A RHOse by any other name:a comparative analysis of animal and plant Rho GTPases

Rho GTPases are molecular switches that act as key regulators of a many cellular processes, including cell movement, morphogenesis, host defense, cell division and gene expression. Rho GTPases are found in all eukaryotic kingdoms. Plants lack clear homologs to conventional Rho GTPases found in yeast and animals; instead, they have over time developed a unique subfamily, ROPs, also known as RAC. The origin of ROP-like proteins appears to precede the appearance of land plants. This review aims to discuss the evolution of ROP/RAC and to compare plant ROP and animal Rho GTPases, focusing on similarities and differences in regulation of the GTPases and their downstream effectors.

Maintenance of mesophyll potassium and regulation of plasma membrane H^+-ATPase are associated with physiological responses of tea plants to drought and subsequent rehydration

Drought stress is one of the main factors limiting yield in tea plants. The plant cell's ability to preserve K^+homeostasis is an important strategy for coping with drought stress. Plasma membrane H^+-ATPase in the mesophyll cell is important for maintaining membrane potential to regulate K^+transmembrane transport. However, no research to date has investigated the possible relationship between plasma membrane H^+-ATPase and mesophyll K^+retention in tea plants under drought and subsequent rehydration conditions. In our experiment, drought stress inhibited plasma membrane H^+-ATPase activities and induced net H^+influx, leading to membrane potential depolarization and inducing a massive K^+efflux in tea plant mesophyll cells. Subsequent rehydration increased plasma membrane H^+-ATPase activity and induced net H^+efflux, leading to membrane potential hyperpolarization and thus lowering K^+loss. A first downregulated and then upregulated plasma membrane H^+-ATPase protein expression level was also observed under drought and subsequent rehydration treatment, a finding in agreement with the change of measured plasma membrane H^+-ATPase activities. Taken together, our results suggest that maintenance of mesophyll K^+in tea plants under drought and rehydration is associated with regulation of plasma membrane H^+-ATPase activity.

Spatial organization of multiple plant species in arid ecosystems:linking patterns and processes

Spatial organization of multiple plant species that appears as a non-random distribution of vegetative patches is one of the mostly observed spatial patterns in arid ecosystems. Yet understanding of ecological processes allowing this spatial pattern to emerge through interspecific interactions is still lacking. With a proposed conceptual model involving interspecific trade-offs between species competitive ability and colonization ability, we have argued that within patch abundance dynamics regulated by the mechanisms of competition are strongly influenced by the between patches colonization dynamics that are maintained via this trade-offs and it holds a positive, intraspecific occupancy-abundance relationship, in which increased patch occupancy increases species density within inhabiting patches. In a constant environment, while local abundance dynamics approach toward a stable equilibrium point, a fixed spatial arrangement of species can be retained through this coupled dynamics. However, in fluctuating environments where existence of such stable equilibriums is highly uncertain, it may involve continuous transitions from one community state to another as species re-organized themselves over space through the rapid changes in local species abundances. While some of the inhabiting patches are destroyed exogenously or endogenously, or species responses to increasing environmental fluctuations vary increasingly with time, discontinuous transitions into an abrupt, irreversible state of the community dynamics may occur, as with this effect the inherent positive relationship between occupancy and abundance of species is no longer maintained.

Plant salt tolerance and Na^+ sensing and transport

Salinity is a global challenge to agricultural production. Understanding Na^+ sensing and transport in plants under salt stress will be of benefit for breeding robustly salt-tolerant crop species. In this review, first, possible salt stress sensor candidates and the root meristem zone as a tissue harboring salt stress-sensing components are proposed. Then,the importance of Na^+ exclusion and vacuolar Na^+ sequestration in plant overall salt tolerance is highlighted. Other Na^+ regulation processes, including xylem Na^+ loading and unloading, phloem Na^+ recirculation, and Na^+ secretion, are discussed and summarized.Along with a summary of Na^+ transporters and channels, the molecular regulation of Na^+ transporters and channels in response to salt stress is discussed. Finally, some largely neglected issues in plant salt stress tolerance, including Na^+ concentration in cytosol and the role of Na^+ as a nutrient, are reviewed and discussed.

