Mechanisms of Broad Host Range Necrotrophic Pathogenesis in Sclerotinia sclerotiorum

Among necrotrophic fungi, Sclerotinia sclerotiorum is remarkable for its extremely broad host range and for its aggressive host tissue colonization. With full genome sequencing, transcriptomic analyses and the increasing pace of functional gene characterization, the factors underlying the basis of this broad host range necrotrophic pathogenesis are now being elucidated at a greater pace. Among these, genes have been characterized that are required for infection via compound appressoria in addition to genes associated with colonization that regulate oxalic acid (OA) production and OA catabolism. Moreover, virulence-related secretory proteins have been identified, among which are candidates for manipulating host activities apoplastically and cytoplasmically. Coupled with these mechanistic studies, cytological observations of the colonization process have blurred the heretofore clear-cut biotroph versus necrotroph boundary. In this review, we reexamine the cytology of S. sclerotiorum infection and put more recent molecular and genomic data into the context of this cytology. We propose a two-phase infection model in which the pathogen first evades, counteracts and subverts host basal defense reactions prior to killing and degrading host cells. Spatially, the pathogen may achieve this via the production of compatibility factors/effectors in compound appressoria, bulbous subcuticular hyphae, and primary invasive hyphae. By examining the nuances of this interaction, we hope to illuminate new classes of factors as targets to improve our understanding of broad host range necrotrophic pathogens and provide the basis for understanding corresponding host resistance.

Herbivore-Diet Analysis Based on Illumina MiSeq Sequencing: The Potential Use of an ITS2-Barcoding Approach to Establish Qualitative and Quantitative Predictions of Diet Composition of Mongolian Sheep

DNA-barcoding approaches to estimate the diet compositions of grazing animals have received significant attention, and particularly when combined with next-generation sequencing, these techniques have substantially improved in recent years. In this study, the identity and species composition of plant material ingested by Mongolian sheep were estimated through the use of 350 bp ITS2 gene sequences of the vegetation found in fecal samples. Four diets were formulated using varying amounts of eight plant species that are common in the grasslands of northern China. Sixteen Mongolian sheep were taken from pastures and randomly assigned to four groups, and each group received one of four diets. Each sheep was randomly assigned to one of 16 confinement pens and fed its respective diet for 12 consecutive days. Fecal samples were removed from each pen from days 7-12, preserved, and composited for each pen. All herbage species included in the daily diets were detected in each fecal sample, with the exception of Phragmites australis. Moreover, 12 additional different plant species were retrieved from feces of the experimental sheep. The obtained data provided preliminary support for the use of the ITS2 barcode to determine which plants were consumed. Moreover, the proportions of the herbage DNA sequences recovered from sheep feces and those of the herbage masses in the daily diets did not completely match. These results indicate that the non-Gramineae DNA sequences amplified with ITS2 primers (including those of Chenopodium album, Artemisia scoparia, Artemisia tanacetifolia, and Medicago sativa) far exceeded those of the Gramineae species (including Leymus chinensis and Puccinellia distans), which constitute the largest share of the experimental diets. A significant positive correlation (Spearman's ρ = 0.376, P = 0.003) between the actual herbage mass proportions in the experimental diets and the herbage-DNA-sequence proportions provided sufficiently favorable support for the further investigation of DNA barcoding for the quantification of plants in feces. A significant regression coefficient was found between the relative DNA-sequence proportions of L. chinensis ( R² = 0.82, P < 0.0001), P. distans ( R² = 0.64, P = 0.0017), and C. album ( R² = 0.98, P < 0.0001) and their respective herbage mass proportions. The quantitative relationship can be expressed by the linear-regression equations y = 0.90 x - 0.22, y = 0.98 x - 0.03, and y = 5.00 x - 0.25, respectively. Thus, these results demonstrate that dietary-DNA-barcoding methods exhibited potential in providing valuable quantitative information regarding food-item components. However, it should be noted that this explorative data needs to be further improved by using additional genes and by creating a sophisticated reference database, thus enhancing both quality and accuracy of the obtained results.

Evolutionary history and functional traits determine the spatial pattern of multifaceted plant diversity in a typical temperate desert disturbed by an expressway

Temperate desert is one of the globally important biomes with unique and valuable biodiversity, which might be threatened by environmental stresses and human disturbance associated with rapid development. However, few studies have documented the spatial distribution of the multifaceted plant diversity of the temperate desert and their relationships with external impacting factors. We sampled multifaceted plant species diversity including taxonomic diversity, functional diversity and phylogenetic diversity in the Alashan Desert along Beijing-Xinjiang Expressway (G6) in Northern China to identify the key factors and process which regulate the multifaceted plant diversity of the temperate desert. We found that the dynamics of species richness, functional richness, and phylogenetic richness along the elevational gradient corresponded to the unimodal model. Species phylogenetic development shifted from aggregation to divergence, while species functional traits were the opposite along the elevational gradient. The sites at an elevation around 1200-1400 m were the key habitats for the occurrence of high plant diversity including species richness, functional richness and phylogenetic richness. There were no significant differences (p > 0.05) in plant diversity at different distances from the road (500 m, 1000 m and 1500 m) and human disturbances (the distance from the nearest human settlements). Temperature, temperature variability, precipitation, precipitation variability, soil physical and chemistry properties showed no significant effects on plant diversity. It was concluded that evolutionary history and functional traits, not environmental or anthropogenic factors were the key determinants of the pattern of multifaceted plant diversity.

Multi-Organ Plant Classification Based on Convolutional and Recurrent Neural Networks

Classification of plants based on a multi-organ approach is very challenging. Although additional data provide more information that might help to disambiguate between species, the variability in shape and appearance in plant organs also raises the degree of complexity of the problem. Despite promising solutions built using deep learning enable representative features to be learned for plant images, the existing approaches focus mainly on generic features for species classification, disregarding the features representing plant organs. In fact, plants are complex living organisms sustained by a number of organ systems. In our approach, we introduce a hybrid generic-organ convolutional neural network (HGO-CNN), which takes into account both organ and generic information, combining them using a new feature fusion scheme for species classification. Next, instead of using a CNN-based method to operate on one image with a single organ, we extend our approach. We propose a new framework for plant structural learning using the recurrent neural network-based method. This novel approach supports classification based on a varying number of plant views, capturing one or more organs of a plant, by optimizing the contextual dependencies between them. We also present the qualitative results of our proposed models based on feature visualization techniques and show that the outcomes of visualizations depict our hypothesis and expectation. Finally, we show that by leveraging and combining the aforementioned techniques, our best network outperforms the state of the art on the PlantClef2015 benchmark. The source code and models are available at https://github.com/cs-chan/Deep-Plant.

