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1.  Morphological, photosynthetic and water relations traits underpin the contrasting success of two tropical lichen groups at the interior and edge of forest fragments 
AoB Plants  2010;2010:plq004.
Microclimatic edge effects and morpho-physiological characteristics are shaping lichen functional group distribution. Thus, lichen functional groups may be used as indicator for forest disturbance
Background and aims
Forest edges created by fragmentation strongly affect the abiotic and biotic environment. A rarely studied consequence is the resulting impact on non-vascular plants such as poikilohydric lichens, known to be highly sensitive to changes in the microenvironment. We evaluated the impact of forest edge and forest interior on the distribution of two groups of crustose lichens characterized by the presence or absence of a cortex and sought explanations of the outcome in terms of photosynthetic response and water relations.
Methodology
Microclimate, distribution patterns and physiology of cortical and non-cortical lichens were compared at the edge and in the interior of an Atlantic rainforest fragment in Alagoas, Brazil. Ecophysiological aspects of photosynthesis and water relations were studied using chlorophyll a fluorescence analysis, and hydration and rehydration characteristics.
Principal results
Cortical and non-cortical functional groups showed a clear preference for interior and edge habitats, respectively. The cortical lichens retained liquid water more efficiently and tolerated low light. This explains their predominance in the forest interior, where total area cover on host tree trunks reached ca. 40 % (versus ca. 5 % for non-cortical lichens). Although non-cortical lichens exchanged water vapour efficiently, they required high light intensities. Consequently, they were able to exploit well-lit edge conditions where they achieved an area cover of ca. 19 % (versus ca. 7 % for cortical lichens). We provide some of the first data for lichens giving the relative quantity of incident light absorbed by the photosystem (absorptivity). The cortical group achieved higher absorptivity and quantum efficiencies, but at the expense of physiological plasticity; non-cortical lichens showed much decreased values of Fv/Fm and electron transport rates in the forest interior.
Conclusions
Morphological and physiological features largely determine the ecophysiological interaction of lichen functional groups with their abiotic environment and, as a consequence, determine their habitat preference across forest habitats. In view of the distinctiveness of their distribution patterns and ecophysiological strategies, the occurrence of cortical versus non-cortical lichens can be a useful indicator of undisturbed forest interiors in tropical forest fragments.
doi:10.1093/aobpla/plq004
PMCID: PMC2965038  PMID: 22476062
2.  Struggle in the flood: tree responses to flooding stress in four tropical floodplain systems 
AoB Plants  2010;2010:plq003.
This review examines species diversity and structural, physiological and biochemical characteristics associated with survival of annual deep flooding of trees in four contrasting tropical floodplain ecosystems.
Background and aims
In the context of the 200th anniversary of Charles Darwin's birth in 1809, this study discusses the variation in structure and adaptation associated with survival and reproductive success in the face of environmental stresses in the trees of tropical floodplains.
Scope
We provide a comparative review on the responses to flooding stress in the trees of freshwater wetlands in tropical environments. The four large wetlands we evaluate are: (i) Central Amazonian floodplains in South America, (ii) the Okavango Delta in Africa, (iii) the Mekong floodplains of Asia and (iv) the floodplains of Northern Australia. They each have a predictable ‘flood pulse’. Although flooding height varies between the ecosystems, the annual pulse is a major driving force influencing all living organisms and a source of stress for which specialized adaptations for survival are required.
Main points
The need for trees to survive an annual flood pulse has given rise to a large variety of adaptations. However, phenological responses to the flood are similar in the four ecosystems. Deciduous and evergreen species respond with leaf shedding, although sap flow remains active for most of the year. Growth depends on adequate carbohydrate supply. Physiological adaptations (anaerobic metabolism, starch accumulation) are also required.
Conclusions
Data concerning the ecophysiology and adaptations of trees in floodplain forests worldwide are extremely scarce. For successful floodplain conservation, more information is needed, ideally through a globally co-ordinated study using reproducible comparative methods. In the light of climatic change, with increasing drought, decreased groundwater availability and flooding periodicities, this knowledge is needed ever more urgently to facilitate fast and appropriate management responses to large-scale environmental change.
doi:10.1093/aobpla/plq003
PMCID: PMC2965040  PMID: 22476061
3.  Sodium nitroprusside-mediated alleviation of iron deficiency and modulation of antioxidant responses in maize plants 
AoB Plants  2010;2010:plq002.
The nitric oxide donor sodium nitroprusside (SNP) promotes regreening of Fe-deficient maize plants. The effect is not the outcome of increased tissue Fe but of NO-modulation of oxidative changes that may favour conversions of internal Fe to more readily available ferrous iron.
Background and aims
Nitric oxide (NO) has been reported to alleviate Fe-deficiency effects, possibly by enhancing the functional Fe status of plants. This study examines changes in tissue Fe status and oxidative metabolism in Fe-deficient maize (Zea mays L.) plants enriched with NO using sodium nitroprusside (SNP) as a source.
Methodology
Measurements included changes in concentrations of H2O2, non-protein thiols, levels of lipid peroxidation and activities of superoxide dismutase (SOD) and of the Fe-requiring antioxidant haem enzymes catalase, peroxidase and ascorbate peroxidases. Internal NO in Fe-deficient maize plants was manipulated with SNP and the NO scavenger, methylene blue (MB). A key control was treatment with sodium ferrocyanide (SF), a non-NO-supplying analogue of SNP.