Human induced dryland degradation in Ordos Plateau,China,revealed by multilevel statistical modeling of normalized difference vegetation index and rainfall time-series

Land degradation causes serious environmental problems in many regions of the world, and although it can be effectively assessed and monitored using a time series of rainfall and a normalized difference vegetation index （NDVI） from remotely-sensed imagery, dividing human-induced land degradation from vegetation dynamics due to climate change is not a trivial task. This paper presented a multilevel statistical modeling of the NDVI-rainfall relationship to detect human-induced land degradation at local and landscape scales in the Ordos Plateau of Inner Mongolia, China, and recognized that anthropogenic activities result in either positive （land restoration and re-vegetation） or negative （degradation） trends. Linear regressions were used to assess the accuracy of the multi- level statistical model. The results show that： （1） land restoration was the dominant process in the Ordos Plateau between 1998 and 2012; （2） the effect of the statistical removal of precipitation revealed areas of human-induced land degradation and improvement, the latter reflecting successful restoration projects and changes in land man- agement in many parts of the Ordos; （3） compared to a simple linear regression, multilevel statistical modeling could be used to analyze the relationship between the NDVI and rainfall and improve the accuracy of detecting the effect of human activities. Additional factors should be included when analyzing the NDVI-rainfall relationship and detecting human-induced loss of vegetation cover in drylands to improve the accuracy of the approach and elimi- nate some observed non-significant residual trends.

Spatio-temporal pattern and changes of evapotranspiration in arid Central Asia and Xinjiang of China

Accurate inversion of land surface evapotranspiration （ET） in arid areas is of great significance for understanding global eco-hydrological process and exploring the spatio-temporal variation and ecological response of water resources. It is also important in the functional evaluation of regional water cycle and water balance, as well as the rational allocation and management of water resources. This study, based on model validation analysis at varied scales in fiwe Central Asian countries and China＇s Xinjiang, developed an appropriate approach for ET inversion in arid lands. The actual ET during growing seasons of the study area was defined, and the changes in water participating in evaporation in regional water cycle were then educed. The results show the simulation error of SEBS （Surface Energy Balance System） model under cloud amount consideration was 1.34% at 30-m spatial scale, 2.75% at 1-km spatial scale and 6,37% at 4-kin spatial scale. ET inversion for 1980-2007 applying SEBS model in the study area indicates： （1） the evaporation depth （May-September） by land types descends in the order of waters （660.24 ram） 〉 cultivated land （464.66 mm） 〉 woodland （388.44 mm） 〉 urbanized land （168.16 mm） 〉 grassland （160.48 mm） 〉 unused land （83.08 mm）; and （2） ET during the 2005 growing season in Xinjiang and Central Asia was 2,168.68x108 m3 （with an evaporation/precipitation ratio of 1.05） and 9,741.03x108 m3 （with an evaporation/precipitation ratio of 1.4）, respectively. The results unveiled the spatio-temporal variation rules of ET process in arid areas, providing a reference for further research on the water cycle and water balance in similar arid regions.

Mapping of QTLs and candidate genes associated with multiple phenotypic traits for Huanglongbing tolerance in citrus

Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.

The effect of total carbon on microscopic soil properties and implications for crop production

Soil structure is a dynamic property affected by physical, chemical, and microbiological processes. Addition of organic matter to soils and the use of different management practices have been reported to impact soil structure and crop production. Moderation in soil temperature and increases in microbial activity and soil water retention are often suggested as reasons for the rise in crop yield when organic matter is added to the soil. Less is known about the direct effect of changes in soil structure on crop production. A field experiment was conducted to study the effect of summer cover crop and in-season management system on soil structure. The experiment was a nested design with summer cover crop as the main plot and management system as the subplot. Summer cover crop treatments included cowpea （Vigna unguiculata L. Walp.） incorporated into the soil in the fall （CI）, cowpea used as mulch in the fall （CM）, sudangrass （Sorghum vulgare） incorporated into the soil in the fall （S）, and dry fallow or bare ground （B）. Management systems were organic （ORG） and conventional （CNV） systems. Lettuce （Lactuca sativa L.） and cantaloupes （Cucumis melo L.） were cultivated in rotation in the plots for three consecutive years using the same cover crops and management systems for each plot. Disturbed and undisturbed soil cores were collected at the end of the third year and used for laboratory experiments to measure physical, chemical, and hy- draulic properties. Image analysis was used to quantify soil structure properties using a scanning electron micro- scope on thin sections prepared from the undisturbed soil cores. We found that total soil carbon was correlated with porosity, saturation percentage, and pore roughness. Pore roughness was correlated with crop production in gen- eral and with marketable production in particular. We found that the higher the complexity of the pore space, the more water retained in the soil, which may increase soil water residence and reduce plant water stress.

