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1.  Racemose inflorescences of monocots: structural and morphogenetic interaction at the flower/inflorescence level 
Annals of Botany  2012;112(8):1553-1566.
Background
Understanding and modelling early events of floral meristem patterning and floral development requires consideration of positional information regarding the organs surrounding the floral meristem, such as the flower-subtending bracts (FSBs) and floral prophylls (bracteoles). In common with models of regulation of floral patterning, the simplest models of phyllotaxy consider only unbranched uniaxial systems. Racemose inflorescences and thyrses offer a useful model system for investigating morphogenetic interactions between organs belonging to different axes.
Scope
This review considers (1) racemose inflorescences of early-divergent and lilioid monocots and their possible relationship with other inflorescence types, (2) hypotheses on the morphogenetic significance of phyllomes surrounding developing flowers, (3) patterns of FSB reduction and (4) vascular patterns in the primary inflorescence axis and lateral pedicels.
Conclusions
Racemose (partial) inflorescences represent the plesiomorphic condition in monocots. The presence or absence of a terminal flower or flower-like structure is labile among early-divergent monocots. In some Alismatales, a few-flowered racemose inflorescence can be entirely transformed into a terminal ‘flower’. The presence or absence and position of additional phyllomes on the lateral pedicels represent important taxonomic markers and key features in regulation of flower patterning. Racemose inflorescences with a single floral prophyll are closely related to thyrses. Floral patterning is either unidirectional or simultaneous in species that lack a floral prophyll or possess a single adaxial floral prophyll and usually spiral in the outer perianth whorl in species with a transversely oriented floral prophyll. Inhibitory fields of surrounding phyllomes are relevant but insufficient to explain these patterns; other important factors are meristem space economy and/or the inhibitory activity of the primary inflorescence axis. Two patterns of FSB reduction exist in basal monocots: (1) complete FSB suppression (cryptic flower-subtending bract) and (2) formation of a ‘hybrid’ organ by overlap of the developmental programmes of the FSB and the first abaxial organ formed on the floral pedicel. FSB reduction affects patterns of interaction between the conductive systems of the flower and the primary inflorescence axis.
doi:10.1093/aob/mcs246
PMCID: PMC3828938  PMID: 23172413
Bracteole; flower; flower-subtending bract; inflorescence; inhibitory field; pattern formation; prophyll; regulation of development; vasculature
2.  The interplay between inflorescence development and function as the crucible of architectural diversity 
Annals of Botany  2012;112(8):1477-1493.
Background
Most angiosperms present flowers in inflorescences, which play roles in reproduction, primarily related to pollination, beyond those served by individual flowers alone. An inflorescence's overall reproductive contribution depends primarily on the three-dimensional arrangement of the floral canopy and its dynamics during its flowering period. These features depend in turn on characteristics of the underlying branching structure (scaffold) that supports and supplies water and nutrients to the floral canopy. This scaffold is produced by developmental algorithms that are genetically specified and hormonally mediated. Thus, the extensive inflorescence diversity evident among angiosperms evolves through changes in the developmental programmes that specify scaffold characteristics, which in turn modify canopy features that promote reproductive performance in a particular pollination and mating environment. Nevertheless, developmental and ecological aspects of inflorescences have typically been studied independently, limiting comprehensive understanding of the relations between inflorescence form, reproductive function, and evolution.
Scope
This review fosters an integrated perspective on inflorescences by summarizing aspects of their development and pollination function that enable and guide inflorescence evolution and diversification.