Principal results
SNP but not SF caused re-greening of leaves in Fe-deficient maize plants over 10–20 days, increased in vivo NO content, raised chlorophyll and carotenoid concentrations, promoted growth in dry weight, increased the activities of H2O2-scavenging haem enzymes and enhanced lipid peroxidation, while decreasing SOD activity and H2O2 concentrations. The NO scavenger, MB, blocked the effects of the SNP. Although SNP and SF each donated Fe and increased active Fe, only SNP increased leaf chlorophyll.
Conclusions
NO plays a role in Fe nutrition, independently of its effect on total or active Fe status. The most probable mechanism of NO involvement is to increase the intracellular availability of Fe by means of modulating redox. This is likely to be achieved by enhancing the chemical reduction of foliar Fe(III) to Fe(II).
doi:10.1093/aobpla/plq002
PMCID: PMC2965042  PMID: 22476060
4.  Interactions between rootstock, inter-stem and scion xylem vessel characteristics of peach trees growing on rootstocks with contrasting size-controlling characteristics 
AoB Plants  2010;2010:plq013.
This paper documents that while characteristics of the xylem anatomy and calculated hydraulic conductance of peach rootstock genotypes differ according to their effects on vigour of the scion they do not strongly influence the xylem characteristics of the scion. Furthermore xylem characteristics of a dwarfing rootstock genotype used as an inter-stem do not substantially influence anatomical characteristics of a vigorous rootstock below the inter-stem or the scion above it.
Background and aims
The primary physiological mechanism influencing tree vigour in size-controlling rootstocks of peach has been related to the hydraulic conductance of the rootstock. Differences in rootstock hydraulic conductance are a function of rootstock xylem vessel characteristics. The present research examined whether the vigour and xylem vessel characteristics of the rootstock influence the xylem characteristics of the scion. We tested whether using a size-controlling rootstock genotype as an inter-stem influences the xylem vessel characteristics of either the rootstock below the inter-stem or the scion above it and vice versa.
Methodology
Anatomical measurements (diameter and frequency) of xylem vessels were determined above and below the graft unions of the trunks of peach trees with differing scion/rootstock combinations. The three peach rootstocks were ‘Nemaguard’ (vigorous), ‘P30-135’ (intermediate vigour) and ‘K146-43’ (dwarfing). The vigorous scion cultivar was ‘O'Henry’. The inter-stem experiment involved trees with ‘Nemaguard’ (vigorous) as the rootstock, ‘K146-43’ (dwarfing) as the inter-stem and ‘O'Henry’ as the scion. Based on anatomical measurements, we calculated the theoretical axial xylem conductance of each stem piece and rootstock genotype with the Hagen–Poiseuille law.
Principal results
Xylem vessel dimensions of rootstocks varied in conjunction with tree vigour. Scion xylem vessel dimensions of different scion/rootstock combinations were only marginally affected by rootstock genotype. The inter-stem sections from the dwarfing genotype (‘K146-43’) had narrower vessels and a lower calculated hydraulic conductance than the xylem from either the vigorous rootstock below (‘Nemaguard’) or the scion above (‘O'Henry’).
Conclusions
Rootstock genotype only marginally affected scion xylem vessel characteristics. Thus the xylem vessel characteristics of the dwarfing rootstock genotypes appear to influence tree growth directly rather than through an effect on the xylem characteristics of the scion. A dwarfing rootstock genotype used as an inter-stem appeared to work as a physical restriction to water movement, reducing potential xylem flow and conductance of the whole tree.
doi:10.1093/aobpla/plq013
PMCID: PMC2975467  PMID: 22476071
5.  Nitrification inhibition activity, a novel trait in root exudates of rice 
AoB Plants  2010;2010:plq014.
Screening numerous genotypes for nitrification inhibition activity provides first evidence that root exudates of rice can slow the nitrification of ammonium to nitrate in soil. This offers promising possibilities for exploiting molecular and genetic tools to improve nitrogen use efficiency by inhibiting wasteful nitrification.
Background and aims
Nitrification is an important process in soil--plant systems for providing plant-available nitrate (NO3−). However, NO3− is less stable in soils compared with ammonium (NH4+) and is more easily lost through leaching, runoff or denitrification. This study tested whether biological nitrification inhibition (BNI) activity is present in the root exudates of rice (Oryza sativa) and also the extent of variation between different genotypes.
Methodology
The BNI activity of root exudates was estimated by a bioluminescence assay using a recombinant Nitrosomonas europaea strain. Afterwards, the effect of a single application of concentrated root exudates and that of exudates deposited in the rhizosphere soil was tested on BNI using soil incubation. Soil was added with (NH4)2SO4 and water to reach 60 % of the water-holding capacity and incubated at 30 °C for different periods. Amounts of NH4+ and NO3− were determined using a continuous-flow auto-analyser.
Principal results
In an initial screening experiment, BNI activity in the exudates of 36 different rice genotypes was evaluated using a bioassay based on a recombinant Nitrosomonas strain. Significant genotypic variation was detected with the upland cultivar IAC25 demonstrating consistently high BNI activity, while modern lowland varieties like Nipponbare or IR64 exhibited lower activity. Subsequent experiments ruled out the possibility that BNI activity is simply due to non-specific (solute) leakage from roots. Soil incubation studies with concentrated root exudates of IAC25 showed significant reductions in NO3− formation. This effect was confirmed by detecting lower NO3− levels in incubation experiments using rhizosphere soil obtained from IAC25.
