The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity.

We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.

The potential of remote sensing of cover crops to benefit sustainable and precision fertilization.

Cover crops and precision fertilization are two core strategies to advance sustainable agriculture. Based on a review of proven achievements in remote sensing of vegetation, a novel approach is proposed to use remote-sensing of cover crops to map soil nutrient availability and to produce prescription maps for precision basal fertilization prior to sowing the following cash crop. The first goal of this manuscript is to introduce the concept of using remote-sensing of cover crops as 'reflectors' or 'bio-indicators' of soil nutrient availability. This concept has two components: 1. mapping nitrogen availability using remote-sensing of cover crops; 2. using remotely-detected visual symptoms of cover crops' nutrient deficiencies to guide sampling schemes. The second goal was to describe two case studies that initially evaluated the feasibility of this concept in a 20 ha field. In the first case study, cover crops mixtures containing legumes and cereals were sown during two seasons in soils with different nitrogen levels. Cereals dominated the mixture when soil nitrogen levels were low, while legumes dominated when levels were high. Plant height and texture analysis derived from UAV-RGB-images were used to measure differences between the dominant species as an indicator of soil nitrogen availability. In the second case study, in an oat cover crop, three different appearances of visual symptoms (phenotypes) were observed throughout the field, and laboratory analysis showed they significantly differed in their nutrient levels. Spectral vegetation indices and plant height derived from UAV-RGB-images were analyzed by a multi-stage classification procedure to differentiate between the phenotypes. The classified product was interpreted and interpolated to generate a high-resolution map showing nutrient uptake for the whole field. The suggested concept essentially elevates the services cover crops can provide to benefit sustainable agriculture if incorporated with remote-sensing. The potentials, limitations and open questions concerning the suggested concept are discussed.

Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica.

Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress-ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.

Plant ecological genomics at the limits of life in the Atacama Desert.

The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a "genetic goldmine" to engineer crop resilience to face climate change.

Soil health assessment: A critical review of current methodologies and a proposed new approach.

The wellbeing of soils is crucial for securing food production worldwide. The soil health (SH) concept has been introduced due to an evolving understanding that soil is not just a growing medium for crops but that it provides a foundation for other essential ecosystem services (ES). The SH concept requires development of a holistic index for reliable and quantitative assessment of soil wellbeing related to the effects of different soil management practices and land uses. The aims of this paper are to: (1) review current approaches and methods to assess SH, (2) highlight the role of soil ES in characterizing soil function and (3) propose a new approach to assess SH via monitoring of ES provided by soils. We introduce a brief critical review of the following three main steps required for assessment of common SH indices: (1) selection of relevant attributes; (2) quantification and scoring approaches; and (3) integration of the selected attributes to construct the SH index. These steps usually include statistical or expert opinion-based approaches. In addition, we present a new approach that highlights the relevance and importance of soil ES, i.e., provisioning, regulating and supporting services that must be quantified for comprehensive assessment of soil functions and for fitting models that relate selected soil attributes to ES. This will allow practitioners and scholars to identify the most significant and universal attributes, quantify the relative contribution of each attribute to each ES, and subsequently assess the overall health of soils.

Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

Halophytes are able to thrive in salt concentrations that would kill 99% of other plant species, and identifying their salt-adaptive mechanisms has great potential for improving the tolerance of crop plants to salinized soils. Much research has focused on the physiological basis of halophyte salt tolerance, whereas the elucidation of molecular mechanisms has traditionally lagged behind due to the absence of a model halophyte system. However, over the last decade and a half, two Arabidopsis (Arabidopsis thaliana) relatives, Eutrema salsugineum and Schrenkiella parvula, have been established as transformation-competent models with various genetic resources including high-quality genome assemblies. These models have facilitated powerful comparative analyses with salt-sensitive Arabidopsis to unravel the genetic adaptations that enable a halophytic lifestyle. The aim of this review is to explore what has been learned about halophytism using E. salsugineum and S. parvula We consider evidence from physiological and molecular studies suggesting that differences in salt tolerance between related halophytes and salt-sensitive plants are associated with alterations in the regulation of basic physiological, biochemical, and molecular processes. Furthermore, we discuss how salt tolerance mechanisms of the halophytic models are reflected at the level of their genomes, where evolutionary processes such as subfunctionalization and/or neofunctionalization have altered the expression and/or functions of genes to facilitate adaptation to saline conditions. Lastly, we summarize the many areas of research still to be addressed with E. salsugineum and S. parvula as well as obstacles hindering further progress in understanding halophytism.