Conclusions
The architecture of flowering inflorescences comprises three related components: topology (branching patterns, flower number), geometry (phyllotaxis, internode and pedicel lengths, three-dimensional flower arrangement) and phenology (flower opening rate and longevity, dichogamy). Genetic and developmental evidence reveals that these components are largely subject to quantitative control. Consequently, inflorescence evolution proceeds along a multidimensional continuum. Nevertheless, some combinations of topology, geometry and phenology are represented more commonly than others, because they serve reproductive function particularly effectively. For wind-pollinated species, these combinations often represent compromise solutions to the conflicting physical influences on pollen removal, transport and deposition. For animal-pollinated species, dominant selective influences include the conflicting benefits of large displays for attracting pollinators and of small displays for limiting among-flower self-pollination. The variety of architectural components that comprise inflorescences enable diverse resolutions of these conflicts.
doi:10.1093/aob/mcs252
PMCID: PMC3828939  PMID: 23243190
Inflorescence; angiosperm; form and function; evolution; development; architecture; floral display; pollination; geitonogamy; heterochrony
3.  Papilionoid inflorescences revisited (Leguminosae-Papilionoideae) 
Annals of Botany  2012;112(8):1567-1576.
Background and Aims
The inflorescence structure determines the spatiotemporal arrangement of the flowers during anthesis and is therefore vital for reproductive success. The Leguminosae are among the largest angiosperm plant families and they include some important crop plants. In papilionoid legumes, the raceme is the most common type of inflorescence. However, a range of other inflorescence types have evolved via various developmental processes. A (re-)investigation of inflorescences in Swainsona formosa, Cicer arietinum, Abrus precatorius, Hardenbergia violacea and Kennedia nigricans leads to new insights into reduction mechanisms and to a new hypothesis on the evolution of the papilionoid pseudoraceme.
Methods
Inflorescence morphology and ontogeny were studied using scanning electron microscopy (SEM).
Key Results
The inflorescence in S. formosa is an umbel with a rare type of pendulum symmetry which may be triggered by the subtending leaf. Inflorescences in C. arietinum are reduced to a single flower. An early formed adaxial bulge is the sterile apex of the inflorescence (i.e. the inflorescence is open and not terminated by a flower). In partial inflorescences of A. precatorius, the axis is reduced and its meristem is relocated towards the main inflorescence. Flower initiation follows a peculiar pendulum pattern. Partial inflorescences in H. violacea and in K. nigricans show reduction tendencies. In both taxa, initiated but early reduced bracteoles are present.
Conclusions
Pendulum symmetry in S. formosa is probably associated with distichous phyllotaxis. In C. arietinum, strong reduction tendencies are revealed. Based on studies of A. precatorius, the papilionoid pseudoraceme is reinterpreted as a compound raceme with condensed lateral axes. From an Abrus-like inflorescence, other types can be derived via reduction of flower number and synchronization of flower development. A plea is made for uniform usage of inflorescence terminology.
doi:10.1093/aob/mcs258
PMCID: PMC3828940  PMID: 23235698
Abrus precatorius; Cicer arietinum; Hardenbergia violacea; Kennedia nigricans; inflorescence; Leguminosae; Papilionoideae; pseudoraceme; Swainsona formosa
4.  Strigolactones activate different hormonal pathways for regulation of root development in response to phosphate growth conditions 
Annals of Botany  2012;112(2):409-415.
Background
Strigolactones (SLs) – a group of plant hormones and their derivatives – have been found to play a role in the regulation of root development, in addition to their role in suppression of lateral shoot branching: they alter root architecture and affect root-hair elongation, and SL signalling is necessary for the root response to low phosphate (Pi) conditions. These effects of SLs have been shown to be associated with differential activation of the auxin and ethylene signalling pathways.
Scope
The present review highlights recent findings on the activity of SLs as regulators of root development, in particular in response to low Pi stress, and discusses the different hormonal networks putatively acting with SLs in the root's Pi response.
Conclusions
SLs are suggested to be key regulators of the adaptive responses to low Pi in the root by modulating the balance between auxin and ethylene signalling. Consequently, they impact different developmental programmes responsible for the changes in root system architecture under differential Pi supply.
doi:10.1093/aob/mcs216
PMCID: PMC3698373  PMID: 23059852
Strigolactones; root; phosphate; hormones; ethylene; auxin; root hairs; primary root; lateral root
5.  A paradigm shift towards low-nitrifying production systems: the role of biological nitrification inhibition (BNI) 
Annals of Botany  2012;112(2):297-316.