Conclusions
Our results provide first evidence that root exudates of rice can reduce nitrification rates in soil. Having shown this for a model crop, rice, offers possibilities for further exploitation of this phenomenon through molecular and genetic tools.
doi:10.1093/aobpla/plq014
PMCID: PMC2992353  PMID: 22476072
6.  Genome size variation in diploid and tetraploid wild wheats 
AoB Plants  2010;2010:plq015.
Low but significant intraspecific genome size variations were found in diploid and tetraploid wild wheats. This limited variation is not correlated with geographical and climate variables. It can be concluded that the genome size of Triticum species is generally stable, despite of the presence of many potentially active retroelements.
Background and aims
Intra- and interspecific variations of C-values and the relationship between habitat factors and genome size were studied in natural populations of diploid and tetraploid wild wheats.
Methodology
The 1C nuclear DNA content of 376 individual plants representing 41 populations of diploid and tetraploid wild wheats was determined by flow cytometry (FCM) and correlated with geographical and bioclimate variables.
Principal results
Based on analysis of variance, significant differences between diploid and tetraploid Triticum species were found. Differences among populations of T. boeoticum and T. dicoccoides were also statistically significant and argue for isolation between populations, except for T. araraticum. However, the variation among individuals of the same population was not statistically significant. Maximum genome size differences among populations for T. boeoticum (0.143 pg; 2.32 %), T. dicoccoides (0.314 pg; 2.49 %) and T. araraticum (0.116 pg; 0.98 %) argue for genome constancy in these species. There was no significant correlation between intra-population variance and geographical and bioclimate variables for T. boeoticum and T. dicoccoides. In contrast to the limited genome size variation at the intraspecific level, the interspecific variation was large: ∼0.5 pg/1C (8 %) at the diploid level (T. boeoticum vs. T. urartu) and ∼1 pg/1C (9.7 %) at the tetraploid level (T. dicoccoides vs. T. araraticum).
Conclusions
Low intraspecific genome size variation occurs in diploid and tetraploid wild wheats, and this limited variation is not correlated with geographical and climate variables. However, interspecific variation is significant at the diploid and tetraploid level. It can be concluded that the genome size of wild self-fertilizing Triticum species is generally stable, despite the presence of many potentially active retroelements. In natural habitats, it is very difficult to distinguish wild wheats from each other. However, all four species can be distinguished easily, quickly and unambiguously by using the FCM technique.
doi:10.1093/aobpla/plq015
PMCID: PMC2992354  PMID: 22476073
7.  Plastid division 
AoB Plants  2010;2010:plq016.
This review considers the nature of the plastid division machinery that enables binary fission of plastids, from a cell biology perspective and considers how the cell might control aspects of plastid population control and segregation during plant development.
Background and aims
Plastids undergo a process of binary fission in order to replicate. Plastid replication is required at two distinct stages of plant growth: during cell division to ensure correct plastid segregation, and during cell expansion and development to generate large populations of functional plastids, as in leaf mesophyll cells. This review considers some of the recent advances in the understanding of how plastids undergo binary fission, a process which uses several different proteins, both internal and external to the plastid, which have been derived from the original endosymbiont's genome as well as new proteins that have been recruited from the host genome.
Key points
Several of the proteins currently used in this process in higher plants have homologues in modern-day bacteria. An alternative mode of replication by a budding-type mechanism also appears to be used in some circumstances. The review also highlights how most of our knowledge of plastid division is centred on the chloroplast developing in leaf mesophyll cells and a role for plastid division during the development of other plastid types is poorly understood. Whilst models for a protein-based mechanism have been devised, exactly how the division process is controlled at the plastid level and at the plastid population level is poorly understood.
doi:10.1093/aobpla/plq016
PMCID: PMC2995336  PMID: 22476074
8.  Biogeography and divergence times of genus Macroptilium (Leguminosae) 
AoB Plants  2010;2010:plq018.
The biogeographic history pattern for Macroptilium, a legume genus closely related to Phaseolus, is proposed. By using ITS sequences, molecular analysis revealed that the genus has its origin on South America, with an estimate age of 2.9 to 4 My.
Background and aims
Macroptilium is a herbaceous legume genus with 18 currently accepted species, seven of them with economic importance due to their use as forage, green fertilizer and in medicine. The genus is strictly American, with an unknown biogeographic history. The aim of this study was to infer a biogeographic pattern of Macroptilium and to estimate its divergence times, using sequences from the nuclear ribosomal DNA internal transcribed spacers.
Methodology
To study the historical biogeography of Macroptilium, two approaches were used: area optimization on a previously obtained phylogeny and a dispersal–vicariance analysis. Divergence times were calculated by Bayesian methods.
Principal results
The analyses revealed that Macroptilium has its origin in the middle Pliocene, with an estimated age that ranges from 2.9 to 4 million years. The biogeographic analyses placed its origin in South America, specifically on the Chaquean sub-region, where most of the cladogenetic events of the genus took place.
Conclusions
Macroptilium constitutes a further example of the geographic pattern displayed by numerous Neotropical taxa that moved north from South America to dominate the Central American lowlands after the land connection across the Isthmus of Panama was established.
doi:10.1093/aobpla/plq018
PMCID: PMC2995337  PMID: 22476076
9.  Population rules can apply to individual plants and affect their architecture: an evaluation on the cushion plant Mulinum spinosum (Apiaceae) 
AoB Plants  2010;2010:plq019.
