Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify

Functional analysis of CYP71AV1 reveals the evolutionary landscape of artemisinin biosynthesis

Artemisinin biosynthesis, unique to Artemisia annua, is suggested to have evolved from the ancestral costunolide biosynthetic pathway commonly found in the Asteraceae family. However, the evolutionary landscape of this process is not fully understood. The first oxidase in artemisinin biosynthesis, CYP71AV1, also known as amorpha-4,11-diene oxidase (AMO), has specialized from ancestral germacrene A oxidases (GAOs). Unlike GAO, which exhibits catalytic promiscuity toward amorpha-4,11-diene, the natural substrate of AMO, AMO has lost its ancestral activity on germacrene A. Previous studies have suggested that the loss of the GAO copy in A. annua is responsible for the abolishment of the costunolide pathway. In the genome of A. annua, there are two copies of AMO, each of which has been reported to be responsible for the different product profiles of high- and low-artemisinin production chemotypes. Through analysis of their tissue-specific expression and comparison of their sequences with those of other GAOs, it was discovered that one copy of AMO (AMOHAP) exhibits a different transcript compared to the reported artemisinin biosynthetic genes and shows more sequence similarity to other GAOs in the catalytic regions. Furthermore, in a subsequent in vitro enzymatic assay, the recombinant protein of AMOHAP unequivocally demonstrated GAO activity. This result clearly indicates that AMOHAP is a GAO rather than an AMO and that its promiscuous activity on amorpha-4,11-diene has led to its misidentification as an AMO in previous studies. In addition, the divergent expression pattern of AMOHAP compared to that of the upstream germacrene A synthase may have contributed to the abolishment of costunolide biosynthesis in A. annua. Our findings reveal a complex evolutionary landscape in which the emergence of a new metabolic pathway replaces an ancestral one.

The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development

MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. By analyzing loss-of-function and overexpression lines, we found that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas SOC1 overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in xal2-2 roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.

Diversity of Arbuscular Mycorrhizal fungi under different agroforestry practices in the drylands of Southern Ethiopia

The conversion of an agroforestry based agricultural system to a monocropping farming system influences the distribution and composition of arbuscular mycorrhizal fungi (AMF). The aim of this paper was to analyze AMF species diversity, spore density, and root colonization across different agroforestry practices (AFP) in southern Ethiopia. Soil and root samples were collected from homegarden, cropland, woodlot, and trees on soil and water conservation-based AFP. AMF spores were extracted from the soil and species diversity was evaluated using morphological analysis and root colonization from root samples. The AMF spore density, root colonization and composition were significantly different among the AFP (P < 0.05). In this study, 43 AMF morphotypes belonging to eleven genera were found, dominated by Acaulospora (32.56%), followed by Claroideoglomus (18.60%). Home gardens had the highest spore density (7641.5 spore100 g- 1 dry soil) and the lowest was recorded in croplands (683.6 spore100 g- 1 dry soil). Woodlot had the highest root colonization (54.75%), followed by homegarden (48.25%). The highest isolation frequency (63.63%) was recorded for Acaulospora scrobiculata. The distribution of AMF species and diversity were significantly related to soil total nitrogen and organic carbon. The homegarden and woodlot AFP were suitable for soil AMF reserve and conservation.

Multiomics studies with co-transformation reveal microRNAs via miRNA-TF-mRNA network participating in wood formation in Hevea brasiliensis

Introduction

MicroRNAs (miRNAs) are small endogenous non-coding RNAs that play an important role in wood formation in plants. However, the significance of the link between miRNAs and their target transcripts in wood formation remains unclear in rubber tree (Hevea brasiliensis).

Methods

In this study, we induced the formation of reaction wood by artificially bending rubber trees for 300 days and performed small RNA sequencing and transcriptome deep sequencing (RNA-seq) to describe the complement of miRNAs and their targets contributing to this process.

Results and discussion

We identified 5, 11, and 2 differentially abundant miRNAs in normal wood (NW) compared to tension wood (TW), in NW relative to opposite wood (OW), and between TW and OW, respectively. We also identified 12 novel miRNAs and 39 potential miRNA-mRNA pairs with different accumulation patterns in NW, TW, and OW. We noticed that many miRNAs targeted transcription factor genes, which were enriched in KEGG pathways associated with phenylpropanoid biosynthesis, phenylalanine metabolism, and pyruvate metabolism. Thus, miRNA-TF-mRNA network involved in wood formation via tension wood model were constructed. We validated the differential accumulation of miRNAs and their targets by RT-qPCR analysis and overexpressed miRNA in Nicotiana benthamiana with its potential target gene. These results will provide a reference for a deep exploration of growth and development in rubber tree.