Pesticide load dynamics during stormwater flow events in Mediterranean coastal streams: Alexander stream case study.

Cultivated land is a major source of pesticides, which are transported with the runoff water and eroded soil during rainfall events and pollute riverine and estuarine environments. Common ecotoxicological assessments of riverine systems are mainly based on water sampling and analysis of only the dissolved phase, and address a single pesticide's toxicological impact under laboratory conditions. A clear overview of mixtures of pesticides in the adsorbed and dissolved phases is missing, and therefore the full ecotoxicological impact is not fully addressed. The aim of this study was to characterize and quantify pesticide concentrations in both suspended sediment and dissolved phases, to provide a better understanding of pesticide-load dynamics during storm events in coastal streams in a Mediterranean climate. High-resolution sampling campaigns of seven flood events were conducted during two rainy seasons in Alexander stream, Israel. Samples of suspended sediments were separated from the solution and both media were analyzed separately for 250 pesticides. A total of 63 pesticides were detected; 18 and 16 pesticides were found solely in the suspended sediments and solution, respectively. Significant differences were observed among the pesticide groups: only 7% of herbicide, 20% of fungicide and 42% of insecticide load was transported with the suspended sediments. However, in both dissolved and adsorbed phases, a mix of pesticides was found which were graded from "mobile" to "non-mobile" with varied distribution coefficients. Diuron, and tebuconazole were frequently found in large quantities in both phases. Whereas insecticide and fungicide transport is likely governed by application time and method, the governing factor for herbicide load was the magnitude of the stream discharge. The results show a complex dynamic of pesticide load affected by excessive use of pesticides, which should be taken into consideration when designing projects to monitor riverine and estuarine water quality.

Anastatica hierochuntica, an Arabidopsis Desert Relative, Is Tolerant to Multiple Abiotic Stresses and Exhibits Species-Specific and Common Stress Tolerance Strategies with Its Halophytic Relative, Eutrema (Thellungiella) salsugineum.

The search for novel stress tolerance determinants has led to increasing interest in plants native to extreme environments - so called "extremophytes." One successful strategy has been comparative studies between Arabidopsis thaliana and extremophyte Brassicaceae relatives such as the halophyte Eutrema salsugineum located in areas including cold, salty coastal regions of China. Here, we investigate stress tolerance in the desert species, Anastatica hierochuntica (True Rose of Jericho), a member of the poorly investigated lineage III Brassicaceae. We show that A. hierochuntica has a genome approximately 4.5-fold larger than Arabidopsis, divided into 22 diploid chromosomes, and demonstrate that A. hierochuntica exhibits tolerance to heat, low N and salt stresses that are characteristic of its habitat. Taking salt tolerance as a case study, we show that A. hierochuntica shares common salt tolerance mechanisms with E. salsugineum such as tight control of shoot Na+ accumulation and resilient photochemistry features. Furthermore, metabolic profiling of E. salsugineum and A. hierochuntica shoots demonstrates that the extremophytes exhibit both species-specific and common metabolic strategies to cope with salt stress including constitutive up-regulation (under control and salt stress conditions) of ascorbate and dehydroascorbate, two metabolites involved in ROS scavenging. Accordingly, A. hierochuntica displays tolerance to methyl viologen-induced oxidative stress suggesting that a highly active antioxidant system is essential to cope with multiple abiotic stresses. We suggest that A. hierochuntica presents an excellent extremophyte Arabidopsis relative model system for understanding plant survival in harsh desert conditions.

Novel approach for quantitatively estimating element retention and material balances in soil profiles of recharge basins used for wastewater reclamation.