Growth units of individual plants may be seen as equivalent to individual plants in plant populations. Some of the principles known to rule plant-to-plant interactions in crowded populations may apply to the interactions between growth units in plants.
Background and aims
Plants are regarded as populations of modules such as axes and growth units (GUs, i.e. seasonally produced axis segments). Due to their dense arrays of GUs, cushion plants may resemble crowded plant populations in the way the number of components (GUs in plants, individuals in populations) relates to their individual sizes.
Methodology
The morphological differentiation of GUs and its relationship with biomass accumulation and plant size were studied for the cushion subshrub Mulinum spinosum (Apiaceae), a widespread species in dry areas of Patagonia. In 2009, GUs were sampled from one-quarter of each of 24 adult plants. Within- and between-plant variations in GU length, diameter, number of nodes and biomass were analysed and related to whole-plant size.
Principal results
Each year, an M. spinosum cushion develops flowering GUs and vegetative GUs. Flowering GUs are larger, twice as numerous and contain two to four times more dry mass (excluding reproductive structures) than vegetative GUs. The hemispherical area of the cushions was positively correlated with the biomass of last-year GUs. The biomass of flowering GUs was negatively correlated with the density of GUs. Mulinum spinosum plants exhibited a notable differentiation between flowering and vegetative GUs, but their axes, i.e. the sequences of GUs, were not differentiated throughout the plants. Flowering GUs comprised a major proportion of each plant's photosynthetic tissues.
Conclusions
A decrease in the size of flowering GUs and in their number relative to the total number of GUs per plant, parallel to an increase in GU density, is predicted as M. spinosum plants age over years. The assimilative role of vegetative GUs is expected to increase in summer because of their less exposed position in the cushion. These GUs would therefore gain more from warm and dry conditions than flowering GUs.
doi:10.1093/aobpla/plq019
PMCID: PMC2995345  PMID: 22476077
10.  Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume 
AoB Plants  2010;2010:plq017.
Molecular marker studies provide valid guidelines for collection, characterization and selective cultivation of elite Pongamia germplasm that can be exploited further for its improvement through breeding and marker assisted selection for improved characters and oil yield towards biodiesel production.
Background and aims
Pongamia pinnata, a legume tree, has many traditional uses and is a potential biodiesel plant. Despite its importance and the availability of appropriate molecular genetic tools, the full potential of Pongamia is yet to be realized. The objective of this study was to assess genetic diversity among 10 systematically characterized candidate plus trees (CPTs) of P. pinnata from North Guwahati.
Methodology
The application and informativeness of polymerase chain reaction-based molecular markers [random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP)] to assess the genetic variability and relatedness among 10 CPTs of P. pinnata were investigated.
Principal results
Polymorphism rates of 10.48, 10.08 and 100 % were achieved using 18 RAPD, 12 ISSR and 4 AFLP primer combinations, respectively. Polymorphic information content (PIC) varied in the range 0.33–0.49, 0.18–0.49 and 0.26–0.34 for RAPD, ISSR and AFLP markers, respectively, whereas the corresponding average marker index (MI) values for the above markers were 7.48, 6.69 and 30.75. Based on Nei's gene diversity and Shannon's information index, inter-population diversity (hsp) was highest when compared with intra-population diversity (hpop) and the gene flow (Nm) ranged from a moderate value of 0.607 to a high value of 6.287 for the three DNA markers. Clustering of individuals was not similar when RAPD- and ISSR-derived dendrogram analyses were compared with that of AFLP. The Mantel test cophenetic correlation coefficient was higher for AFLP (r = 0.98) than for ISSR (r = 0.73) and RAPD (r = 0.84). Molecular markers discriminated the individuals efficiently and generated a high similarity in dendrogram topologies derived using unweighted pair-group arithmetic average, although some differences were observed. The three-dimensional scaling by principal coordinate analysis supported the result of clustering.
Conclusions
Comparing the results obtained with the three DNA markers, AFLP indicated higher efficiency for estimating the levels of genetic diversity and proved to be reliable for fingerprinting, mapping and diversity studies in Pongamia in view of their suitability for energy production purposes.
doi:10.1093/aobpla/plq017
PMCID: PMC2997655  PMID: 22476075
11.  Ability of crassulacean acid metabolism plants to overcome interacting stresses in tropical environments 
AoB Plants  2010;2010:plq005.
The characteristic high morphological and physiological plasticity of tropical CAM plants as adaptations to multistress locations is reviewed against the background of a realisation that tropical forests contain many more CAM species than do drier areas such as semi-desert.
Background and aims
Single stressors such as scarcity of water and extreme temperatures dominate the struggle for life in severely dry desert ecosystems or cold polar regions and at high elevations. In contrast, stress in the tropics typically arises from a dynamic network of interacting stressors, such as availability of water, CO2, light and nutrients, temperature and salinity. This requires more plastic spatio-temporal responsiveness and versatility in the acquisition and defence of ecological niches.
Crassulacean acid metabolism
The mode of photosynthesis of crassulacean acid metabolism (CAM) is described and its flexible expression endows plants with powerful strategies for both acclimation and adaptation. Thus, CAM plants are able to inhabit many diverse habitats in the tropics and are not, as commonly thought, successful predominantly in dry, high-insolation habitats.
