C/CBF2, DREB1D/CBF4, DREB1E/DDF2, and DREB1F/DDF1 were strongly significantly induced throughout the entire triggering. During triggering, genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or detoxifiers of reactive oxygen species (ROS) were higher expressed compared with priming. Examples of early triggering responders were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling, while late responders were identified to act in fine‐tuning the stress response and developmental regulation. Induction of non‐typical members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced CBF regulon genes and a slower accumulation of selected cold stress associated metabolites indicate that a cold triggering stimulus might be sensed as milder stress in plants compared with priming. Further, strong induction of CBF4 throughout triggering suggests a unique function of this gene for the response to alternating temperatures.
Quantification of gene expression is crucial to connect genome sequences with phenotypic and physiological data. RNA-Sequencing (RNA-Seq) has taken a prominent role in the study of transcriptomic ...reactions of plants to various environmental and genetic perturbations. However, comparative tests of different tools for RNA-Seq read mapping and quantification have been mainly performed on data from animals or humans, which necessarily neglect, for example, the large genetic variability among natural accessions within plant species. Here, we compared seven computational tools for their ability to map and quantify Illumina single-end reads from the
accessions Columbia-0 (Col-0) and N14. Between 92.4% and 99.5% of all reads were mapped to the reference genome or transcriptome and the raw count distributions obtained from the different mappers were highly correlated. Using the software DESeq2 to determine differential gene expression (DGE) between plants exposed to 20 °C or 4 °C from these read counts showed a large pairwise overlap between the mappers. Interestingly, when the commercial CLC software was used with its own DGE module instead of DESeq2, strongly diverging results were obtained. All tested mappers provided highly similar results for mapping Illumina reads of two polymorphic Arabidopsis accessions to the reference genome or transcriptome and for the determination of DGE when the same software was used for processing.
High night temperatures (HNT) affect rice yield in the field and induce chlorosis symptoms in leaves in controlled chamber experiments. However, little is known about molecular changes in leaf ...segments under these conditions. Transcript and metabolite profiling were performed for leaf segments of six rice cultivars with different HNT sensitivity. The metabolite profile of the sheath revealed a lower metabolite abundance compared to segments of the leaf blade. Furthermore, pre-adaptation to stress under control conditions was detected in the sheath, whereas this segment was only slightly affected by HNT. No unique significant transcriptomic changes were observed in the leaf base, including the basal growth zone at HNT conditions. Instead, selected metabolites showed correlations with HNT sensitivity in the base. The middle part and the tip were most highly affected by HNT in sensitive cultivars on the transcriptomic level with higher expression of jasmonic acid signaling related genes, genes encoding enzymes involved in flavonoid metabolism and a gene encoding galactinol synthase. In addition, gene expression of expansins known to improve stress tolerance increased in tolerant and sensitive cultivars. The investigation of the different leaf segments indicated highly segment specific responses to HNT. Molecular key players for HNT sensitivity were identified.
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the ...lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant
cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.
Rice (
) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice ...yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS.
Alternating temperatures require fast and coordinated adaptation responses of plants. Cold acclimation has been extensively investigated and results in increased freezing tolerance in Arabidopsis ...thaliana. Here, we show that the two Arabidopsis accessions, Col‐0 and N14, which differ in their freezing tolerance, showed memory of cold acclimation, that is, cold priming. Freezing tolerance was higher in plants exposed to cold priming at 4°C, a lag phase at 20°C, and a second triggering cold stress (4°C) than in plants that were only cold primed. To our knowledge, this is the first report on cold memory improving plant freezing tolerance. The triggering response was distinguishable from the priming response at the levels of gene expression (RNA‐Seq), lipid (ultraperformance liquid chromatography–mass spectrometry), and metabolite composition (gas chromatography–mass spectrometry). Transcriptomic responses pointed to induced lipid, secondary metabolism, and stress in Col‐0 and growth‐related functions in N14. Specific accumulation of lipids included arabidopsides with possible functions as signalling molecules or precursors of jasmonic acid. Whereas cold‐induced metabolites such as raffinose and its precursors were maintained in N14 during the lag phase, they were strongly accumulated in Col‐0 after the cold trigger. This indicates genetic differences in the transcriptomic and metabolic patterns during cold memory.
Cold acclimation results in increased freezing tolerance that is lost upon transfer back to warm conditions. Arabidopsis thaliana shows cold memory, leading to higher freezing tolerance during a second cold treatment that is related to specific transcriptomic, lipidomic, and metabolomic responses.