We investigated changes in element content and distribution in soil profiles in a study designed to monitor the geochemical changes accruing in soil due to long-term secondary effluent recharge, and its impact on the sustainability of the Soil Aquifer Treatment (SAT) system. Since the initial elemental contents of the soils at the studied site were not available, we reconstructed them using scandium (Sc) as a conservative tracer. By using this approach, we were able to produce a mass-balance for 18 elements and evaluate the geochemical changes resulting from 19 years of effluent recharge. This approach also provides a better understanding of the role of soils as an adsorption filter for the heavy metals contained in the effluent. The soil mass balance suggests 19 years of effluent recharge cause for a significant enrichment in Cu, Cr, Ni, Zn, Mg, K, Na, S and P contents in the upper 4m of the soil profile. Combining the elements lode record during the 19 years suggest that Cr, Ni, and P inputs may not reach the groundwater (20 m deep), whereas the other elements may. Conversely, we found that 58, 60, and 30% of the initial content of Mn, Ca and Co respectively leached from the upper 2-m of the soil profile. These high percentages of Mn and Ca depletion from the basin soils may reduce the soil's ability to buffer decreases in redox potential pe and pH, respectively, which could initiate a reduction in the soil's holding capacity for heavy metals.

Low induction of non-photochemical quenching and high photochemical efficiency in the annual desert plant Anastatica hierochuntica.

Non-photochemical quenching (NPQ) plays a major role in photoprotection. Anastatica hierochuntica is an annual desert plant found in hot deserts. We compared A. hierochuntica to three other different species: Arabidopsis thaliana, Eutrema salsugineum and Helianthus annuus, which have different NPQ and photosynthetic capacities. Anastatica hierochuntica plants had very different induction kinetics of NPQ and, to a lesser extent, of photosystem II electron transport rate (PSII ETR), in comparison to all other plants species in the experiments. The major components of the unusual photosynthetic and photoprotective response in A. hierochuntica were: (1) Low NPQ at the beginning of the light period, at various light intensities and CO2 concentrations. The described low NPQ cannot be explained by low leaf absorbance or by low energy distribution to PSII, but was related to the de-epoxidation state of xanthophylls. (2) Relatively high PSII ETR at various CO2 concentrations in correlation with low NPQ. PSII ETR responded positively to the increase of CO2 concentrations. At low CO2 concentrations PSII ETR was mostly O2 dependent. At moderate and high CO2 concentrations the high PSII ETR in A. hierochuntica was accompanied by relatively high CO2 assimilation rates. We suggest that A. hierochuntica have an uncommon NPQ and PSII ETR response. These responses in A. hierochuntica might represent an adaptation to the short growing season of an annual desert plant.

Quantitative assessment of hydrocarbon contamination in soil using reflectance spectroscopy: a "multipath" approach.

Petroleum hydrocarbons are contaminants of great significance. The commonly used analytic method for assessing total petroleum hydrocarbons (TPH) in soil samples is based on extraction with 1,1,2-Trichlorotrifluoroethane (Freon 113), a substance prohibited to use by the Environmental Protection Agency. During the past 20 years, a new quantitative methodology that uses the reflected radiation of solids has been widely adopted. By using this approach, the reflectance radiation across the visible, near infrared-shortwave infrared region (400-2500 nm) is modeled against constituents determined using traditional analytic chemistry methods and then used to predict unknown samples. This technology is environmentally friendly and permits rapid and cost-effective measurements of large numbers of samples. Thus, this method dramatically reduces chemical analytical costs and secondary pollution, enabling a new dimension of environmental monitoring. In this study we adapted this approach and developed effective steps in which hydrocarbon contamination in soils can be determined rapidly, accurately, and cost effectively solely from reflectance spectroscopy. Artificial contaminated samples were analyzed chemically and spectrally to form a database of five soils contaminated with three types of petroleum hydrocarbons (PHCs), creating 15 datasets of 48 samples each at contamination levels of 50-5000 wt% ppm (parts per million). A brute force preprocessing approach was used by combining eight different preprocessing techniques with all possible datasets, resulting in 120 different mutations for each dataset. The brute force was done based on an innovative computing system developed for this study. A new parameter for evaluating model performance scoring (MPS) is proposed based on a combination of several common statistical parameters. The effect of dividing the data into training validation and test sets on modeling accuracy is also discussed. The results of this study clearly show that predicting TPH levels at low concentrations in selected soils at high precision levels is viable. Dividing a dataset into training, validation, and test groups affects the modeling process, and different preprocessing methods, alone or in combination, need to be selected based on soil type and PHC type. MPS was found to be a better parameter for selecting the best performing model than ratio of prediction to deviation, yielding models with the same performance but less complicated and more stable. The use of the "all possibilities" system proved to be mandatory for efficient optimal modeling of reflectance spectroscopy data.