Tropical CAM habitats
Typical tropical CAM habitats or ecosystems include exposed lava fields, rock outcrops of inselbergs, salinas, savannas, restingas, high-altitude páramos, dry forests and moist forests.
Morphotypical and physiotypical plasticity of CAM
Morphotypical and physiotypical plasticity of CAM phenotypes allow a wide ecophysiological amplitude of niche occupation in the tropics. Physiological and biochemical plasticity appear more responsive by having more readily reversible variations in performance than do morphological adaptations. This makes CAM plants particularly fit for the multi-factor stressor networks of tropical forests. Thus, while the physiognomy of semi-deserts outside the tropics is often determined by tall succulent CAM plants, tropical forests house many more CAM plants in terms of quantity (biomass) and quality (species diversity).
doi:10.1093/aobpla/plq005
PMCID: PMC3000696  PMID: 22476063
12.  Effect of salinity on water relations of wild barley plants differing in salt tolerance 
AoB Plants  2010;2010:plq006.
Root hydraulic conductivity was decreased by salinity in barley plants in parallel with slower transpiration rates and a down-regulation of aquaporin expression in the roots. The effects were larger and faster in a more salinity-tolerant line.
Background and aims
Certain lines of wild barley (Hordeum spontaneum) are more tolerant of salinity than others. The physiological basis of this difference is examined in a comparative study of a saline-tolerant and saline-intolerant line that emphasizes plant water relations.
Methodology
Effects of salt-treatment (75 mM maximum) extending from a few hours to 3 weeks were quantified in 8-day-old seedlings of a saline-sensitive wild barley line (‘T-1’) and a less saline-sensitive line (‘20-45’). Plants were grown in nutrient culture. Levels of mRNA of the HtPIP2;4 aquaporin (AQP) gene were determined together with a range of physiological responses including root hydraulic conductivity, osmotic potential of root xylem sap, transpiration, leaf relative water content, root water content, leaf water potential, leaf sap osmolality, leaf length, leaf area and chlorophyll content.
Principal results
Salt treatment inhibited transpiration and hydraulic conductivity more in salt-tolerant ‘20-45’ plants than in salt-sensitive ‘T-1’. In ‘20-45’, the effect was paralleled by a fast (within a few hours) and persistent (3 days) down-regulation of aquaporin. In salt-sensitive ‘T-1’ plants, aquaporin down-regulation was delayed for up to 24 h. Greater tolerance in ‘20-45’ plants was characterized by less inhibition of leaf area, root fresh weight, leaf water content and chlorophyll concentration. Leaf water potentials were similar in both lines.
Conclusions
(i) Decline in hydraulic conductivity in salt-treated barley plants is important for stomatal closure, (ii) lowered transpiration rate is beneficial for salt tolerance, at least at the seedling stage and (iii) changes in AQP expression are implicated in the control of whole plant hydraulic conductivity and the regulation of shoot water relations.
doi:10.1093/aobpla/plq006
PMCID: PMC3000697  PMID: 22476064
13.  Nucleated succession by an endemic palm Phoenix pusilla enhances diversity of woody species in the arid Coromandel Coast of India 
AoB Plants  2010;2010:plq007.
Endemic Phoenix pusilla acaulescent palms can act as nurse plants promoting establishment of 11 primary dry-forest species in degraded arid open ground (nucleation), in part, through ameliorating abiotic stress. The phenomenon is long-recognized by the Irula tribe of South India.
Background and aims
Phoenix pusilla, an endemic shrubby palm, was used as a model nurse plant in degraded tropical dry evergreen forest (TDEF) landscapes. This choice was informed by traditional ecological knowledge of the Irula tribe of south India. We tested whether the presence of P. pusilla in water-stressed arid regions improves conditions for other species to establish, resulting in nucleated succession. Success would point the way forward for establishing species-rich woodland in abandoned farm land on the south-eastern Coromandel Coast of India.
Methodology
Spatial associations of woody species in the natural landscape were studied. Experimental tests of nurse plant potential examined the extent to which P. pusilla (i) promoted seed germination, (ii) seedling emergence and (iii) establishment of two TDEF species, and (iv) ameliorated soil and microclimatic conditions over 8 months.
Principal results
Phoenix pusilla cooled the soil by up to 50 % and decreased radiation by up to 9-fold, especially in summer. Soil organic matter and water-holding capacity increased, as did seedling number and seedling height of tested TDEF species. The presence of P. pusilla favoured a greater abundance (20 %) of woody plants with a bias towards primary (11) rather than secondary (2) species, indicating species specificity of the effect.
Conclusions
Phoenix pusilla ameliorated abiotic stresses present in open ground to create a patchy species-rich mosaic. This nucleated succession created using P. pusilla provided an important refuge for primary TDEF species. This effect can be expected to have impact at the landscape scale and may prove useful in managing landscapes and in biodiversity conservation. The conservation value of these patchy landscapes deserves to be more widely recognized as they persist in populated areas and thus merit protection. The value of traditional tribal knowledge in identifying a highly effective nurse species is highlighted by this study.
doi:10.1093/aobpla/plq007
PMCID: PMC3000698  PMID: 22476065
14.  Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature 
AoB Plants  2010;2010:plq008.