Environment and Genotype Influence Quantitative and Qualitative Variation in Condensed Tannins in Aspen

Condensed tannins (CTs) are abundant, ecologically-relevant secondary metabolites in many plants, which respond to variables associated with anthropogenic environmental change. While many studies have reported how genetic and environmental factors affect CT concentrations, few have explored how they influence CT molecular structure. Here, using trembling aspen (Populus tremuloides) as a model organism, we report how foliar CT concentrations, polymer sizes, representation of procyanidins and prodelphinidins, and stereochemistry vary in response to changes in air temperature (warming and freeze damage), air composition (elevated CO2 and O3), soil quality (nutrients and microbiome), and herbivory (mammal and lepidopteran). Use of multiple aspen genotypes enabled assessment of genetic influences on aspen CTs. CT concentration and composition were analyzed by thiolysis-ultra high performance liquid chromatography/mass spectrometry in archived leaf samples from prior experiments. All environmental variables explored except for soil microbiome influenced both CT quantity and quality, with climate factors appearing to have larger effect magnitudes than herbivory. Climate, soil, and herbivory effects varied among genotypes, while air composition effects were consistent across genotypes. Considering that CT properties (concentrations and molecular structures) mediate functions at the organismal through ecosystem scales, intraspecific variation in responses of CT properties to environmental factors could provide a pathway through which environmental change exerts selective pressure on Populus populations. Future studies are needed to identify the molecular-level mechanisms by which environmental factors influence CT concentrations and structures, and to establish their ecological and evolutionary significance.

Trait-dependent diversification in angiosperms: Patterns, models and data

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.

JustDeepIt: Software tool with graphical and character user interfaces for deep learning-based object detection and segmentation in image analysis

Image processing and analysis based on deep learning are becoming mainstream and increasingly accessible for solving various scientific problems in diverse fields. However, it requires advanced computer programming skills and a basic familiarity with character user interfaces (CUIs). Consequently, programming beginners face a considerable technical hurdle. Because potential users of image analysis are experimentalists, who often use graphical user interfaces (GUIs) in their daily work, there is a need to develop GUI-based easy-to-use deep learning software to support their work. Here, we introduce JustDeepIt, a software written in Python, to simplify object detection and instance segmentation using deep learning. JustDeepIt provides both a GUI and a CUI. It contains various functional modules for model building and inference, and it is built upon the popular PyTorch, MMDetection, and Detectron2 libraries. The GUI is implemented using the Python library FastAPI, simplifying model building for various deep learning approaches for beginners. As practical examples of JustDeepIt, we prepared four case studies that cover critical issues in plant science: (1) wheat head detection with Faster R-CNN, YOLOv3, SSD, and RetinaNet; (2) sugar beet and weed segmentation with Mask R-CNN; (3) plant segmentation with U2-Net; and (4) leaf segmentation with U2-Net. The results support the wide applicability of JustDeepIt in plant science applications. In addition, we believe that JustDeepIt has the potential to be applied to deep learning-based image analysis in various fields beyond plant science.

A Positive Feedback Loop of BBX11-BBX21-HY5 Promotes Photomorphogenic Development in Arabidopsis

Light is the most important environmental factor affecting many aspects of plant development. In this study, we report that B-box protein 11 (BBX11) acts as a positive regulator of red light signaling. BBX11 loss-of-function mutant seedlings display significantly elongated hypocotyls under conditions of both red light and long day, whereas BBX11 overexpression causes markedly shortened hypocotyls under various light states. BBX11 binds to the HY5 promoter to activate its transcription, while both BBX21 and HY5 associate with the promoter of BBX11 to positively regulate its expression. Taken together, our results reveal positive feedback regulation of photomorphogenesis consisting of BBX11, BBX21, and HY5, thus substantiating a transcriptional regulatory mechanism in the response of plants to light during normal development.

Mobilization and Cellular Distribution of Phosphate in the Diatom Phaeodactylum tricornutum

Unicellular organisms that live in marine environments must cope with considerable fluctuations in the availability of inorganic phosphate (P_i). Here, we investigated the extracellular P_i concentration-dependent expression, as well as the intracellular or extracellular localization, of phosphatases and phosphate transporters of the diatom Phaeodactylum tricornutum. We identified P_i-regulated plasma membrane-localized, ER-localized, and secreted phosphatases, in addition to plasma membrane-localized, vacuolar membrane-localized, and plastid-surrounding membrane-localized phosphate transporters that were also regulated in a P_i concentration-dependent manner. These studies not only add further knowledge to already existing transcriptomic data, but also highlight the capacity of the diatom to distribute P_i intracellularly and to mobilize P_i from extracellular and intracellular resources.

A Versatile Plant Rhabdovirus-Based Vector for Gene Silencing, miRNA Expression and Depletion, and Antibody Production

Plant virus vectors are ideal tools for delivery of genetic cargo into host cells for functional genomics studies and protein overexpression. Although a vast number of plant virus vectors have been developed for different purposes, the utility of a particular virus vector is generally limited. Here, we report a multipurpose plant rhabdovirus-based vector system suitable for a wide range of applications in Nicotiana benthamiana. We engineered sonchus yellow net rhabdovirus (SYNV)-based gene silencing vectors through expressing a sense, antisense, or double-stranded RNAs of target genes. Robust target gene silencing was also achieved with an SYNV vector expressing a designed artificial microRNA. In addition, ectopic expression of a short tandem target mimic RNA using the SYNV vector led to a significant depletion of the target miR165/166 and caused abnormal leaf development. More importantly, SYNV was able to harbor two expression cassettes that permitted simultaneous RNA silencing and overexpression of large reporter gene. This dual capacity vector also enabled systemic expression of a whole-molecule monoclonal antibody consisting of light and heavy chains. These results highlight the utility of the SYNV vector system in gene function studies and agricultural biotechnology and provide a technical template for developing similar vectors of other economically important plant rhabdoviruses.