Eco-vegetation Construction of the Community Gardens in US and Its Implications

Community garden is a popular vegetation landscape mode with production,ecology and life functions. On the basis of eco-service functions of community garden,this paper selected 14 such gardens in Los Angeles and studies them by field survey. It researched the response of diversity of urban vegetation varieties and distribution pattern to planters' ethnic background and construction mode,then it analyzed its implications for China's urban green space construction and leisure agriculture. A total of 439 varieties of plant were studied,indicating that community garden is an important species pool of urban ecosystem; it can maintain rich native taxa resources; plant function is mainly edible plant, which plays a great role in protecting ethnic traditional culture and regional native culture; landscape structure and function of vegetation are influenced by ethnic background and construction mode. Researches show that the community garden,as the intersection landscape of ecological diversity and cultural diversity,is a feasible construction mode for realizing urban green infrastructure construction and leisure agricultural development. China should learn from this experience,take into consideration interested parties when making green space planning and conducting eco-vegetation construction. This is of great significance to launching urban eco-vegetation construction and developing leisure agriculture in China.Community garden is a popular vegetation landscape mode with production,ecology and life functions. On the basis of eco-service functions of community garden,this paper selected 14 such gardens in Los Angeles and studies them by field survey. It researched the response of diversity of urban vegetation varieties and distribution pattern to planters' ethnic background and construction mode,then it analyzed its implications for China's urban green space construction and leisure agriculture. A total of 439 varieties of plant were studied,indicating that community garden is an important species pool of urban ecosystem; it can maintain rich native taxa resources; plant function is mainly edible plant, which plays a great role in protecting ethnic traditional culture and regional native culture; landscape structure and function of vegetation are influenced by ethnic background and construction mode. Researches show that the community garden,as the intersection landscape of ecological diversity and cultural diversity,is a feasible construction mode for realizing urban green infrastructure construction and leisure agricultural development. China should learn from this experience,take into consideration interested parties when making green space planning and conducting eco-vegetation construction. This is of great significance to launching urban eco-vegetation construction and developing leisure agriculture in China.

Variation in soil organic matter accumulation and metabolic activity along an elevation gradient in the Santa Rosa Mountains of Southern California, USA

Variations in soil organic matter accumulation across an elevation can be used to explain the control of substrate supply and variability on soil metabolic activity. We investigated geographic changes in soil organic matter and metabolic rates along an elevation gradient（289–2,489 m） in the Santa Rosa Mountains, California, USA from subalpine and montane pine forests through chaparral to desert. From base（289 m） to summit（2,489 m）, 24 sites were established for collecting soil samples under canopies and inter-canopy spaces, at 0–5 and 5–15 cm soil depths increments. Soil organic matter（SOM） content was determined using weight loss on ignition at 550°C and soil CO2 efflux（R） was measured at day 5（R5） and day 20（R20） of incubation. Changes in SOM content along the elevation gradient showed a significant relationship（P〈0.05） but R5 and R20 were not related to either elevation or SOM content. However, the ratio of R and SOM（R5/SOM） showed a strong relationship across the mountains at both soil depths. R5/SOM, as an indicator of carbon use efficiency, may be applicable to other semi-arid transects at larger scale modeling of soil metabolic processes.

Plant-to-plant direct competition for belowground resource in an overlapping depletion zone

In response to limited availability of soil resources in basal root zone, plant extends its roots into nearby resource-rich zones to fulfill essential resource demands for survival and reproduction. This root proliferation into that enriched zones occupied by other plants constitutes interplant overlapping rooting zones and thereby the overlapping depletion zones, causing reduction in resource uptake by neighboring plants. By incorporating this mechanism into the classic resource competition model, we study interplant direct competition through their rooting system in an overlapping depletion zone. The model results indicate an extension of Tilman’s R* rule that has already been proved true when plants compete indirectly through their effect on shared resources. The results reveal that plant’s direct competitive ability (i.e., the ability to occupy an overlapping depletion zone by excluding others) can be characterized by its R*-value, where a best competitor having lowest R*-value excludes others from an overlapping zone and occupies the zone by depleting the resource level to the lowest as in its non-overlapping depletion zone. By analyzing the model, we find a suite of traits that confers R* variation among directly competing plants. This suite of traits would be a useful proxy measure for R* that do not necessarily require to establish equilibrium field monoculture—a requirement for R* measurement in the field.