The ‘Crop Ontology’ database we describe provides a controlled vocabulary for several economically important crops. It facilitates data integration and discovery from global databases and digital literature. This allows researchers to exploit comparative phenotypic and genotypic information of crops to elucidate functional aspects of traits.
Background and aims
Agricultural crop databases maintained in gene banks of the Consultative Group on International Agricultural Research (CGIAR) are valuable sources of information for breeders. These databases provide comparative phenotypic and genotypic information that can help elucidate functional aspects of plant and agricultural biology. To facilitate data sharing within and between these databases and the retrieval of information, the crop ontology (CO) database was designed to provide controlled vocabulary sets for several economically important plant species.
Methodology
Existing public ontologies and equivalent catalogues of concepts covering the range of crop science information and descriptors for crops and crop-related traits were collected from breeders, physiologists, agronomists, and researchers in the CGIAR consortium. For each crop, relationships between terms were identified and crop-specific trait ontologies were constructed following the Open Biomedical Ontologies (OBO) format standard using the OBO-Edit tool. All terms within an ontology were assigned a globally unique CO term identifier.
Principal results
The CO currently comprises crop-specific traits for chickpea (Cicer arietinum), maize (Zea mays), potato (Solanum tuberosum), rice (Oryza sativa), sorghum (Sorghum spp.) and wheat (Triticum spp.). Several plant-structure and anatomy-related terms for banana (Musa spp.), wheat and maize are also included. In addition, multi-crop passport terms are included as controlled vocabularies for sharing information on germplasm. Two web-based online resources were built to make these COs available to the scientific community: the ‘CO Lookup Service’ for browsing the CO; and the ‘Crops Terminizer’, an ontology text mark-up tool.
Conclusions
The controlled vocabularies of the CO are being used to curate several CGIAR centres' agronomic databases. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases will be important steps in comparative phenotypic and genotypic studies across species and gene-discovery experiments.
doi:10.1093/aobpla/plq008
PMCID: PMC3000699  PMID: 22476066
15.  Plant reproduction in the Central Amazonian floodplains: challenges and adaptations 
AoB Plants  2010;2010:plq009.
We review strategies of sexual and asexual reproduction and persistence in plants of flood-prone Central Amazonia. Adaptations in response to the strong instability of these environments are highlighted together with the importance of river connectivity for species dispersal and persistence.
Background
The Central Amazonian floodplain forests are subjected to extended periods of flooding and to flooding amplitudes of 10 m or more. The predictability, the length of the flood pulse, the abrupt transition in the environmental conditions along topographic gradients on the banks of major rivers in Central Amazonia, and the powerful water and sediment dynamics impose a strong selective pressure on plant reproduction systems.
Scope
In this review, we examine how the hydrological cycle influences the strategies of sexual and asexual reproduction in herbaceous and woody plants. These are of fundamental importance for the completion of the life cycle. Possible constraints to seed germination, seedling establishment and formation of seed banks are also covered. Likewise, we also discuss the importance of river connectivity for species propagation and persistence in floodplains.
Conclusions
The propagation and establishment strategies employed by the highly diversified assortment of different plant life forms result in contrasting successional stages and a zonation of plant assemblages along the flood-level gradient, whose species composition and successional status are continuously changing not only temporally but also spatially along the river channel.
doi:10.1093/aobpla/plq009
PMCID: PMC3000700  PMID: 22476067
16.  Morphological and physiological responses of lowland purple nutsedge (Cyperus rotundus L.) to flooding 
AoB Plants  2010;2010:plq010.
Comparing a lowland and an upland ecotype of Cyperus rotundus, the former had greater carbohydrate reserves in tubers, thicker roots and stems with larger air spaces and, under hypoxia, it maintained relatively lower activities of alcohol dehydrogenase and lactate dehydrogenase.
Background and aims
Purple nutsedge (Cyperus rotundus L.) is a major weed of upland crops and vegetables. Recently, a flood-tolerant ecotype evolved as a serious weed in lowland rice. This study attempted to establish the putative growth and physiological features that led to this shift in adaptation.
Methodology
Tubers of upland C. rotundus (ULCR) and lowland C. rotundus (LLCR) ecotypes were collected from their native habitats and maintained under the respective growth conditions in a greenhouse. Five experiments were conducted to assess the variation between the two ecotypes in germination, growth and tuber morphology when grown in their native or ‘switched’ conditions. Carbohydrate storage and mobilization, and variation in anaerobic respiration under hypoxia were compared.
Principal results
Tubers of LLCR were larger than those of ULCR, with higher carbohydrate content, and larger tubers developed with increasing floodwater depth. Stems of LLCR had larger diameter and proportionally larger air spaces than those of ULCR: a method of aerating submerged plant parts. The LLCR ecotype can also mobilize and use carbohydrate reserves under hypoxia, and it maintained relatively lower and steadier activity of alcohol dehydrogenase (ADH) as a measure of sustained anaerobic respiration. In contrast, ADH activity in ULCR increased faster upon a shift to hypoxia and then sharply decreased, suggesting depletion of available soluble sugar substrates. The LLCR ecotype also maintained lower lactate dehydrogenase activity under flooded conditions, which could reduce chances of cellular acidosis.
