Expression of major photosynthetic and salt-resistance genes in invasive reed lineages grown under elevated CO2 and temperature

Choose Wisely: Great Variation among Genotypes of Promising Paludiculture Crop Phragmites australis

Measures mitigating the climate crisis, such as paludiculture, which is the agriculture on rewetted peatlands, are urgently needed. The cosmopolitan species Phragmites australis has the potential to be used in paludiculture worldwide but is known for its high intraspecific variation. This raises the questions of whether (i) P. australis genotypes differ even at a regional scale, making them differently well suited for paludiculture and (ii) P. australis performance can be predicted by linking the variation in genotypes to strategies in the plant economics spectrum. Five P. australis genotypes from Mecklenburg-Western Pomerania were cultivated in two 10-month mesocosm experiments along gradients of water level and nutrient addition. We compared growth, morphology (height, growing density), above- and belowground biomass, functional and ecophysiological traits (SLA, LDMC, SRL, RDMC, root porosity, photosynthetic rate) as well as gene expression. Our results demonstrate a high variability of P. australis genotypes even at a regional scale, revealing genotype-specific productivity, morphology, and gene expression and implying that the selection of suitable genotypes will be crucial for the success of a paludiculture. However, trait covariation did not indicate distinct plant economic strategies to predict genotype performance. Instead, large-scale genotype trials are needed to select suitable genotypes for paludiculture.

Discovery of Euryhaline Phycoerythrobilin-Containing Synechococcus and Its Mechanisms for Adaptation to Estuarine Environments

Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment.

Synechococcus are among the most abundant and widely distributed picocyanobacteria on earth. Cluster 5 phycoerythrobilin-containing (PEB-containing) Synechococcus, the major marine Synechococcus, were considered to prefer high salinity, and they are absent in estuarine ecosystems. However, we have detected PEB-containing Synechococcus in some low-salinity (<15-ppt) areas of the Pearl River estuary at an abundance up to 1.0 × 10⁵ cells ml⁻¹. Two PEB-containing Synechococcus strains (HK01 and LTW-R) were isolated, and tests on them revealed their ability to cope with variations in the salinity (from 14 to 44 ppt). Phylogenetic analysis showed that HK01 belonged to a novel Synechococcus clade (HK1), whereas LTW-R was clustered with S5.2 strains. Whole-genome analysis revealed that a membrane channel protein with glycine zipper motifs is unique to euryhaline Synechococcus. The upregulation of this protein, the osmotic sensors, and the heat shock protein HSP20 and the downregulation of the osmolyte biosynthesis enable euryhaline Synechococcus to well adapt to the low and fluctuating salinity in the estuarine environment. In addition, decreasing the salinity in LTW-R strongly downregulated several important metabolic pathways, including photosynthesis, and the Calvin-Benson cycle, whereas its growth was not significantly affected. Moreover, obtaining PEB genes from horizontal gene transfer expands the light niche significantly for euryhaline Synechococcus. These results provided new insights into the life strategies and ecological function of marine PEB-containing Synechococcus under the unique environmental condition of estuarine waters, particularly in response to salinity variations.

IMPORTANCE Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment. This study expands current understanding on mechanisms involved in niche separation of marine Synechococcus lineages.

The Importance of Biological and Ecological Properties of Phragmites Australis (Cav.) Trin. Ex Steud., in Phytoremendiation of Aquatic Ecosystems—The Review

Phragmites australis (common reed) is one of the most extensively distributed species of emergent plant worldwide. The adaptive features of this plant show its competitive character. Owing to high intraspecific diversity of common reed, as well as its phenotypic plasticity, the plant shows a broad ecological amplitude. Moreover, the plant exhibits a high capacity for acclimatization to environmental conditions which are considered adverse. This plant has been used for many years in phytoremediation to purify various types of wastewater. Phragmites australis has a high ability to accumulate various nutrients, heavy metals, and micropollutants, and in this respect, it is superior to other aquatic plants. This review examines the existing literature on the biological and ecological properties of common reed, the use of common reed in wastewater treatment for removing pollutants and tolerance for metals, and in hydrophyte treatment systems. It seems vital to conduct further research on the physiology and biochemistry of the common reed, with the aim of increasing the plant’s efficiency for pollutants removal.

Plant science's next top models

BACKGROUND

Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models.

SCOPE

Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers.

CONCLUSIONS

Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance

With the rapidly deteriorating environmental conditions, the development of stress tolerant plants has become a priority for sustaining agricultural productivity. Therefore, studying the process of stress tolerance in naturally tolerant species hold significant promise. Phragmites karka is an invasive plant species found abundantly in tropical and sub tropical regions, fresh water regions and brackish marshy areas, such as river banks and lake shores. The plant possesses the ability to adapt and survive under conditions of high salinity. We subjected P. karka seedlings to salt stress and carried out whole transcriptome profiling of leaf and root tissues. Assessing the global transcriptome changes under salt stress resulted in the identification of several genes that are differentially regulated under stress conditions in root and leaf tissue. A total of 161,403 unigenes were assembled and used as a reference for digital gene expression analysis. A number of key metabolic pathways were found to be over-represented. Digital gene expression analysis was validated using qRT-PCR. In addition, a number of different transcription factor families including WRKY, MYB, CCCH, NAC etc. were differentially expressed under salinity stress. Our data will facilitate further characterisation of genes involved in salinity stress tolerance in P. karka. The DEGs from our results are potential candidates for understanding and engineering abiotic stress tolerance in plants.