Asymmetric warming resulting in a faster increase in night compared to day temperatures affects crop yields negatively. Physiological characterization and agronomic findings have been complemented ...more recently by molecular biology approaches including transcriptomic, proteomic, metabolomic and lipidomic investigations in crops exposed to high night temperature (HNT) conditions. Nevertheless, the understanding of the underlying mechanisms causing yield decline under HNT is still limited. The discovery of significant differences between HNT‐tolerant and HNT‐sensitive cultivars is one of the main research directions to secure continuous food supply under the challenge of increasing climate change. With this review, we provide a summary of current knowledge on the physiological and molecular basis of contrasting HNT tolerance in rice and wheat cultivars. Requirements for HNT tolerance and the special adaptation strategies of the HNT‐tolerant rice cultivar Nagina‐22 (N22) are discussed. Putative metabolite markers for HNT tolerance useful for marker‐assisted breeding are suggested, together with future research directions aimed at improving food security under HNT conditions.
Recent findings on physiological and molecular responses of rice and wheat to high night temperature (HNT) are highlighted. Special focus is directed on special adaptation strategies of HNT‐tolerant cultivars (e.g., N22) and putative metabolite markers for future marker‐assisted breeding to secure food supply under increasing HNT are suggested.
Climate change in Arctic ecosystems fosters permafrost thaw and makes massive amounts of ancient soil organic carbon (OC) available to microbial breakdown. However, fractions of the organic matter ...(OM) may be protected from rapid decomposition by their association with minerals. Little is known about the effects of mineral‐organic associations (MOA) on the microbial accessibility of OM in permafrost soils and it is not clear which factors control its temperature sensitivity. In order to investigate if and how permafrost soil OC turnover is affected by mineral controls, the heavy fraction (HF) representing mostly MOA was obtained by density fractionation from 27 permafrost soil profiles of the Siberian Arctic. In parallel laboratory incubations, the unfractionated soils (bulk) and their HF were comparatively incubated for 175 days at 5 and 15°C. The HF was equivalent to 70 ± 9% of the bulk CO2 respiration as compared to a share of 63 ± 1% of bulk OC that was stored in the HF. Significant reduction of OC mineralization was found in all treatments with increasing OC content of the HF (HF‐OC), clay‐size minerals and Fe or Al oxyhydroxides. Temperature sensitivity (Q10) decreased with increasing soil depth from 2.4 to 1.4 in the bulk soil and from 2.9 to 1.5 in the HF. A concurrent increase in the metal‐to‐HF‐OC ratios with soil depth suggests a stronger bonding of OM to minerals in the subsoil. There, the younger 14C signature in CO2 than that of the OC indicates a preferential decomposition of the more recent OM and the existence of a MOA fraction with limited access of OM to decomposers. These results indicate strong mineral controls on the decomposability of OM after permafrost thaw and on its temperature sensitivity. Thus, we here provide evidence that OM temperature sensitivity can be attenuated by MOA in permafrost soils.
The study investigated the temperature sensitivity of organic carbon in Siberian permafrost soils. The results showed that although substantial amounts of soil organic carbon are prone to degradation under rising global temperatures, strong mineral controls affect the temperature sensitivity of organic carbon mineralization. We here provide evidence that OM temperature sensitivity can be attenuated by mineral‐organic associations in permafrost soil.
Soil microorganisms are key players of the nitrogen cycle and relevant for soil development. While the community structure of nitrogen-cycling microorganisms during initial soil development is ...already well investigated, knowledge about the patterns during long-term ecosystem development is limited. In this study, nitrogen functional genes of ammonia-oxidizers (amoA), nitrate-reducers (narG), and chitin-degraders (chiA) were determined via quantitative PCR and the functional community composition of archaeal ammonia-oxidizers was analyzed via clone libraries and DNA sequencing (amoA) in soil depth profiles along the 120,000-year Franz Josef chronosequence (New Zealand). The results show that absolute nitrogen functional gene abundances change significantly during long-term soil development. In organic layers, narG and chiA gene abundances were highest in young to intermediate-aged soils and then decreased following progressive and retrogressive development of the vegetation. While relative archaeal amoA gene abundance (proportional to total cell counts) decreased in the oldest phosphorus-limited topsoils, relative narG and chiA gene abundances remained constant. In subsoils, archaeal amoA and narG gene abundances also decreased with ecosystem retrogression that coincided with the increasing content of iron and aluminum oxides as well as other clay-sized minerals. In contrast, subsoil chiA gene abundances were hardly affected by soil age. The analysis of the archaeal amoA community revealed a compositional shift during long-term ecosystem development. Our study provides evidence that the community structure of nitrogen-cycling microorganisms in top- and subsoils is significantly affected by long-term ecosystem development and suggests an important role of the mineral phase in subsoils.
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•Analysis of N functional gene abundances along soil chronosequence via qPCR.•Individual N functional genes were differently affected by long-term ecosystem development.•narG and chiA gene abundances highest in intermediate-aged topsoils.•Archaeal amoA and narG gene abundances decrease in old subsoils.•Gene abundance dynamics in subsoils also linked to soil mineralogical properties.
Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the ...dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O
status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to
suggesting that
may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the
, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils.
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