Conclusions
These adaptive traits in the LLCR ecotype were expressed constitutively, but some of them, such as tuber growth and aerenchyma development, are enhanced with stress severity. The LLCR ecotype attained numerous adaptive traits that could have evolved as a consequence of natural evolution or repeated management practices, and alternative strategies are necessary because flooding is no longer a feasible management option.
doi:10.1093/aobpla/plq010
PMCID: PMC3000701  PMID: 22476068
17.  Strong positive growth responses to salinity by Ceriops tagal, a commonly occurring mangrove of the Gujarat coast of India 
AoB Plants  2010;2010:plq011.
Ceriops tagal commonly occurs along the Gujarat coast of India. It has evolved a high degree of salinity tolerance and optimal growth occurs at 12.6 ppt. This is related to an adaptive regulation of hydration and ionic content.
Background and aims
Mangroves of Western Gujarat (India) are subject to die-back. Salinity intolerance is one possible cause, especially in young plants. We therefore quantified the extent to which young plants of one widely occurring mangrove species (Ceriops tagal) tolerate high salt in terms of establishment, growth, water status, proline content and mineral accumulation.
Methodology
In a greenhouse study, juvenile plants were established from mature propagules over 40 days in soil containing added NaCl, raising soil water salinity to 0.2, 2.5, 5.1, 7.7, 10.3, 12.6, 15.4, 17.9, 20.5 and 23.0 ppt (w/v). Growth and physiological characteristics were monitored over the subsequent 6 months.
Principal results
Despite a negative relationship between the percentage of young plant establishment and salt concentration (50 % loss at 22.3 ppt), the remaining plants proved highly tolerant. Growth, in dry weight, was significantly promoted by low salinity, which is optimal at 12.6 ppt. Water content, leaf expansion and dry matter accumulation in tissues followed a similar optimum curve with leaf area being doubled at 12.6 ppt NaCl. Salinity >12.6 and <23 ppt inhibited plant growth, but never to below control levels. Root:shoot dry weight ratios were slightly reduced by salinity (maximum 19 %), but the water potential of roots, leaves and stems became more negative as salinity increases while proline increases in all tissues. The concentration of Na increased, whereas concentrations of K, Ca, N and P decreased and that of Mg remained stable.
Conclusions
Ceriops tagal has a remarkably high degree of salinity tolerance, and shows an optimal growth when soil water salinity is 12.6 ppt. Salinity tolerance is linked to an adaptive regulation of hydration and ionic content. The cause of localized die-back along the coastal region of Gujarat is thus unlikely to be a primary outcome of salinity stress although amendments with Ca and K, and perhaps proline, may help protect against extreme salinity.
doi:10.1093/aobpla/plq011
PMCID: PMC3000702  PMID: 22476069
18.  Bolting and flowering control in sugar beet: relationships and effects of gibberellin, the bolting gene B and vernalization 
AoB Plants  2010;2010:plq012.
Using a co-dominant genotypic PCR marker we show for the first time that, in sugar beet, the GA and B-gene pathways are independent for bolt initiation. We show that vernalization permits GA-dependant stem elongation and that the B-allele influences subsequent flowering.
Background and aims
Bolting, the first visible sign of reproductive transition in beets (Beta vulgaris), is controlled by the dominant bolting gene B (B allele), which allows for flowering under long days (LDs, >14 h light) without prior vernalization. The B-locus carries recessive alleles (bb) in sugar beet (Beta vulgaris L. spp. vulgaris), so that vernalization and LDs are required for bolting and flowering. Gibberellin growth hormones (GAs) control stem elongation and reproductive development, but their role during these processes in sugar beet is not defined. We aimed to investigate the involvement of GAs in bolting and flowering in sugar beet, and also its relationship with the vernalization requirement as defined by the B-gene.
Methodology
Plants segregating for the B allele were treated with exogenous GA4 under inductive (16 h light) and non-inductive (8 h light) photoperiods, with and without prior vernalization treatment. A co-dominant polymerase chain reaction (PCR) marker was used to genotype the B-gene locus. Bolting and flowering dates were scored, and bolt heights were measured as appropriate. Analysis of variance was used to determine the effects and interactions of GAs, the B allele and vernalization on bolting and flowering. The effects of the B allele on bolting were also verified in the field.
Principal results
Application of GAs or the B allele could initiate bolting independently. When the B allele was absent, the applied GAs promoted stem growth, but did so only in vernalized plants, irrespective of photoperiod. Under LDs, bolt height before flowering in plants carrying the B allele (BB; Bb) was not significantly influenced by GAs. The timing and frequency of flowering were influenced by the B allele without interactive effects from GAs.
Conclusions
In sugar beet, GA acts independently of the B allele and photoperiod to induce bolting. Vernalization enables GA action independently of the B allele; hence, the dominant B allele may not directly participate in vernalization-induced bolting.
doi:10.1093/aobpla/plq012
PMCID: PMC3000703  PMID: 22476070
19.  Bilirubin present in diverse angiosperms 
AoB Plants  2010;2010:plq020.
Recently, we discovered bilirubin-IXα, a pigment previously known only in animals as a breakdown product of heme, in Strelitzia nicolai. Here, we show that bilirubin-IXα is present in eight species from three diverse angiosperm orders.