Comparative Proteomic Analysis of Two Manilkara Species Leaves Under NaCl Stress

Background:

Salinity is a major environmental limiting factor, which affect agricultural production. The two Manilkara seedlings (M. roxburghiana and M. zapota) with high economic importance, could not adapt well to higher soil salinity and little is known about their proteomic mechanisms.

Objectives:

The mechanisms responsible for the effects of salinity on the two Manilkara species leaves were examined by means of proteomic analysis.

Material and Methods:

The seedlings were cultivated in a greenhouse and treated with NaCl. Leaves of control and the salt-stressed seedlings were sampled for phenol protein extraction. Proteins were separated by two-dimensional gel electrophoresis coupled with mass spectroscopy to study the change of proteins under different NaCl concentration.

Results:

For M. roxburghiana leaves, 21 protein spots exhibited significant abundance variations between the control and the 6‰, 8‰ NaCl treatments, of these 13 proteins were identified. They included L-ascorbate peroxidase, chloroplast carbonic anhydrase, phosphoglycerate kinase, 5 heat-shock proteins(HSPs) which were all down- regulated; For M. zapota leaves, 35 protein spots exhibited significant abundance variations, then 24 proteins were identified, including 7 down-regulated HSPs as well as glyceraldehyde-3-phosphate dehydrogenase, Cell division protein, putative mitochondrial NAD-dependent malate dehydrogenase, ATP synthase, Rubisco large subunit-binding protein, Cytochrome c peroxidase.

Conclusions:

Based on the common identified proteins between the two M. species, our results indicated that the identificated proteins in the two Manilkara species were involved in carbohydrate metabolism, photosynthesis, defense and stress. HSPs exhibited variation strictly related to NaCl stress. The down-regulated HSPs meant the function to repair cells that have suffered damage weaken during stress process. Furthermore, except for HSP70 in M. zapota leaves, the HSPs in the two species were all small heat shock proteins (sHSPs) with molecular weights ranging from 15 to 42 kDa.

Cosmopolitan Species As Models for Ecophysiological Responses to Global Change: The Common Reed Phragmites australis

Phragmites australis is a cosmopolitan grass and often the dominant species in the ecosystems it inhabits. Due to high intraspecific diversity and phenotypic plasticity, P. australis has an extensive ecological amplitude and a great capacity to acclimate to adverse environmental conditions; it can therefore offer valuable insights into plant responses to global change. Here we review the ecology and ecophysiology of prominent P. australis lineages and their responses to multiple forms of global change. Key findings of our review are that: (1) P. australis lineages are well-adapted to regions of their phylogeographic origin and therefore respond differently to changes in climatic conditions such as temperature or atmospheric CO2; (2) each lineage consists of populations that may occur in geographically different habitats and contain multiple genotypes; (3) the phenotypic plasticity of functional and fitness-related traits of a genotype determine the responses to global change factors; (4) genotypes with high plasticity to environmental drivers may acclimate or even vastly expand their ranges, genotypes of medium plasticity must acclimate or experience range-shifts, and those with low plasticity may face local extinction; (5) responses to ancillary types of global change, like shifting levels of soil salinity, flooding, and drought, are not consistent within lineages and depend on adaptation of individual genotypes. These patterns suggest that the diverse lineages of P. australis will undergo intense selective pressure in the face of global change such that the distributions and interactions of co-occurring lineages, as well as those of genotypes within-lineages, are very likely to be altered. We propose that the strong latitudinal clines within and between P. australis lineages can be a useful tool for predicting plant responses to climate change in general and present a conceptual framework for using P. australis lineages to predict plant responses to global change and its consequences.

Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones

Common Reed (Phragmites australis) is a frequent component of inland and coastal wetlands in temperate zones worldwide. Ongoing environmental changes have resulted in the decline of this species in many areas and invasive expansion in others. In the Gippsland Lakes coastal waterway system in south-eastern Australia, increasing salinity is thought to have contributed to the loss of fringing P. australis reed beds leading to increased shoreline erosion. A major goal of restoration in this waterway is to address the effect of salinity by planting a genetically diverse range of salt-tolerant P. australis plants. This has prompted an interest in examining the variation in salinity tolerance among clones and the underlying basis of this variation. Transcriptomics is an approach for identifying variation in genes and their expression levels associated with the exposure of plants to environmental stressors. In this paper we present initial results of the first comparative culm transcriptome analysis of P. australis clones. After sampling plants from sites of varied surface water salinity across the Gippsland Lakes, replicates from three clones from highly saline sites (>18 g L(-1) TDS) and three from low salinity sites (<6 g L(-1)) were grown in containers irrigated with either fresh (<0.1 g L(-1)) or saline water (16 g L(-1)). An RNA-Seq protocol was used to generate sequence data from culm tissues from the 12 samples allowing an analysis of differential gene expression. Among the key findings, we identified several genes uniquely up- or down-regulated in clones from highly saline sites when irrigated with saline water relative to clones from low salinity sites. These included the higher relative expression levels of genes associated with photosynthesis and lignan biosynthesis indicative of a greater ability of these clones to maintain growth under saline conditions. Combined with growth data from a parallel study, our data suggests local adaptation of certain clones to salinity and provides a basis for more detailed studies.