The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon

The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social1-10 and natural sciences11,12. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data8, modern vegetation13, modern ethnographic data3 or a limited integration of archaeological and palaeoecological data12. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered11. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

From Plant Compounds to Botanicals and Back: A Current Snapshot

This work aims at giving an updated picture of the strict interaction between main plant biologically active compounds and botanicals. The main features of the emerging class of dietary supplements, the botanicals, are highlighted. Focus is also on the definition of actual possibilities of study approach and research strategies. Examples of innovative directions are given: assessment of interaction of bioactive compounds, chemometrics and the new goal of biorefineries. Current models of existing databases, such as plant metabolic pathways, food composition, bioactive compounds, dietary supplements, and dietary markers, are described as usable tools for health research. The need for categorization of botanicals as well as for the implementation of specific and dedicated databases emerged, based on both analytical data and collected data taken from literature throughout a harmonized and standardized approach for the evaluation of an adequate dietary intake.

DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.

Disturbance from traditional fire management in subalpine heathlands increases Afro-alpine plant resilience to climate change

Species are often controlled by biotic factors such as competition at the warm edge of their distribution range. Disturbances at the treeline, disrupting competitive dominance, may thus enable alpine species to utilize lower altitudes. We searched for evidence for range expansion in grazed, fire-managed Ethiopian subalpine Erica heathlands across a 25-year chronosequence. We examined vascular plant composition in 48 plots (5 × 5 m) across an altitudinal range of 3,465-3,711 m.a.s.l. and analyzed how community composition changed in relation to increasing competition over time (using a Shade index based on Erica shrub height and cover) and altitude. Species' habitats and altitudinal ranges were derived from literature. Time since fire explained more variation (r²  = .41) in species composition than altitude did (r²  = .32) in an NMDS analysis. Community-weighted altitudinal optima for species in a plot decreased strongly with increasing shade (GLM, Standardized Regression Coefficient SRC = -.41, p = .003), but increased only weakly with altitude (SRC = .26, p = .054). In other words, young stands were dominated by species with higher altitudinal optima than old stands. Forest species richness increased with Log Shade index (SRC = .12, p = .008), but was unaffected by altitude (SRC = -.07, p = .13). However, richness of alpine and heathland species was not highest in plots with lowest Shade index, but displayed a unimodal pattern with an initial increase, followed by a decrease when shading increased (altitude was not significant). Our results indicate that disturbance from the traditional patch burning increases the available habitat for less competitive high-altitude plants and prevents tree line ascent. Therefore, maintaining, but regulating, the traditional land use increases the Afro-alpine flora's resilience to global warming. However, this system is threatened by a new REDD+ program attempting to increase carbon storage via fire suppression. This study highlights the importance of understanding traditional management regimes for biodiversity conservation in cultural landscapes in an era of global change.

Effects of Plant Diversity, Vegetation Composition, and Habitat Type on Different Functional Trait Groups of Wild Bees in Rural Beijing

The loss of flower-rich habitats and agricultural intensification have resulted in significant losses of wild bee diversity from agricultural landscapes that is increasingly threatening the pollination of zoochorous agricultural crops and agricultural sustainability. However, the links of different wild bee functional trait groups with habitat types and plant resources in agricultural landscapes remain poorly understood, thus impeding the formulation of effective policies for bee conservation. We therefore analyzed how bees representing different functional groups responded to variations in habitat type, vegetation composition and plant diversity. Natural shrubland sustained the highest diversity in bees overall, in large-sized bees, solitary bees and belowground-nesting bees, while each habitat harbored unique species. In half of the functional bee groups, species were negatively linked to tree coverage and herb coverage, respectively, while plant diversity was positively related to all functional groups except large-sized bees and aboveground-nesting bees. Overall bee abundance was positively related to abundance of plants in the Sympetalae, and negatively related to abundance of plants in the Archichlamydeae. Different bee functional groups showed distinct preferences for different plant communities. In order to conserve the diversity of wild bees across functional groups to optimize associated pollination services, a diverse habitat mosaic, and particularly plant species in Sympetalae need to be promoted in agricultural landscapes. Future studies should aim to enhance our understanding of plant-pollinator associations and specific food requirement of different wild bee species for their effective conservation.

Phylogenetic diversity and plant trait composition predict multiple ecosystem functions in green roofs

Plant selection and diversity can influence the provision of key ecosystem services in extensive green roofs. While species richness does predict ecosystem services, functional and phylogenetic community structure may provide a stronger mechanistic link to such services than species richness alone. In this study, we assessed the relationship between community-weighted trait values from four key leaf and canopy functional traits (plant height, leaf area, specific leaf area, dry leaf matter content), functional diversity, and phylogenetic diversity to ten different green roof functions, including ecosystem multifunctionality, in experimental polycultures. Functional traits of dominant plant species were a major driver for indicators of multiple green roof functions, such as substrate nitrate-N, substrate phosphorus, aboveground biomass and ecosystem multifunctionality. In contrast, functional diversity alone increased substrate organic matter. Moreover, both functional/phylogenetic diversity and identity predicted canopy density, substrate cooling. This study highlights the first line of evidence that distinct aspects of phylogenetic and functional diversity play a major role in predicting multiple green roof services. Therefore, we provide further evidence that to maximize green roof functioning, a very careful selection of plant traits and polycultures are needed.

Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties

Anthropogenic processes and socio-economic factors play important roles in shaping plant diversity in urban parks. To investigate how plant diversity of Ma' anling urban volcano park in Hainan Province, China respond to these factors, we carried out a field investigation on the taxonomic and phylogenetic diversity of vascular plants and soil properties in this area. We found 284 species of vascular plants belonging to 88 families and 241 genera, which included 194 native species, 23 invasive species, 31 naturalized species, 40 cultivars, and 4 rare / endangered plant species. Tree composition and richness significantly varied between different vegetation formations (plantation, secondary forest, and abandoned land). Plant species richness and community composition were significantly affected by elevation (El), soil water content (WC), total soil nitrogen (TN) and soil organic matter (SOM). There were significant diversity differences between plantations and abandoned lands, but not between the plantations and secondary forests. The flora in the study site was tropical in nature, characterized by pantropic distributions. Compared to adjacent areas, floristic composition in the study site was most similar to that of Guangdong, followed by that of Vietnam. Our study revealed the diversity patterns of volcanic plants and provided the basis for future planning of plant conservation, such as preserving plant species, maintaining plant habitats, and coordinating plant management in this region.

Genetic drift precluded adaptation of an insect seed predator to a novel host plant in a long-term selection experiment

Host specialization is considered a primary driver of the enormous diversity of herbivorous insects. Trade-offs in host use are hypothesized to promote this specialization, but they have mostly been studied in generalist herbivores. We conducted a multi-generation selection experiment to examine the adaptation of the specialist seed-feeding bug, Lygaeus equestris, to three novel host plants (Helianthus annuus, Verbascum thapsus and Centaurea phrygia) and to test whether trade-offs promote specialization. During the selection experiment, body size of L. equestris increased more on the novel host plant H. annuus compared to the primary host plant, Vincetoxicum hirundinaria, but this effect was not observed in other fitness related traits. In addition to selection, genetic drift caused variation among the experimental herbivore populations in their ability to exploit the host plants. Microsatellite data indicated that the level of within-population genetic variation decreased and population differentiation increased more in the selection line feeding on H. annuus compared to V. hirundinaria. We found a negative correlation between genetic differentiation and heterozygosity at the end of the experiment, suggesting that differentiation was significantly affected by genetic drift. We did not find fitness trade-offs between L. equestris feeding on the four hosts. Thus, trade-offs do not seem to promote specialization in L. equestris. Our results suggest that this insect herbivore is not likely to adapt to a novel host species in a time-scale of 20 generations despite sufficient genetic variation and that genetic drift disrupted the response to selection.