Prokaryotic branch of the Tree of Life： A composition vector approach

The Composition Vector Tree (CVTree) is a parameter-free and alignment-free method to infer pro-karyotic phylogeny from their complete genomes. It is distinct from the traditional 16S rRNA analysis in both the input data and the methodology. The prokaryotic phylogenetic trees constructed by using the CVTree method agree well with the Bergey’s taxonomy in all major groupings and fine branching patterns. Thus, combined use of the CVTree approach and the 16S rRNA analysis may provide an objective and reliable reconstruction of the prokaryotic branch of the Tree of Life.

Contribution of biodiversity to ecosystem functioning:a non-equilibrium thermodynamic perspective

Ecosystem stays far from thermodynamic equilibrium. Through the interactions among biotic and abiotic components, and encompassing physical environments, ecosystem forms a dissipative struc- ture that allows it to dissipate energy continuously and thereby remains functional over time. Biotic regulation of energy and material fluxes in and out of the ecosystem allows it to maintain a homeostatic state which corresponds to a self-organized state emerged in a non-equilibrium thermodynamic system. While the associated self-organizational processes approach to homeostatic state, entropy （a measure of irre- versibility） degrades and dissipation of energy increases. We propose here that at a homeostatic state of ecosystem, biodiversity which includes both phenotypic and functional diversity, attains optimal values. As long as biodiversity remains within its optimal range, the corresponding homeostatic state is maintained. However, while embedded environmental conditions fluctuate along the gradient of accelerating changes, phenotypic diversity and functional diversity contribute inversely to the associated self-organizing proc- esses. Furthermore, an increase or decrease in biodiversity outside of its optimal range makes the eco- system vulnerable to transition into a different state.

Special Issue Introduction-The Whitefly Bemisia tabaci Species Complex and Begomoviruses:Research Progress and Future Prospects

The whitefly Bemisia tabaci species complex and the begomoviruses they transmit are devastating agricultural pests worldwide.With the rapid and further inva-sions by some members of the whitefly species complex into new regions,their impacts on human society are likely to increase in the years to come.

Emergence of spatiotemporal chaos arising from far-field breakup of spiral waves in the plankton ecological systems

It has been reported that the minimal spatially extended phytoplankton-zooplankton system exhibits both temporal regular/chaotic behaviour, and spatiotemporal chaos in a patchy environment. As a further investigation by means of computer simulations and theoretical analysis, in this paper we observe that the spiral waves may exist and the spatiotemporal chaos emerge when the parameters are within the mixed Turing-Hopf bifurcation region, which arises from the far-field breakup of the spiral waves over a large range of diffusion coefficients of phytoplankton and zooplankton. Moreover, the spatiotemporal chaos arising from the far-field breakup of spiral waves does not gradually invade the whole space of that region. Our results are confirmed by nonlinear bifurcation of wave trains, We also discuss ecological implications of these spatially structured patterns.

Activation of stress-response genes by retrograde signaling-mediated destabilization of nuclear importin IMPα-9 and its interactor TPR2