The effect of steepness of temporal resource gradients on spatial root allocation.

Plants are able to discriminately allocate greater biomass to organs that grow under higher resource levels. Recent evidence demonstrates that split-root plants also discriminately allocate more resources to roots that grow under dynamically improving nutrient levels, even when their other roots grow in richer patches. Here, we further tested whether, besides their responsiveness to the direction of resource gradients, plants are also sensitive to the steepness of environmental trajectories. Split-root Pisum sativum plants were grown so that one of their roots developed under constantly-high nutrient levels and the other root was subjected to dynamically improving nutrient levels of variable steepness. As expected, plants usually allocated a greater proportion of their biomass to roots that developed under constantly high resource availability; however, when given a choice, they allocated greater biomass to roots that initially experienced relatively low but steeply improving nutrient availabilities than to roots that developed under continuously-high nutrient availability. Such discrimination was not observed when the roots in the poor patch experienced only gentler improvements in nutrient availability. The results are compatible with the notion that responsiveness to the direction and steepness of environmental gradients could assist annual plants to increase their performance by anticipating resource availabilities foreseeable before the end of their growing season. The results exemplify the ability of plants to integrate and utilize environmental information and execute adaptive behaviours which, until recently, were attributed only to animals with central nervous systems.

In situ accumulation of copper, chromium, nickel, and zinc in soils used for long-term waste water reclamation.

We studied the long-term in situ accumulation of Cu, Cr, Ni, and Zn in the soil profile of a large-scale effluent recharge basin after 24 yr of operation in a wastewater reclamation plant using the Soil Aquifer System approach in the Coastal Plain of Israel. The objective was to quantify metals accumulation in the basin's soil profile, clarify retention mechanisms, and calculate material balances and metal removal efficiency as the metal loads increase. Effluent recharge led to measurable accumulation, relative to the pristine soil, of Ni and Zn in the 0- to 4-m soil profile, with concentration increases of 0.3 to 1.3 mg kg(-1) and 2.9 to 6.4 mg kg(-1), respectively. Copper accumulated only in the 0- to 1-m top soil layer, with concentration increase of 0.28 to 0.76 mg kg(-1). Chromium concentration increased by 3.1 to 7.3 mg kg(-1) in the 0- to 1-m horizon and 0.9 to 2.3 mg kg(-1) at deeper horizons. Sequential selective extraction showed Cu tended to be preferentially retained by Fe oxides and organic matter (OM), Cr by OM, Ni by OM, and carbonate and Zn by carbonate. The average total retained amounts of Cu, Cr, Ni, and Zn were 0.7 +/- 1.0, 13.6 +/- 4.8, 4.3 +/- 3.6, and 28.7 +/- 5.4 g per a representative unit soil slab (1 m(2) x 4 m) of the basin, respectively. This amounts to 3.6 +/- 4.9%, 79.5 +/- 28.0%, 8.0 +/- 6.9%, and 9.3 +/- 1.8% of the Cu, Cr, Ni, and Zn loads, respectively, applied during 24 yr of effluent recharge (total of approximately 1880 m effluent load). The low long-term overall removal efficiency of the metals from the recharged effluent in the top horizon may be due to the metals' low concentrations in the recharged effluent and the low adsorption affinity and retention capacity of the sandy soil toward them. This leads to attainment of a quasi-equilibrium and a steady state in element distribution between the recharged effluent solution and the soil after few years of recharge and relatively small cumulative effluent loadings.