DNA barcoding and a precise morphological comparison revealed a cryptic species in the Nippolachnus piri complex (Hemiptera: Aphididae: Lachninae)

Nippolachnus is a small Palaearctic-Oriental genus of very characteristic aphids that live on the leaves of woody Rosaceae. One species, N. piri, has hitherto been regarded to be widely distributed and relatively polyphagous. Members of this genus are considered to be easy to recognize due to the absence of the ocular tubercle and triommatidia on the head. We conducted research on the morphology and generic characters of Nippolachnus piri complex using scanning electron microscopy (for the first time) and DNA barcoding. We analyzed N. piri populations on Pyrus and other plants (Eriobotrya, Rhaphiolepis and Sorbus) in Japan and the Republic of Korea. Specifically, a high genetic divergence value was found between the N. piri populations associated with different host plants. SEM investigation of the head capsule revealed that a triommatidium is present under the compound eye, despite their lack of an ocular tubercle. We propose Nippolachnus micromeli Shinji, 1924 stat. nov. as a cryptic species in the N. piri complex based on a morphological comparison, DNA barcoding and different host-plant associations. Illustrations and descriptions of studied species are given. Morphological keys to the apterae and alatae of all known species of the genus Nippolachnus are also provided.

Using co-occurrence information and trait composition to understand individual plant performance in grassland communities

Depending on the strength of environmental filtering and competitive exclusion, successful colonizers of plant communities show varying degrees of similarity to resident species with respect to functional traits. For the present study, colonizer's performance was assessed in relation to the degree of fit with the resident community, and in addition, in relation to the community's trait profile and the environmental factors at the study locations. The two-year field experiment investigated the relative growth rates of 130 species that had been transplanted into German grassland communities varying in intensities of land-use. The transplanted species were selected in accordance with the following scenarios: species with highly similar or dissimilar traits to residents, species with highest degree of co-occurrence with resident species and species chosen randomly from the local species pool. The performance of transplanted phytometers depended on the scenario according to which the species were selected, on community trait diversity, and in addition, often on the interaction of both and on land use intensity. The total amount of explained variance in performance was low, but increased considerably when species identity was taken into account. In general, individuals in the co-occurrence scenario performed better than those selected based on trait information or those selected randomly. Different predictors were important in different seasons, demonstrating a limited temporal validity of performance models.

Tracing trends in plant physiology and biochemistry: Need of databases from genetic to kingdom level

With the rapid advancement in technologies over recent decades, abundant data regarding plant physiological/biochemical responses to stress conditions are now available. Comparing plant stress responses using latest statistical software and analytical models can trace very interesting and useful trends in literature data, which can be of high use for future research and policy making. This model study uses principal component analysis (PCA) to compare physiological/biochemical responses of Vicia faba plant against Pb stress chelated by ethylenediaminetetraacetic acid (EDTA) or citric acid (CA). PCA confirmed the descriptive analysis and divided all the treatments into two main groups: toxic (Pb alone, Pb-CA-a and Pb-CA-b), and non-toxic (control, EDTA-b, CA-b, Pb-EDTA-a and Pb-EDTA-b) treatments. PCA analysis further revealed the effectiveness of different plant physiological/biochemical responses under Pb stress: glutathione reductase (GR) and ascorbate peroxidase (APX) are the main enzymes reacting against Pb toxicity in relation with Pb uptake by V. faba roots, while GR reacts alone in leaves. It is proposed, using latest statistical tests and software, that the comparison and correlation of physiological responses and analytical techniques can be applied at various levels and types of stresses and responses of living organisms to develop a larger dataset based on existing literature. The trends marked out can be correlated with biochemical and physiological processes/mechanisms taking place at genetic-cellular level.

Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits

There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa). The composition of all soil community groups was affected by plant species identity, both in monocultures and in mixed communities. Moreover, plant community composition predicted additional variation in soil community composition beyond what could be predicted from soil abiotic characteristics. In addition, analysis of the field aboveground plant community composition and the composition of plant roots suggests that plant community attributes are better predictors of soil communities than root distributions. However, neither plant phylogeny nor plant traits were strong predictors of soil communities in either experiment. Our results demonstrate that grassland plant species form specific associations with soil community members and that information on plant species distributions can improve predictions of soil community composition. These results indicate that specific associations between plant species and complex soil communities are key determinants of biodiversity patterns in grassland soils.

'A more perfect arrangement of plants': the botanical model in psychiatric nosology, 1676 to the present day

Psychiatric classification remains a complex endeavour; since the Enlightenment, nosologists have made use of various models and metaphors to describe their systems. Here we present the most common model, botanical taxonomy, and trace its history from the nosologies of Sydenham, Sauvages and Linnaeus; to evolutionary models; to the later contributions of Hughlings-Jackson, Kraepelin and Jaspers. Over time, there has been a shift from explicit attempts to pattern disease classification on botanical systems, to a more metaphorical use. We find that changes in the understanding of plants and plant relationships parallel changes in the conceptualization of mental illness. Not only have scientific discoveries influenced the use of metaphor, but the language of metaphor has also both illuminated and constrained psychiatric nosology.

Recommending plant taxa for supporting on-site species identification

BACKGROUND

Predicting a list of plant taxa most likely to be observed at a given geographical location and time is useful for many scenarios in biodiversity informatics. Since efficient plant species identification is impeded mainly by the large number of possible candidate species, providing a shortlist of likely candidates can help significantly expedite the task. Whereas species distribution models heavily rely on geo-referenced occurrence data, such information still remains largely unused for plant taxa identification tools.

RESULTS

In this paper, we conduct a study on the feasibility of computing a ranked shortlist of plant taxa likely to be encountered by an observer in the field. We use the territory of Germany as case study with a total of 7.62M records of freely available plant presence-absence data and occurrence records for 2.7k plant taxa. We systematically study achievable recommendation quality based on two types of source data: binary presence-absence data and individual occurrence records. Furthermore, we study strategies for aggregating records into a taxa recommendation based on location and date of an observation.

CONCLUSION

We evaluate recommendations using 28k geo-referenced and taxa-labeled plant images hosted on the Flickr website as an independent test dataset. Relying on location information from presence-absence data alone results in an average recall of 82%. However, we find that occurrence records are complementary to presence-absence data and using both in combination yields considerably higher recall of 96% along with improved ranking metrics. Ultimately, by reducing the list of candidate taxa by an average of 62%, a spatio-temporal prior can substantially expedite the overall identification problem.

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

BACKGROUND

Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny.

RESULTS

We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled.

CONCLUSIONS

TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .

HeLM: a macrophyte-based method for monitoring and assessment of Greek lakes

The Water Framework Directive (WFD) requires Member States to develop appropriate assessment methods for the classification of the ecological status of their surface waters. Mediterranean region has lagged behind in this task, so we propose here the first developed method for Greek lakes, Hellenic Lake Macrophyte (HeLM) assessment method. This method is based on two metrics, a modified trophic index and maximum colonization depth C_max that quantify the degree of changes in lake macrophytic vegetation, as a response to eutrophication and general degradation pressures. The method was developed on the basis of a data set sampled from 272 monitoring transects in 16 Greek lakes. Sites from three lakes were selected as potential reference sites by using a screening process. Ecological quality ratios were calculated for each metric and for each lake, and ecological status class boundaries were defined. For the evaluation of effectiveness of the method, the correlations between individual metrics and final HeLM values and common pressure indicators, such as total phosphorus, chlorophyll a and Secchi depth, were tested and found highly significant and relatively strong. In addition, the ability of HeLM values and its individual metrics to distinguish between different macrophytic communities' structure was checked using aquatic plant life-forms and found satisfactory. The HeLM method gave a reliable assessment of the macrophytic vegetation's condition in Greek lakes and may constitute a useful tool for the classification of ecological status of other Mediterranean lakes.

DNA from lake sediments reveals long-term ecosystem changes after a biological invasion

What are the long-term consequences of invasive species? After invasion, how long do ecosystems require to reach a new equilibrium? Answering these questions requires long-term, high-resolution data that are vanishingly rare. We combined the analysis of environmental DNA extracted from a lake sediment core, coprophilous fungi, and sedimentological analyses to reconstruct 600 years of ecosystem dynamics on a sub-Antarctic island and to identify the impact of invasive rabbits. Plant communities remained stable from AD 1400 until the 1940s, when the DNA of invasive rabbits was detected in sediments. Rabbit detection corresponded to abrupt changes of plant communities, with a continuous decline of a dominant plant species. Furthermore, erosion rate abruptly increased with rabbit abundance. Rabbit impacts were very fast and were stronger than the effects of climate change during the 20th century. Lake sediments can allow an integrated temporal analysis of ecosystems, revealing the impact of invasive species over time and improving our understanding of underlying mechanisms.

New insights on plant phenological response to temperature revealed from long-term widespread observations in China

Constraints of temperature on spring plant phenology are closely related to plant growth, vegetation dynamics, and ecosystem carbon cycle. However, the effects of temperature on leaf onset, especially for winter chilling, are still not well understood. Using long-term, widespread in situ phenology observations collected over China for multiple plant species, this study analyzes the quantitative response of leaf onset to temperature, and compares empirical findings with existing theories and modeling approaches, as implemented in 18 phenology algorithms. Results show that the growing degree days (GDD) required for leaf onset vary distinctly among plant species and geographical locations as well as at organizational levels (species and community), pointing to diverse adaptation strategies. Chilling durations (CHD) needed for releasing bud dormancy decline monotonously from cold to warm areas with very limited interspecies variations. Results also reveal that winter chilling is a crucial component of phenology models, and its effect is better captured with an index that accounts for the inhomogeneous effectiveness of low temperature to chilling rate than with the conventional CHD index. The impact of spring warming on leaf onset is nonlinear, better represented by a logistical function of temperature than by the linear function currently implemented in biosphere models. The optimized base temperatures for thermal accumulation and the optimal chilling temperatures are species-dependent and average at 6.9 and 0.2°C, respectively. Overall, plants' chilling requirement is not a constant, and more chilling generally results in less requirement of thermal accumulation for leaf onset. Our results clearly demonstrate multiple deficiencies of the parameters (e.g., base temperature) and algorithms (e.g., method for calculating GDD) in conventional phenology models to represent leaf onset. Therefore, this study not only advances our mechanistic and quantitative understanding of temperature controls on leaf onset but also provides critical information for improving existing phenology models.

Precipitation frequency alters peatland ecosystem structure and CO2 exchange: Contrasting effects on moss, sedge, and shrub communities

Climate projections forecast a redistribution of seasonal precipitation for much of the globe into fewer, larger events spaced between longer dry periods, with negligible changes in seasonal rainfall totals. This intensification of the rainfall regime is expected to alter near-surface water availability, which will affect plant performance and carbon uptake. This could be especially important in peatland systems, where large stores of carbon are tightly coupled to water surpluses limiting decomposition. Here, we examined the role of precipitation frequency on vegetation growth and carbon dioxide (CO₂ ) balances for communities dominated by a Sphagnum moss, a sedge, and an ericaceous shrub in a cool temperate poor fen. Field plots and laboratory monoliths received one of three rainfall frequency treatments, ranging from one event every three days to one event every 14 days, while total rain delivered in a two-week cycle and the entire season to each treatment remained the same. Separating incident rain into fewer but larger events increased vascular cover in all peatland communities: vascular plant cover increased 6× in the moss-dominated plots, nearly doubled in the sedge plots, and tripled in the shrub plots in Low-Frequency relative to High-Frequency treatments. Gross ecosystem productivity was lowest in moss communities receiving low-frequency rain, but higher in sedge and shrub communities under the same conditions. Net ecosystem exchange followed this pattern: fewer events with longer dry periods increased CO₂ flux to the atmosphere from the moss while vascular plant-dominated communities became more of a sink for CO₂ . Results of this study suggest that changes to rainfall frequency already occurring and predicted to continue will lead to increased vascular plant cover in peatlands and will impact their carbon-sink function.

Sporophytes of polysporangiate land plants from the early Silurian period may have been photosynthetically autonomous

The colonization of land by vascular plants is an extremely important phase in Earth's life history. This key evolutionary process is thought to have begun during the Middle Cambrian ¹ period and culminated in the Silurian/Early Devonian period (interval about 509-393 million years ago (Ma)), and is documented primarily by microfossils (that is, by dispersed spores, phytodebris including fragments of algae, tissues, sporangia and cuticles), tubes and rare megafossils ² . A newly recognized fossil cooksonioid plant with in situ spores from the Barrandian area, Czech Republic, is of the highest importance because it represents extremely ancient megafossil evidence of land plant diploid generation: sporophytes (~432 Ma). The robust size of this plant places it among the largest known early polysporangiate land plants and it is probable that it attained adequate size for both aeration and effective photosynthetic competence. This would mean not only that sporophytes were photosynthetically autonomous but also that the they might have been able to sustain a relatively gametophyte-independent existence.

Aridity drives plant biogeographical sub regions in the Caatinga, the largest tropical dry forest and woodland block in South America

Our aims were to quantify and map the plant sub regions of the the Caatinga, that covers 844,453 km² and is the largest block of seasonally dry forest in South America. We performed spatial analyses of the largest dataset of woody plant distributions in this region assembled to date (of 2,666 shrub and tree species; 260 localities), compared these distributions with the current phytogeographic regionalizations, and investigated the potential environmental drivers of the floristic patterns in these sub regions. Phytogeographical regions were identified using quantitative analyses of species turnover calculated as Simpson dissimilarity index. We applied an interpolation method to map NMDS axes of compositional variation over the entire extent of the Caatinga, and then classified the compositional dissimilarity according to the number of biogeographical sub regions identified a priori using k-means analysis. We used multinomial logistic regression models to investigate the influence of contemporary climatic productivity, topographic complexity, soil characteristics, climate stability since the last glacial maximum, and the human footprint in explaining the identified sub regions. We identified nine spatially cohesive biogeographical sub regions. Current productivity, as indicated by an aridity index, was the only explanatory variable retained in the best model, explaining nearly half of the floristic variability between sub regions. The highest rates of endemism within the Caatinga were in the Core and Periphery Chapada Diamantina sub regions. Our findings suggest that the topographic complexity, soil variation, and human footprint in the Caatinga act on woody plant distributions at local scales and not as determinants of broad floristic patterns. The lack of effect of climatic stability since the last glacial maximum probably results from the fact that a single measure of climatic stability does not adequately capture the highly dynamic climatic shifts the region suffered during the Pleistocene. There was limited overlap between our results and previous Caatinga classifications.

Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation

Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.

A CsMYB6-CsTRY module regulates fruit trichome initiation in cucumber

Fruit epidermal features such as the number and size of trichomes or spines are important fruit quality traits in cucumber production. Little is known about the molecular mechanisms underlying fruit spine formation in cucumber. Here, we report functional characterization of the cucumber CsMYB6 gene, which encodes a MIXTA-like MYB transcription factor that plays an important role in regulating fruit trichome development. Spatial-temporal expression analyses revealed high-level expression of CsMYB6 in the epidermis of cucumber ovaries during fruit spine initiation, which was similar to the expression of CsTRY, a homolog of the Arabidopsis TRY gene that also plays a key role in trichome development. Overexpression of CsMYB6 and CsTRY in cucumber and Arabidopsis revealed that CsMYB6 and CsTRY act as negative regulators of trichome initiation in both species, and that CsMYB6 acted upstream of CsTRY in this process. CsMYB6 was found to bind to the three MYB binding sites inside the promoter region of CsTRY, and protein-protein interaction assays suggested that CsTRY also directly interacted with CsMYB6 protein. The results also revealed conserved and divergent roles of CsMYB6 and its Arabidopsis homolog AtMYB106 in trichome development. Collectively, our results reveal a novel mechanism in which the CsMYB6-CsTRY complex negatively regulates fruit trichome formation in cucumber.

Automated plant species identification-Trends and future directions

Current rates of species loss triggered numerous attempts to protect and conserve biodiversity. Species conservation, however, requires species identification skills, a competence obtained through intensive training and experience. Field researchers, land managers, educators, civil servants, and the interested public would greatly benefit from accessible, up-to-date tools automating the process of species identification. Currently, relevant technologies, such as digital cameras, mobile devices, and remote access to databases, are ubiquitously available, accompanied by significant advances in image processing and pattern recognition. The idea of automated species identification is approaching reality. We review the technical status quo on computer vision approaches for plant species identification, highlight the main research challenges to overcome in providing applicable tools, and conclude with a discussion of open and future research thrusts.

Plant identification is not exclusively the job of botanists and plant ecologists. It is required or useful for large parts of society, from professionals (such as landscape architects, foresters, farmers, conservationists, and biologists) to the general public (like ecotourists, hikers, and nature lovers). But the identification of plants by conventional means is difficult, time consuming, and (due to the use of specific botanical terms) frustrating for novices. This creates a hard-to-overcome hurdle for novices interested in acquiring species knowledge. In recent years, computer science research, especially image processing and pattern recognition techniques, have been introduced into plant taxonomy to eventually make up for the deficiency in people's identification abilities. We review the technical status quo on computer vision approaches for plant species identification, highlight the main research challenges to overcome in providing applicable tools, and conclude with a discussion of open and future research thrusts.

Decline in atmospheric sulphur deposition and changes in climate are the major drivers of long-term change in grassland plant communities in Scotland

The predicted long lag time between a decrease in atmospheric deposition and a measured response in vegetation has generally excluded the investigation of vegetation recovery from the impacts of atmospheric deposition. However, policy-makers require such evidence to assess whether policy decisions to reduce emissions will have a positive impact on habitats. Here we have shown that 40 years after the peak of SO_x emissions, decreases in SO_x are related to significant changes in species richness and cover in Scottish Calcareous, Mestrophic, Nardus and Wet grasslands. Using a survey of vegetation plots across Scotland, first carried out between 1958 and 1987 and resurveyed between 2012 and 2014, we test whether temporal changes in species richness and cover of bryophytes, Cyperaceae, forbs, Poaceae, and Juncaceae can be explained by changes in sulphur and nitrogen deposition, climate and/or grazing intensity, and whether these patterns differ between six grassland habitats: Acid, Calcareous, Lolium, Nardus, Mesotrophic and Wet grasslands. The results indicate that Calcareous, Mesotrophic, Nardus and Wet grasslands in Scotland are starting to recover from the UK peak of SO_x deposition in the 1970's. A decline in the cover of grasses, an increase in cover of bryophytes and forbs and the development of a more diverse sward (a reversal of the impacts of increased SO_x) was related to decreased SO_x deposition. However there was no evidence of a recovery from SO_x deposition in the Acid or Lolium grasslands. Despite a decline in NO_x deposition between the two surveys we found no evidence of a reversal of the impacts of increased N deposition. The climate also changed significantly between the two surveys, becoming warmer and wetter. This change in climate was related to significant changes in both the cover and species richness of bryophytes, Cyperaceae, forbs, Poaceae and Juncaceae but the changes differed between habitats.

Accelerated increase in plant species richness on mountain summits is linked to warming

Globally accelerating trends in societal development and human environmental impacts since the mid-twentieth century 1-7 are known as the Great Acceleration and have been discussed as a key indicator of the onset of the Anthropocene epoch 6 . While reports on ecological responses (for example, changes in species range or local extinctions) to the Great Acceleration are multiplying 8, 9 , it is unknown whether such biotic responses are undergoing a similar acceleration over time. This knowledge gap stems from the limited availability of time series data on biodiversity changes across large temporal and geographical extents. Here we use a dataset of repeated plant surveys from 302 mountain summits across Europe, spanning 145 years of observation, to assess the temporal trajectory of mountain biodiversity changes as a globally coherent imprint of the Anthropocene. We find a continent-wide acceleration in the rate of increase in plant species richness, with five times as much species enrichment between 2007 and 2016 as fifty years ago, between 1957 and 1966. This acceleration is strikingly synchronized with accelerated global warming and is not linked to alternative global change drivers. The accelerating increases in species richness on mountain summits across this broad spatial extent demonstrate that acceleration in climate-induced biotic change is occurring even in remote places on Earth, with potentially far-ranging consequences not only for biodiversity, but also for ecosystem functioning and services.

Ethylene Exerts Species-Specific and Age-Dependent Control of Photosynthesis

Ethylene regulates many different aspects of photosynthesis in an age-dependent and species-specific manner.

Leveraging contemporary species introductions to test phylogenetic hypotheses of trait evolution

Plant trait evolution is a topic of interest across disciplines and scales. Phylogenetic studies are powerful for generating hypotheses about the mechanisms that have shaped plant traits and their evolution. Introduced plants are a rich source of data on contemporary trait evolution. Introductions could provide especially useful tests of a variety of evolutionary hypotheses because the environments selecting on evolving traits are still present. We review phylogenetic and contemporary studies of trait evolution and identify areas of overlap and areas for further integration. Emerging tools which can promote integration include broadly focused repositories of trait data, and comparative models of trait evolution that consider both intra and interspecific variation.