Stress-induced retrograde signal transmission from the plastids to the nucleus has long puzzled plant biologists.To address this,we performed a suppressor screen of the ceh1 mutant,which contains elevated 2-C-methyl-d-erythritol-2,4-cyclopyrophosphate(MEcPP)levels,and identified the gain-of-function mutant impα-9,which shows reversed dwarfism and suppressed expression of stress-response genes in the ceh1 background despite heightened MEcPP.Subsequent genetic and biochemical analyses established that the accumulation of MEcPP initiates an upsurge in Arabidopsis SKP1-like 1(ASK1)abundance,a pivotal component in the proteasome degradation pathway.This increase in ASK1 prompts the degradation of IMPα-9.Moreover,we uncovered a protein-protein interaction between IMPα-9 and TPR2,a transcriptional co-suppressor and found that a reduction in IMPα-9 levels coincides with a decrease in TPR2 abundance.Significantly,the interaction between IMPα-9 and TPR2 was disrupted in impα-9 mutants,highlighting the critical role of a single amino acid alteration in maintaining their association.Disruption of their interaction results in the reversal of MEcPP-associated phenotypes.Chromatin immunoprecipitation coupled with sequencing analyses revealed that TPR2 binds globally to stress-response genes and suggested that IMPα-9 associates with the chromatin.They function together to suppress the expression of stress-response genes under normal conditions,but this suppression is alleviated in response to stress through the degradation of the suppressing machinery.The biological relevance of our discoveries was validated under high light stress,marked by MEcPP accumulation,elevated ASK1 levels,IMPα-9 degredation,reduced TPR2 abundance,and subsequent activation of a network of stress-response genes.In summary,our study collectively unveils fresh insights into plant adaptive mechanisms,highlighting intricate interactions among retrograde signaling,the proteasome,and nuclear transport machinery.

The Ozone Component of Global Change:Potential Effects on Agricultural and Horticultural Plant Yield,Product Quality and Interactions with Invasive Species

The productivity, product quality and competitive ability of important agricultural and horticultural plants in many regions of the world may be adversely affected by current and anticipated concentrations of ground-level ozone （O_3）. Exposure to elevated O_3 typically results in suppressed photosynthesis, accelerated senescence, decreased growth and lower yields. Various approaches used to evaluate O_3 effects generally concur that current yield losses range from 5% to 15% among sensitive plants. There is, however, considerable genetic variability in plant responses to O_3.

Primary Cell Wall Structure in the Evolution of Land Plants

Investigation of the primary cell walls of lower plants improves our understanding of the cell biology of these organisms but also has the potential to improve our understanding of cell wall structure and function in angiosperms that evolved from lower plants. Cell walls were prepared from eight species, ranging from a moss to advanced gymnosperms, and subjected to sequential chemical extraction to separate the main polysaccharide fractions. The glycosyl compositions of these fractions were then determined by gas chromatography. The results were compared among the eight plants and among data from related studies reported in the existing published reports to identify structural features that have been either highly conserved or clearly modified during evolution. Among the highly conserved features are the presence of a cellulose framework, the presence of certain hemicelluloses such as xyloglucan, and the presence of rhamnogalacturonan II, a domain in pectic polysaccharides. Among the modified features are the abundance of mannosyl-containing hemicelluloses and the presence of methylated sugars.

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants

microRNAs (miRNAs)are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression,leading to gene silencing.We previously developed short tandem target mimic (STTM)technology to deactivate endogenous miRNAs in Arabidopsis.Here,we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis,tomato,rice,and maize,providing a resource for the functional interrogation of miRNAs.We not only revealed the functions of several miRNAs in plant development,but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development.RNA-seq and small RNAseq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation,secondary metabolism,and ion-channel activity-associated electrophysiology,demonstrating that STTM technology is an effective approach for studying miRNA functions.To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks,we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTMinduced miRNA knockdown plants.

The biosynthetic pathway of the hallucinogen mescaline and its heterologous reconstruction

Mescaline,among the earliest identified natural hallucinogens,holds great potential in psychotherapy treatment.Nonetheless,despite the existence of a postulated biosynthetic pathway for more than half a century,the specific enzymes involved in this process are yet to be identified.In this study,we investigated the cactus Lophophora williamsii(Peyote),the largest known natural producer of the phenethylamine mescaline.We employed a multi-faceted approach,combining de novo whole-genome and transcriptome sequencing with comprehensive chemical profiling,enzymatic assays,molecular modeling,and pathway engineering for pathway elucidation.We identified four groups of enzymes responsible for the six catalytic steps in the mescaline biosynthetic pathway,and an N-methyltransferase enzyme that N-methylates all phenethylamine intermediates,likely modulating mescaline levels in Peyote.Finally,we reconstructed the mescaline biosynthetic pathway in both Nicotiana benthamiana plants and yeast cells,providing novel insights into several challenges hindering complete heterologous mescaline production.Taken together,our study opens up avenues for exploration of sustainable production approaches and responsible utilization of mescaline,safeguarding this valuable natural resource for future generations.