Skeletonema marinoi as a new genetic model for marine chain-forming diatoms

Diatoms are ubiquitous primary producers in marine ecosystems and freshwater habitats. Due to their complex evolutionary history, much remains unknown about the specific gene functions in diatoms that underlie their broad ecological success. In this study, we have genetically transformed the centric diatom Skeletonema marinoi, a dominant phytoplankton species in temperate coastal regions. Transformation of S. marinoi is the first for a true chain-forming diatom, with the random genomic integration via nonhomologous recombination of a linear DNA construct expressing the resistance gene to the antibiotic zeocin. A set of molecular tools were developed for reliably identifying the genomic insertion site within each transformant, many of which disrupt recognizable genes and constitute null or knock-down mutations. We now propose S. marinoi as a new genetic model for marine diatoms, representing true chain-forming species that play a central role in global photosynthetic carbon sequestration and the biogeochemical cycling of silicates and various nutrients, as well as having potential biotechnological applications.

Growing Azolla to produce sustainable protein feed: the effect of differing species and CO2 concentrations on biomass productivity and chemical composition

BACKGROUND

Since available arable land is limited and nitrogen fertilizers pollute the environment, cropping systems ought to be developed that do not rely on them. Here we investigate the rapidly growing, N₂ -fixing Azolla/Nostoc symbiosis for its potential productivity and chemical composition to determine its potential as protein feed.

RESULTS

In a small production system, cultures of Azolla pinnata and Azolla filiculoides were continuously harvested for over 100 days, yielding an average productivity of 90.0-97.2 kg dry weight (DW) ha^-1  d^-1 . Under ambient CO₂ levels, N₂ fixation by the fern's cyanobacterial symbionts accounted for all nitrogen in the biomass. Proteins made up 176-208 g kg^-1 DW (4.9 × total nitrogen), depending on species and CO₂ treatment, and contained more essential amino acids than protein from soybean. Elevated atmospheric CO₂ concentrations (800 ppm) significantly boosted biomass production by 36-47%, without decreasing protein content. Choice of species and CO₂ concentrations further affected the biomass content of lipids (79-100 g kg^-1 DW) and (poly)phenols (21-69 g kg^-1 DW).

CONCLUSIONS

By continuous harvesting, high protein yields can be obtained from Azolla cultures, without the need for nitrogen fertilization. High levels of (poly)phenols likely contribute to limitations in the inclusion rate of Azolla in animal diets and need further investigation. © 2018 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The Role of Programmed Cell Death Regulator LSD1 in Nematode-Induced Syncytium Formation

Cyst-forming plant-parasitic nematodes are common pests of many crops. They inject secretions into host cells to induce the developmental and metabolic reprogramming that leads to the formation of a syncytium, which is the sole food source for growing nematodes. As in other host-parasite models, avirulence leads to rapid and local programmed cell death (PCD) known as the hypersensitive response (HR), whereas in the case of virulence, PCD is still observed but is limited to only some cells. Several regulators of PCD were analyzed to understand the role of PCD in compatible plant-nematode interactions. Thus, Arabidopsis plants carrying recessive mutations in LESION SIMULATING DISEASE1 (LSD1) family genes were subjected to nematode infection assays with juveniles of Heterodera schachtii. LSD1 is a negative and conditional regulator of PCD, and fewer and smaller syncytia were induced in the roots of lsd1 mutants than in wild-type Col-0 plants. Mutation in LSD ONE LIKE2 (LOL2) revealed a pattern of susceptibility to H. schachtii antagonistic to lsd1. Syncytia induced on lsd1 roots compared to Col0 showed significantly retarded growth, modified cell wall structure, increased vesiculation, and some myelin-like bodies present at 7 and 12 days post-infection. To place these data in a wider context, RNA-sequencing analysis of infected and uninfected roots was conducted. During nematode infection, the number of transcripts with changed expression in lsd1 was approximately three times smaller than in wild-type plants (1440 vs. 4206 differentially expressed genes, respectively). LSD1-dependent PCD in roots is thus a highly regulated process in compatible plant-nematode interactions. Two genes identified in this analysis, coding for AUTOPHAGY-RELATED PROTEIN 8F and 8H were down-regulated in syncytia in the presence of LSD1 and showed an increased susceptibility to nematode infection contrasting with lsd1 phenotype. Our data indicate that molecular regulators belonging to the LSD1 family play an important role in precise balancing of diverse PCD players during syncytium development required for successful nematode parasitism.