Climbing plants: attachment adaptations and bioinspired innovations

Climbing plants have unique adaptations to enable them to compete for sunlight, for which they invest minimal resources for vertical growth. Indeed, their stems bear relatively little weight, as they traverse their host substrates skyward. Climbers possess high tensile strength and flexibility, which allows them to utilize natural and manmade structures for support and growth. The climbing strategies of plants have intrigued scientists for centuries, yet our understanding about biochemical adaptations and their molecular undergirding is still in the early stages of research. Nonetheless, recent discoveries are promising, not only from a basic knowledge perspective, but also for bioinspired product development. Several adaptations, including nanoparticle and adhesive production will be reviewed, as well as practical translation of these adaptations to commercial applications. We will review the botanical literature on the modes of adaptation to climb, as well as specialized organs-and cellular innovations. Finally, recent molecular and biochemical data will be reviewed to assess the future needs and new directions for potential practical products that may be bioinspired by climbing plants.

Global environmental change effects on plant community composition trajectories depend upon management legacies

The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.

Honeydew Honeys: A Review on the Characterization and Authentication of Botanical and Geographical Origins

The commercial interest in honeydew honeys (from the secretions of plants or the excretions of plant-sucking insects found on plants) is increasing because of their higher therapeutic properties compared with those of most blossom honeys (from nectar). However, honeydew honeys have been less studied than blossom honeys. In this work, studies carried out to characterize and authenticate honeydew honeys by their botanical and geographical origins have been reviewed. The identification of honey origins has been approached by two ways: by the analysis of chemical markers and by the development of analytical methodologies combined with multivariate analyses. Some compounds have been suggested as specific botanical markers of several honeydew honeys, such as quercitol and trans-oak lactone for oak honey, 2-aminoacetophenone and propylanisol for holm oak honey, and 1-chloro-octane and tridecane for pine honey. The presence of 3-carene and an unidentified compound in samples was proposed as a way discriminate between Greek and Turkish pine honeys. Chemometric analyses have been applied on chemical compositions and on physicochemical, microscopic, and spectral parameters and have proved to be valuable methods for authenticating honeydew honeys. Analytical methods based on spectral information are suitable for the routine control of honeydew-honey origins because they are fast and require easy sample preparations.

Optimum water depth ranges of dominant submersed macrophytes in a natural freshwater lake

Macrophytes show a zonal distribution along the lake littoral zone because of their specific preferred water depths while the optimum growth water depths of dominant submersed macrophytes in natural lakes are not well known. We studied the seasonal biomass and frequency patterns of dominant and companion submersed macrophytes along the water depth gradient in Lake Erhai in 2013. The results showed that the species richness and community biomass showed hump-back shaped patterns along the water depth gradient both in polydominant and monodominant communities. Biomass percentage of Potamogenton maackianus showed a hump-back pattern while biomass percentages of Ceratophyllum demersum and Vallisneria natans appeared U-shaped patterns across the water depth gradient in polydominant communities whereas biomass percentage of V. natans increased with the water depth in monodominant communities. Dominant species demonstrated a broader distribution range of water depth than companion species. Frequency and biomass of companion species declined drastically with the water depth whereas those of dominant species showed non-linear patterns across the water depth gradient. Namely, along the water depth gradient, biomass of P. maackianus and V. natans showed hump-back patterns and biomasses of C. demersum displayed a U-shaped pattern in the polydominant communities but biomass of V. natans demonstrated a hump-back pattern in the monodominant communities; frequency of P. maackianus showed a hump-back pattern and C. demersum and V. natans maintained high frequencies in the two types of communities. We can speculate that in Lake Erhai the optimum growth water depths of P. maackianus and C. demersum in the polydominant communities are 2.5–4.5 m and 1–2 m or 5–6 m, respectively and that of V. natans is 3–5 m in the polydominant communities and 2.5–5 m in the monodominant communities. This is the first report that the optimum water depth ranges in the horizontal direction of three dominant submersed macrophytes in a natural freshwater lake were determined.

The timescale of early land plant evolution

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.

Variation in bulk-leaf 13 C discrimination, leaf traits and water-use efficiency-trait relationships along a continental-scale climate gradient in Australia

Large spatial and temporal gradients in rainfall and temperature occur across Australia. This heterogeneity drives ecological differentiation in vegetation structure and ecophysiology. We examined multiple leaf-scale traits, including foliar ¹³ C isotope discrimination (Δ¹³ C), rates of photosynthesis and foliar N concentration and their relationships with multiple climate variables. Fifty-five species across 27 families were examined across eight sites spanning contrasting biomes. Key questions addressed include: (i) Does Δ¹³ C and intrinsic water-use efficiency (WUE_i ) vary with climate at a continental scale? (ii) What are the seasonal and spatial patterns in Δ¹³ C/WUE_i across biomes and species? (iii) To what extent does Δ¹³ C reflect variation in leaf structural, functional and nutrient traits across climate gradients? and (iv) Does the relative importance of assimilation and stomatal conductance in driving variation in Δ¹³ C differ across seasons? We found that MAP, temperature seasonality, isothermality and annual temperature range exerted independent effects on foliar Δ¹³ C/WUE_i . Temperature-related variables exerted larger effects than rainfall-related variables. The relative importance of photosynthesis and stomatal conductance (g_s ) in determining Δ¹³ C differed across seasons: Δ¹³ C was more strongly regulated by g_s during the dry-season and by photosynthetic capacity during the wet-season. Δ¹³ C was most strongly correlated, inversely, with leaf mass area ratio among all leaf attributes considered. Leaf N_mass was significantly and positively correlated with MAP during dry- and wet-seasons and with moisture index (MI) during the wet-season but was not correlated with Δ¹³ C. Leaf P_mass showed significant positive relationship with MAP and Δ¹³ C only during the dry-season. For all leaf nutrient-related traits, the relationships obtained for Δ¹³ C with MAP or MI indicated that Δ¹³ C at the species level reliably reflects the water status at the site level. Temperature and water availability, not foliar nutrient content, are the principal factors influencing Δ¹³ C across Australia.

Responses of phenology and biomass production of boreal fens to climate warming under different water-table level regimes

Climate change affects peatlands directly through increased air temperatures and indirectly through changes in water-table level (WL). The interactions of these two still remain poorly known. We determined experimentally the separate and interactive effects of temperature and WL regime on factors of relevance for the inputs to the carbon cycle: plant community composition, phenology, biomass production, and shoot:root allocation in two wet boreal sedge-dominated fens, "southern" at 62°N and "northern" at 68°Ν. Warming (1.5°C higher average daily air temperature) was induced with open-top chambers and WL drawdown (WLD; 3-7 cm on average) by shallow ditches. Total biomass production varied from 250 to 520 g/m² , with belowground production comprising 25%-63%. Warming was associated with minor effects on phenology and negligible effects on community composition, biomass production, and allocation. WLD clearly affected the contribution of different plant functional types (PFTs) in the community and the biomass they produced: shrubs benefited while forbs and mosses suffered. These responses did not depend on the warming treatment. Following WLD, aboveground biomass production decreased mainly due to reduced growth of mosses in the southern fen. Aboveground vascular plant biomass production remained unchanged but the contribution of different PFTs changed. The observed changes were also reflected in plant phenology, with different PFTs showing different responses. Belowground production increased following WLD in the northern fen only, but an increase in the contributions of shrubs and forbs was observed in both sites, while sedge contribution decreased. Moderate warming alone seems not able to drive significant changes in plant productivity or community composition in these wet ecosystems. However, if warming is accompanied by even modest WL drawdown, changes should be expected in the relative contribution of PFTs, which could lead to profound changes in the function of fens. Consequently, hydrological scenarios are of utmost importance when estimating their future function.