Background and aims
Bilirubin is an orange-yellow tetrapyrrole produced from the breakdown of heme by mammals and some other vertebrates. Plants, algae and cyanobacteria synthesize molecules similar to bilirubin, including the protein-bound bilins and phytochromobilin which harvest or sense light. Recently, we discovered bilirubin in the arils of Strelitzia nicolai, the White Bird of Paradise Tree, which was the first example of this molecule in a higher plant. Subsequently, we identified bilirubin in both the arils and the flowers of Strelitzia reginae, the Bird of Paradise Flower. In the arils of both species, bilirubin is present as the primary pigment, and thus functions to produce colour. Previously, no tetrapyrroles were known to generate display colour in plants. We were therefore interested in determining whether bilirubin is broadly distributed in the plant kingdom and whether it contributes to colour in other species.
Methodology
In this paper, we use HPLC/UV and HPLC/UV/electrospray ionization-tandem mass spectrometry (HPLC/UV/ESI-MS/MS) to search for bilirubin in 10 species across diverse angiosperm lineages.
Principal results
Bilirubin was present in eight species from the orders Zingiberales, Arecales and Myrtales, but only contributed to colour in species within the Strelitziaceae.
Conclusions
The wide distribution of bilirubin in angiosperms indicates the need to re-assess some metabolic details of an important and universal biosynthetic pathway in plants, and further explore its evolutionary history and function. Although colour production was limited to the Strelitziaceae in this study, further sampling may indicate otherwise.
doi:10.1093/aobpla/plq020
PMCID: PMC3000704  PMID: 22476078
20.  The invasive ‘mothcatcher’ (Araujia sericifera Brot.; Asclepiadoideae) co-opts native honeybees as its primary pollinator in South Africa 
AoB Plants  2010;2010:plq021.
Araujia sericifera is a South American milkweed which is an invasive/exotic species in South Africa. This species relies on pollinators for sexual reproduction and we show it has co-opted native South African honeybees as primary pollinators in its adopted country. Moths also visit the flowers of this species, but contribute little to its relatively high pollination success.
Background and aims
Successful invasive plants such as Araujia sericifera usually either are capable of automatic self-pollination or maintain pollinator services by having generalized pollination systems to make use of local pollinators in the invaded range. Alternatively, plants must co-opt new pollinators with similar morphology to native pollinators or reproduce asexually. We aimed to document the pollination biology of A. sericifera in South Africa. Given the success of this species as an invader, we predicted that sexual reproduction occurs either through self-pollination or because A. sericifera has successfully co-opted native insect pollinators.
Methodology
We examined the pollination biology of the South American A. sericifera in South Africa. We documented the effective pollinators including a comparison of the efficacy of nocturnal versus diurnal pollinators as well as the breeding system and long-term natural levels of the pollination success of this species.
Principal results
We found that native honeybees (Apis mellifera) were the main pollinators of A. sericifera in South Africa. Visiting moths are unimportant pollinators despite being attracted by the pale colour and nocturnal scent of the flowers. Plants from the Grahamstown population were incapable of autonomous self-pollination but pollinator-mediated self-pollination does occur. However, the highest fruit initiation resulted from out-crossed pollination treatments. The high pollen transfer efficiency of this species was comparable to other hymenopteran-pollinated exotic and native milkweeds, suggesting that A. sericifera maintains pollinator services at levels experienced by indigenous asclepiad species.
Conclusions
Araujia sericifera reproduces successfully in South Africa due to a combined ability of this species to attract and exploit native honeybees as its pollinators and of individual plants to set fruit from pollinator-mediated self-pollination.
doi:10.1093/aobpla/plq021
PMCID: PMC3035059  PMID: 22476079
21.  Mechanisms of plant adaptation/memory in rice seedlings under arsenic and heat stress: expression of heat-shock protein gene HSP70 
AoB Plants  2010;2010:plq023.
Imprints of stress response by rice seedlings in terms of expression levels of stress response gene HSP70 are characterised . The response to arsenic and/or heat shock are shown to be additive for the same stress or the combined stresses, indicating a commonality of signalling pathways.
Background and aims
Plants can withstand many abiotic stresses. Stress adaptation through retention of imprints of previous stress exposure has also been described in plants. We have characterized the imprint or memory of adaptive stress responses of rice seedlings to arsenic (As) and heat stress.
Methodology
Two-week-old rice seedlings (both with and without As) were given a 45 °C heat shock for 3 h. While under heat shock, the leafy portion of the seedlings was harvested at regular intervals. Subsequently, the seedlings were kept at room temperature for recovery and sampling continued over 3 h. Total RNA and protein were extracted from the leafy portion of the seedlings and complementary DNA (cDNA) was prepared from total RNA. The cDNA was used as a template for the polymerase chain reaction to identify the transcription level of HSP70. Protein extracted from the seedlings was western-blotted. HSP70 and actin (loading control) antibodies were used to recognize the proteins on the same blot.
Principal results
Our studies reveal that HSP70, a cellular chaperone gene, is over-expressed at the mRNA and protein levels when rice seedlings are exposed to As and heat. The effect is cumulative and increases with the duration of stress for 3 h. During 3 h recovery from heat stress at ambient temperatures for 3 h, the chaperone remains expressed at higher levels in plants pre-exposed to As.
Conclusions
Our findings demonstrate a retention of the imprint of previous stress exposure, perhaps through sustained activation of the signalling pathways upstream of over-expression of HSP70. Furthermore, stress-induced HSP70 expression was additive/cumulative for continued exposure to similar or different kinds of stress, indicating that a commonality of signal transduction networks is adopted when plants experience more than one stress.
doi:10.1093/aobpla/plq023
PMCID: PMC3035060  PMID: 22476080

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