Background
Agriculture is the single largest geo-engineering initiative that humans have initiated on planet Earth, largely through the introduction of unprecedented amounts of reactive nitrogen (N) into ecosystems. A major portion of this reactive N applied as fertilizer leaks into the environment in massive amounts, with cascading negative effects on ecosystem health and function. Natural ecosystems utilize many of the multiple pathways in the N cycle to regulate N flow. In contrast, the massive amounts of N currently applied to agricultural systems cycle primarily through the nitrification pathway, a single inefficient route that channels much of this reactive N into the environment. This is largely due to the rapid nitrifying soil environment of present-day agricultural systems.
Scope
In this Viewpoint paper, the importance of regulating nitrification as a strategy to minimize N leakage and to improve N-use efficiency (NUE) in agricultural systems is highlighted. The ability to suppress soil nitrification by the release of nitrification inhibitors from plant roots is termed ‘biological nitrification inhibition’ (BNI), an active plant-mediated natural function that can limit the amount of N cycling via the nitrification pathway. The development of a bioassay using luminescent Nitrosomonas to quantify nitrification inhibitory activity from roots has facilitated the characterization of BNI function. Release of BNIs from roots is a tightly regulated physiological process, with extensive genetic variability found in selected crops and pasture grasses. Here, the current status of understanding of the BNI function is reviewed using Brachiaria forage grasses, wheat and sorghum to illustrate how BNI function can be utilized for achieving low-nitrifying agricultural systems. A fundamental shift towards ammonium (NH4+)-dominated agricultural systems could be achieved by using crops and pastures with high BNI capacities. When viewed from an agricultural and environmental perspective, the BNI function in plants could potentially have a large influence on biogeochemical cycling and closure of the N loop in crop–livestock systems.
doi:10.1093/aob/mcs230
PMCID: PMC3698375  PMID: 23118123
AMO; ammonia mono-oxygenase; biological nitrification inhibition; BNI; BNI capacity; brachialactone; fatty acids; HAO; hydroxylamine oxidoreductase; high-nitrifying production systems; low-nitrifying production systems; nitrification; Nitrosomonas; nitrate leaching; synthetic nitrification inhibitors; nitrous oxide emissions; sustainability
6.  A conceptual model of root hair ideotypes for future agricultural environments: what combination of traits should be targeted to cope with limited P availability? 
Annals of Botany  2012;112(2):317-330.
Background
Phosphorus (P) often limits crop production and is frequently applied as fertilizer; however, supplies of quality rock phosphate for fertilizer production are diminishing. Plants have evolved many mechanisms to increase their P acquisition, and an understanding of these traits could result in improved long-term sustainability of agriculture. This Viewpoint focuses on the potential benefits of root hairs to sustainable production.
Scope
First the various root-related traits that could be deployed to improve agricultural sustainability are catalogued, and their potential costs and benefits to the plant are discussed. A novel mathematical model describing the effects of length, density and longevity of root hairs on P acquisition is developed, and the relative benefits of these three root-hair traits to plant P nutrition are calculated. Insights from this model are combined with experimental data to assess the relative benefits of a range of root hair ideotypes for sustainability of agriculture.
Conclusions
A cost–benefit analysis of root traits suggests that root hairs have the greatest potential for P acquisition relative to their cost of production. The novel modelling of root hair development indicates that the greatest gains in P-uptake efficiency are likely to be made through increased length and longevity of root hairs rather than by increasing their density. Synthesizing this information with that from published experiments we formulate six potential ideotypes to improve crop P acquisition. These combine appropriate root hair phenotypes with architectural, anatomical and biochemical traits, such that more root-hair zones are produced in surface soils, where P resources are found, on roots which are metabolically cheap to construct and maintain, and that release more P-mobilizing exudates. These ideotypes could be used to inform breeding programmes to enhance agricultural sustainability.
doi:10.1093/aob/mcs231
PMCID: PMC3698376  PMID: 23172412
Arabidopsis; barley; Hordeum vulgare; cost/benefit; modelling; phosphorus; root architecture; root anatomy; root function; root hairs
7.  Use of genotype × environment interactions to understand rooting depth and the ability of wheat to penetrate hard soils 
Annals of Botany  2012;112(2):359-368.