Comparative habitat use by takin in the Wanglang and Xiaohegou Nature Reserves

We investigated the habitat use characteristics of takin in Wanglang and Xiaohegou Nature Reserves to detect whether takin has the different habitat use patterns in different environments. We found that takin has similarities and differences in habitat use in these two nature reserves. Takin at Wanglang usually used the habitats with greater bamboo coverage and bamboo density, whereas takin at Xiaohegou usually used the habitats with a lower canopy. The results of a logistic regression analysis showed that bamboo density, herb-cover proportion, and tree size contributed significantly to the difference between takin plots at Wanglang and Xiaohegou, with an overall correct prediction rate of 92.3%, indicating that these are the main factors discriminating habitat use characteristics of takin in these two nature reserves. Considering takin has different habitat use characteristics in different areas, different protection measures should be taken to protect different takin populations. Based on the habitat use characteristics of takin at Wanglang and Xiaohegou, we summarized adaptation of takin to environments as general adaptation, regional adaptation, and special adaptation.

Divergent biodiversity change within ecosystems

The Earth's ecosystems are under unprecedented pressure, yet the nature of contemporary biodiversity change is not well understood. Growing evidence that community size is regulated highlights the need for improved understanding of community dynamics. As stability in community size could be underpinned by marked temporal turnover, a key question is the extent to which changes in both biodiversity dimensions (temporal α- and temporal β-diversity) covary within and among the assemblages that comprise natural communities. Here, we draw on a multiassemblage dataset (encompassing vertebrates, invertebrates, and unicellular plants) from a tropical freshwater ecosystem and employ a cyclic shift randomization to assess whether any directional change in temporal α-diversity and temporal β-diversity exceeds baseline levels. In the majority of cases, α-diversity remains stable over the 5-y time frame of our analysis, with little evidence for systematic change at the community level. In contrast, temporal β-diversity changes are more prevalent, and the two diversity dimensions are decoupled at both the within- and among-assemblage level. Consequently, a pressing research challenge is to establish how turnover supports regulation and when elevated temporal β-diversity jeopardizes community integrity.

An expert botanical feature extraction technique based on phenetic features for identifying plant species

In this paper, we present a new method to recognise the leaf type and identify plant species using phenetic parts of the leaf; lobes, apex and base detection. Most of the research in this area focuses on the popular features such as the shape, colour, vein, and texture, which consumes large amounts of computational processing and are not efficient, especially in the Acer database with a high complexity structure of the leaves. This paper is focused on phenetic parts of the leaf which increases accuracy. Detecting the local maxima and local minima are done based on Centroid Contour Distance for Every Boundary Point, using north and south region to recognise the apex and base. Digital morphology is used to measure the leaf shape and the leaf margin. Centroid Contour Gradient is presented to extract the curvature of leaf apex and base. We analyse 32 leaf images of tropical plants and evaluated with two different datasets, Flavia, and Acer. The best accuracy obtained is 94.76% and 82.6% respectively. Experimental results show the effectiveness of the proposed technique without considering the commonly used features with high computational cost.

Discovery of a diverse cave flora in China

Few studies document plants in caves. Our field observations of a widespread and seemingly angiosperm-rich cave flora in SW China lead us to test the following hypotheses, 1) SW China caves contain a diverse vascular plant flora, 2) that this is a relic of a largely absent forest type lacking endemic species, and 3) that the light environment plants occupy in caves is not distinct from non-cave habitats. To do so we surveyed 61 caves and used species accumulation curves (SAC) to estimate the total diversity of this flora and used a subsample of 14 caves to characterise the light environment. We used regional floras and existing conservation assessments to evaluate the conservation value of this flora. We used observations on human disturbance within caves to evaluate anthropogenic activities. Four-hundred-and-eighteen vascular plant species were documented with SACs predicting a total diversity of 529–846. Ninety-three percent of the species documented are known karst forest species, 7% are endemic to caves and 81% of the species are angiosperms. We demonstrate that the light environment in caves is distinct to that of terrestrial habitats and that a subset of the flora likely grow in the lowest light levels documented for vascularised plants. Our results suggest that the proportion of species threatened with extinction is like that for the terrestrial habitat and that almost half of the entrance caverns sampled showed signs of human disturbance. We believe that this is the first time that such an extensive sample of cave flora has been undertaken and that such a diverse vascular plant flora has been observed in caves which we predict occurs elsewhere in SE Asia. We argue that the cave flora is an extension of the karst forest understory present prior to catastrophic deforestation in the 20thC. We suggest that within SW China caves serve as both refuges and a valuable source of germplasm for the restoration of karst forest. We also propose that caves represent a distinct habitat for plants that is most similar to that of the forest understory, but distinct with respect to the absence of trees, leaf litter, root mats, higher levels of atmospheric CO2, and lower diurnal and annual variation in temperature and humidity. We highlight tourism, agriculture and the absence of legislated protection of caves as the main current threats to this flora.

Plant Cation-Chloride Cotransporters (CCC): Evolutionary Origins and Functional Insights

Genomes of unicellular and multicellular green algae, mosses, grasses and dicots harbor genes encoding cation-chloride cotransporters (CCC). CCC proteins from the plant kingdom have been comparatively less well investigated than their animal counterparts, but proteins from both plants and animals have been shown to mediate ion fluxes, and are involved in regulation of osmotic processes. In this review, we show that CCC proteins from plants form two distinct phylogenetic clades (CCC1 and CCC2). Some lycophytes and bryophytes possess members from each clade, most land plants only have members of the CCC1 clade, and green algae possess only the CCC2 clade. It is currently unknown whether CCC1 and CCC2 proteins have similar or distinct functions, however they are both more closely related to animal KCC proteins compared to NKCCs. Existing heterologous expression systems that have been used to functionally characterize plant CCC proteins, namely yeast and Xenopus laevis oocytes, have limitations that are discussed. Studies from plants exposed to chemical inhibitors of animal CCC protein function are reviewed for their potential to discern CCC function in planta. Thus far, mutations in plant CCC genes have been evaluated only in two species of angiosperms, and such mutations cause a diverse array of phenotypes-seemingly more than could simply be explained by localized disruption of ion transport alone. We evaluate the putative roles of plant CCC proteins and suggest areas for future investigation.

Vegetation Changes in a Native Forest Produced by Atta vollenweideri Forel 1893 (Hymenoptera: Formicidae) Nests

Herbivory is an important factor to generate spatial mosaics with variations in a plant community composition and organization. The objective of this work was to determine the impact of Atta vollenweideri Forel 1893 nests on herbaceous and shrub vegetation in a degraded native forest of the Espinal ecoregion. The study was carried out in the Protected Area and Multiple Use Nature Reserve called Estancia "El Carayá" (Entre Ríos, Argentina). Ten A. vollenweideri nests were selected by simple random sampling through internal roads, and two transects were drawn from the center of the nest (0 m) up to 60 m away in opposite directions. The line intercept method was used to quantify the percentage of vegetation cover of herbaceous and shrub species, while the floristic composition was estimated by the Canfield method. Afterwards, a nonparametric test between positions and a conglomerate analysis to evaluated distance were applied. Grass species, legumes, and sedges fell in the adjacent areas to nests, highlighting the bare soil at the crest and base of the nests. Fifteen plant species were identified, and two families correspond to monocotyledonous and dicotyledonous species. In conclusion, the nests of A. vollenweideri affect the community of herbaceous and shrub vegetation of the studied degraded native forest of the Espinal ecoregion since these ants perform a high selection of herbaceous species considered as pioneers of plant successions.

Non-coding RNAs and plant male sterility: current knowledge and future prospects

Latest outcomes assign functional role to non-coding (nc) RNA molecules in regulatory networks that confer male sterility to plants. Male sterility in plants offers great opportunity for improving crop performance through application of hybrid technology. In this respect, cytoplasmic male sterility (CMS) and sterility induced by photoperiod (PGMS)/temperature (TGMS) have greatly facilitated development of high-yielding hybrids in crops. Participation of non-coding (nc) RNA molecules in plant reproductive development is increasingly becoming evident. Recent breakthroughs in rice definitively associate ncRNAs with PGMS and TGMS. In case of CMS, the exact mechanism through which the mitochondrial ORFs exert influence on the development of male gametophyte remains obscure in several crops. High-throughput sequencing has enabled genome-wide discovery and validation of these regulatory molecules and their target genes, describing their potential roles performed in relation to CMS. Discovery of ncRNA localized in plant mtDNA with its possible implication in CMS induction is intriguing in this respect. Still, conclusive evidences linking ncRNA with CMS phenotypes are currently unavailable, demanding complementing genetic approaches like transgenics to substantiate the preliminary findings. Here, we review the recent literature on the contribution of ncRNAs in conferring male sterility to plants, with an emphasis on microRNAs. Also, we present a perspective on improved understanding about ncRNA-mediated regulatory pathways that control male sterility in plants. A refined understanding of plant male sterility would strengthen crop hybrid industry to deliver hybrids with improved performance.

Scandinavian perspectives on plant gene technology: applications, policies and progress

Plant research and breeding has a long and successful history in the Scandinavian countries, Denmark, Finland, Norway and Sweden. Researchers in the region have been early in adopting plant gene technologies as they developed. This review gives a background, as well as discuss the current and future progress of plant gene technology in these four countries. Country-specific details of the regulation of genetically modified plants are described, as well as similarities and differences in the approach to regulation of novel genome-editing techniques. Also, the development of a sustainable bioeconomy may encompass the application of plant gene technology and we discuss whether or not this is reflected in current associated national strategies. In addition, country-specific information about the opinion of the public and other stakeholders on plant gene technology is presented, together with a country-wise political comparison and a discussion of the potential reciprocal influence between public opinion and the political process of policy development. The Scandinavian region is unique in several aspects, such as climate and certain agriculturally related regulations, and at the same time the region is vulnerable to changes in plant breeding investments due to the relatively small market sizes. It is therefore important to discuss the role and regulation of innovative solutions in Scandinavian plant research and breeding.

Host plant forensics and olfactory-based detection in Afro-tropical mosquito disease vectors

The global spread of vector-borne diseases remains a worrying public health threat, raising the need for development of new combat strategies for vector control. Knowledge of vector ecology can be exploited in this regard, including plant feeding; a critical resource that mosquitoes of both sexes rely on for survival and other metabolic processes. However, the identity of plant species mosquitoes feed on in nature remains largely unknown. By testing the hypothesis about selectivity in plant feeding, we employed a DNA-based approach targeting trnH-psbA and matK genes and identified host plants of field-collected Afro-tropical mosquito vectors of dengue, Rift Valley fever and malaria being among the most important mosquito-borne diseases in East Africa. These included three plant species for Aedes aegypti (dengue), two for both Aedes mcintoshi and Aedes ochraceus (Rift Valley fever) and five for Anopheles gambiae (malaria). Since plant feeding is mediated by olfactory cues, we further sought to identify specific odor signatures that may modulate host plant location. Using coupled gas chromatography (GC)-electroantennographic detection, GC/mass spectrometry and electroantennogram analyses, we identified a total of 21 antennally-active components variably detected by Ae. aegypti, Ae. mcintoshi and An. gambiae from their respective host plants. Whereas Ae. aegypti predominantly detected benzenoids, Ae. mcintoshi detected mainly aldehydes while An. gambiae detected sesquiterpenes and alkenes. Interestingly, the monoterpenes β-myrcene and (E)-β-ocimene were consistently detected by all the mosquito species and present in all the identified host plants, suggesting that they may serve as signature cues in plant location. This study highlights the utility of molecular approaches in identifying specific vector-plant associations, which can be exploited in maximizing control strategies such as such as attractive toxic sugar bait and odor-bait technology.

Ungulates increase forest plant species richness to the benefit of non-forest specialists

Large wild ungulates are a major biotic factor shaping plant communities. They influence species abundance and occurrence directly by herbivory and plant dispersal, or indirectly by modifying plant-plant interactions and through soil disturbance. In forest ecosystems, researchers' attention has been mainly focused on deer overabundance. Far less is known about the effects on understory plant dynamics and diversity of wild ungulates where their abundance is maintained at lower levels to mitigate impacts on tree regeneration. We used vegetation data collected over 10 years on 82 pairs of exclosure (excluding ungulates) and control plots located in a nation-wide forest monitoring network (Renecofor). We report the effects of ungulate exclusion on (i) plant species richness and ecological characteristics, (ii) and cover percentage of herbaceous and shrub layers. We also analyzed the response of these variables along gradients of ungulate abundance, based on hunting statistics, for wild boar (Sus scrofa), red deer (Cervus elaphus) and roe deer (Capreolus capreolus). Outside the exclosures, forest ungulates maintained higher species richness in the herbaceous layer (+15%), while the shrub layer was 17% less rich, and the plant communities became more light-demanding. Inside the exclosures, shrub cover increased, often to the benefit of bramble (Rubus fruticosus agg.). Ungulates tend to favour ruderal, hemerobic, epizoochorous and non-forest species. Among plots, the magnitude of vegetation changes was proportional to deer abundance. We conclude that ungulates, through the control of the shrub layer, indirectly increase herbaceous plant species richness by increasing light reaching the ground. However, this increase is detrimental to the peculiarity of forest plant communities and contributes to a landscape-level biotic homogenization. Even at population density levels considered to be harmless for overall plant species richness, ungulates remain a conservation issue for plant community composition.