Background
Root systems are well-recognized as complex and a variety of traits have been identified as contributing to plant adaptation to the environment. A significant proportion of soil in south-western Australia is prone to the formation of hardpans of compacted soil that limit root exploration and thus access to nutrients and water for plant growth. Genotypic variation has been reported for root-penetration ability of wheat in controlled conditions, which has been related to field performance in these environments. However, research on root traits in field soil is recognized as difficult and labour intensive. Pattern analysis of genotype × environment (G × E) interactions is one approach that enables interpretation of these complex relationships, particularly when undertaken with probe genotypes with well-documented traits, in this case, for the ability to penetrate a wax layer. While the analytical approach is well-established in the scientific literature, there are very few examples of pattern analysis for G × E interactions applied to root traits of cereal crops.
Scope
In this viewpoint, we aim to review the approach of pattern analysis for G × E interaction and the importance of environment and genotype characterization, with a focus on root traits. We draw on our research on G × E interaction for root depth and related studies on genotypic evaluation for root-penetration ability. In doing so, we wish to explore how pattern analysis can aid in the interpretation of complex root traits and their interaction with the environment and how this may explain patterns of adaptation and inform future research.
Conclusions
With appropriate characterization of environments and genotypes, the G × E approach can be used to aid in the interpretation of the complex interactions of root systems with the environment, inform future research and therefore provide supporting evidence for selecting specific root traits for target environments in a crop breeding programme.
doi:10.1093/aob/mcs251
PMCID: PMC3698378  PMID: 23204508
Hardpan; wax layer; Western Australia; pattern analysis; wheat; Triticum aestivum
8.  Plasticity of rhizosphere hydraulic properties as a key for efficient utilization of scarce resources 
Annals of Botany  2012;112(2):277-290.
Background
It is known that the soil near roots, the so-called rhizosphere, has physical and chemical properties different from those of the bulk soil. Rhizosphere properties are the result of several processes: root and soil shrinking/swelling during drying/wetting cycles, soil compaction by root growth, mucilage exuded by root caps, interaction of mucilage with soil particles, mucilage shrinking/swelling and mucilage biodegradation. These processes may lead to variable rhizosphere properties, i.e. the presence of air-filled gaps between soil and roots; water repellence in the rhizosphere caused by drying of mucilage around the soil particles; or water accumulation in the rhizosphere due to the high water-holding capacity of mucilage. The resulting properties are not constant in time but they change as a function of soil condition, root growth rate and mucilage age.
Scope
We consider such a variability as an expression of rhizosphere plasticity, which may be a strategy for plants to control which part of the root system will have a facilitated access to water and which roots will be disconnected from the soil, for instance by air-filled gaps or by rhizosphere hydrophobicity. To describe such a dualism, we suggest classifying rhizosphere into two categories: class A refers to a rhizosphere covered with hydrated mucilage that optimally connects roots to soil and facilitates water uptake from dry soils. Class B refers to the case of air-filled gaps and/or hydrophobic rhizosphere, which isolate roots from the soil and may limit water uptake from the soil as well water loss to the soil. The main function of roots covered by class B will be long-distance transport of water.
Outlook
This concept has implications for soil and plant water relations at the plant scale. Root water uptake in dry conditions is expected to shift to regions covered with rhizosphere class A. On the other hand, hydraulic lift may be limited in regions covered with rhizosphere class B. New experimental methods need to be developed and applied to different plant species and soil types, in order to understand whether such dualism in rhizosphere properties is an important mechanism for efficient utilization of scarce resources and drought tolerance.
doi:10.1093/aob/mcs262
PMCID: PMC3698379  PMID: 23235697
Rhizosphere; hydraulic properties; root water uptake; mucilage; root–soil contact; gaps
9.  Zinc uptake and radial transport in roots of Arabidopsis thaliana: a modelling approach to understand accumulation 
Annals of Botany  2012;112(2):369-380.
Background and Aims
Zinc uptake in roots is believed to be mediated by ZIP (ZRT-, IRT-like proteins) transporters. Once inside the symplast, zinc is transported to the pericycle, where it exits by means of HMA (heavy metal ATPase) transporters. The combination of symplastic transport and spatial separation of influx and efflux produces a pattern in which zinc accumulates in the pericycle. Here, mathematical modelling was employed to study the importance of ZIP regulation, HMA abundance and symplastic transport in creation of the radial pattern of zinc in primary roots of Arabidopsis thaliana.
Methods
A comprehensive one-dimensional dynamic model of radial zinc transport in roots was developed and used to conduct simulations. The model accounts for the structure of the root consisting of symplast and apoplast and includes effects of water flow, diffusion and cross-membrane transport via transporters. It also incorporates the radial geometry and varying porosity of root tissues, as well as regulation of ZIP transporters.
Key Results
Steady-state patterns were calculated for various zinc concentrations in the medium, water influx and HMA abundance. The experimentally observed zinc gradient was reproduced very well. An increase of HMA or decrease in water influx led to loss of the gradient. The dynamic behaviour for a change in medium concentration and water influx was also simulated showing short adaptation times in the range of seconds to minutes. Slowing down regulation led to oscillations in expression levels, suggesting the need for rapid regulation and existence of buffering agents.
Conclusions
The model captures the experimental findings very well and confirms the hypothesis that low abundance of HMA4 produces a radial gradient in zinc concentration. Surprisingly, transpiration was found also to be a key parameter. The model suggests that ZIP regulation takes place on a comparable timescale as symplastic transport.
doi:10.1093/aob/mcs263
PMCID: PMC3698380  PMID: 23258417
Modelling; zinc uptake; ZIP; HMA; Arabidopsis thaliana; Arabidopsis halleri; advection; diffusion; radial transport; root; gradient; pattern; regulation
10.  Root–shoot allometry of tropical forest trees determined in a large-scale aeroponic system 
Annals of Botany  2012;112(2):291-296.
Background and Aims
This study is a first step in a multi-stage project aimed at determining allometric relationships among the tropical tree organs, and carbon fluxes between the various tree parts and their environment. Information on canopy–root interrelationships is needed to improve understanding of above- and below-ground processes and for modelling of the regional and global carbon cycle. Allometric relationships between the sizes of different plant parts will be determined.
Methods
Two tropical forest species were used in this study: Ceiba pentandra (kapok), a fast-growing tree native to South and Central America and to Western Africa, and Khaya anthotheca (African mahogany), a slower-growing tree native to Central and Eastern Africa. Growth and allometric parameters of 12-month-old saplings grown in a large-scale aeroponic system and in 50-L soil containers were compared. The main advantage of growing plants in aeroponics is that their root systems are fully accessible throughout the plant life, and can be fully recovered for harvesting.
Key Results
The expected differences in shoot and root size between the fast-growing C. pentandra and the slower-growing K. anthotheca were evident in both growth systems. Roots were recovered from the aeroponically grown saplings only, and their distribution among various diameter classes followed the patterns expected from the literature. Stem, branch and leaf allometric parameters were similar for saplings of each species grown in the two systems.
Conclusions
The aeroponic tree growth system can be utilized for determining the basic allometric relationships between root and shoot components of these trees, and hence can be used to study carbon allocation and fluxes of whole above- and below-ground tree parts.
doi:10.1093/aob/mcs275
PMCID: PMC3698382  PMID: 23250916
Aeroponics; African mahogany; allometry; Ceiba pentandra; Khaya anthotheca; root–shoot relationships; specific root length; wood density
11.  The phylogenetic distribution of extrafloral nectaries in plants 
Annals of Botany  2012;111(6):1251-1261.
Background and Aims
Understanding the evolutionary patterns of ecologically relevant traits is a central goal in plant biology. However, for most important traits, we lack the comprehensive understanding of their taxonomic distribution needed to evaluate their evolutionary mode and tempo across the tree of life. Here we evaluate the broad phylogenetic patterns of a common plant-defence trait found across vascular plants: extrafloral nectaries (EFNs), plant glands that secrete nectar and are located outside the flower. EFNs typically defend plants indirectly by attracting invertebrate predators who reduce herbivory.
Methods
Records of EFNs published over the last 135 years were compiled. After accounting for changes in taxonomy, phylogenetic comparative methods were used to evaluate patterns of EFN evolution, using a phylogeny of over 55 000 species of vascular plants. Using comparisons of parametric and non-parametric models, the true number of species with EFNs likely to exist beyond the current list was estimated.
Key Results
To date, EFNs have been reported in 3941 species representing 745 genera in 108 families, about 1–2 % of vascular plant species and approx. 21 % of families. They are found in 33 of 65 angiosperm orders. Foliar nectaries are known in four of 36 fern families. Extrafloral nectaries are unknown in early angiosperms, magnoliids and gymnosperms. They occur throughout monocotyledons, yet most EFNs are found within eudicots, with the bulk of species with EFNs being rosids. Phylogenetic analyses strongly support the repeated gain and loss of EFNs across plant clades, especially in more derived dicot families, and suggest that EFNs are found in a minimum of 457 independent lineages. However, model selection methods estimate that the number of unreported cases of EFNs may be as high as the number of species already reported.
Conclusions
EFNs are widespread and evolutionarily labile traits that have repeatedly evolved a remarkable number of times in vascular plants. Our current understanding of the phylogenetic patterns of EFNs makes them powerful candidates for future work exploring the drivers of their evolutionary origins, shifts, and losses.
doi:10.1093/aob/mcs225
PMCID: PMC3662505  PMID: 23087129
Extrafloral; extranuptial; foliar; nectary; extrafloral nectary; phylogeny; taxonomy; distribution; mutualism; angiosperms; rosids; asteriids
12.  Diversity and evolution of a trait mediating ant–plant interactions: insights from extrafloral nectaries in Senna (Leguminosae) 
Annals of Botany  2012;111(6):1263-1275.
Background and Aims
Plants display a wide range of traits that allow them to use animals for vital tasks. To attract and reward aggressive ants that protect developing leaves and flowers from consumers, many plants bear extrafloral nectaries (EFNs). EFNs are exceptionally diverse in morphology and locations on a plant. In this study the evolution of EFN diversity is explored by focusing on the legume genus Senna, in which EFNs underwent remarkable morphological diversification and occur in over 80 % of the approx. 350 species.
Methods
EFN diversity in location, morphology and plant ontogeny was characterized in wild and cultivated plants, using scanning electron microscopy and microtome sectioning. From these data EFN evolution was reconstructed in a phylogenetic framework comprising 83 Senna species.
Key Results
Two distinct kinds of EFNs exist in two unrelated clades within Senna. ‘Individualized’ EFNs (iEFNs), located on the compound leaves and sometimes at the base of pedicels, display a conspicuous, gland-like nectary structure, are highly diverse in shape and characterize the species-rich EFN clade. Previously overlooked ‘non-individualized’ EFNs (non-iEFNs) embedded within stipules, bracts, and sepals are cryptic and may represent a new synapomorphy for clade II. Leaves bear EFNs consistently throughout plant ontogeny. In one species, however, early seedlings develop iEFNs between the first pair of leaflets, but later leaves produce them at the leaf base. This ontogenetic shift reflects our inferred diversification history of iEFN location: ancestral leaves bore EFNs between the first pair of leaflets, while leaves derived from them bore EFNs either between multiple pairs of leaflets or at the leaf base.
Conclusions
EFNs are more diverse than previously thought. EFN-bearing plant parts provide different opportunities for EFN presentation (i.e. location) and individualization (i.e. morphology), with implications for EFN morphological evolution, EFN–ant protective mutualisms and the evolutionary role of EFNs in plant diversification.
doi:10.1093/aob/mcs226
PMCID: PMC3662506  PMID: 23104672
Ant–plant mutualism; ant protection; extrafloral nectaries; Senna; Fabaceae; functional morphology; homology; key innovation; morphological evolution; ontogeny; phylogeny
13.  Congratulations, you have been carefully chosen to represent an important developmental regulator! 
Annals of Botany  2012;111(3):329-333.
Background
Studying a process in a new species often relies on focusing our attention to a candidate gene, encoding a protein similar to one with a known function. Not all the choices seem to be prudent.
Scope
This Viewpoint includes an overview of issues that are encountered during research of candidate genes. Defining a match for a gene of interest, deciding whether variation in ESTs or RNAseq data for a certain transcript, represent more than one gene. The problem of incorrect annotation of genes due to incorrect in-silico splicing, is also mentioned. The author's humble opinion on how to deal with these issues is provided.
Conclusions
The vast amount of new sequence data provides us with great possibilities for giant leaps in our understanding. Still, we cannot afford to skip over the tedious steps required to confirm that we are indeed studying the correct gene, and try to be sure that the complex expression pattern we observe is not a composite of several genes.
doi:10.1093/aob/mcs161
PMCID: PMC3579433  PMID: 22811510
Homology; orthology; MADS box; FLOWERING LOCUS T; FLC; candidate gene; citrus; Citrus clementina; apple; Malus domestica
14.  Current methods for detecting ethylene in plants 
Annals of Botany  2012;111(3):347-360.
Background
In view of ethylene's critical developmental and physiological roles the gaseous hormone remains an active research topic for plant biologists. Progress has been made to understand the ethylene biosynthesis pathway and the mechanisms of perception and action. Still numerous questions need to be answered and findings to be validated. Monitoring gas production will very often complete the picture of any ethylene research topic. Therefore the search for suitable ethylene measuring methods for various plant samples either in the field, greenhouses, laboratories or storage facilities is strongly motivated.
Scope
This review presents an update of the current methods for ethylene monitoring in plants. It focuses on the three most-used methods – gas chromatography detection, electrochemical sensing and optical detection – and compares them in terms of sensitivity, selectivity, time response and price. Guidelines are provided for proper selection and application of the described sensor methodologies and some specific applications are illustrated of laser-based detector for monitoring ethylene given off by Arabidopsis thaliana upon various nutritional treatments.
Conclusions
Each method has its advantages and limitations. The choice for the suitable ethylene sensor needs careful consideration and is driven by the requirements for a specific application.
doi:10.1093/aob/mcs259
PMCID: PMC3579434  PMID: 23243188
Ethylene; Arabidopsis thaliana; gas sampling; gas chromatography; electrochemical sensing; laser-based detector
15.  Altitudinal changes in temperature responses of net photosynthesis and dark respiration in tropical bryophytes 
Annals of Botany  2012;111(3):455-465.
Background and Aims
There is a conspicuous increase of poikilohydric organisms (mosses, liverworts and macrolichens) with altitude in the tropics. This study addresses the hypothesis that the lack of bryophytes in the lowlands is due to high-temperature effects on the carbon balance. In particular, it is tested experimentally whether temperature responses of CO2-exchange rates would lead to higher respiratory carbon losses at night, relative to potential daily gains, in lowland compared with lower montane forests.
Methods
Gas-exchange measurements were used to determine water-, light-, CO2- and temperature-response curves of net photosynthesis and dark respiration of 18 tropical bryophyte species from three altitudes (sea level, 500 m and 1200 m) in Panama.
Key Results
Optimum temperatures of net photosynthesis were closely related to mean temperatures in the habitats in which the species grew at the different altitudes. The ratio of dark respiration to net photosynthesis at mean ambient night and day temperatures did not, as expected, decrease with altitude. Water-, light- and CO2-responses varied between species but not systematically with altitude.
Conclusions
Drivers other than temperature-dependent metabolic rates must be more important in explaining the altitudinal gradient in bryophyte abundance. This does not discard near-zero carbon balances as a major problem for lowland species, but the main effect of temperature probably lies in increasing evaporation rates, thus restricting the time available for photosynthetic carbon gain, rather than in increasing nightly respiration rates. Since optimum temperatures for photosynthesis were so fine tuned to habitat temperatures we analysed published temperature responses of bryophyte species worldwide and found the same pattern on the large scale as we found along the tropical mountain slope we studied.
doi:10.1093/aob/mcs267
PMCID: PMC3579435  PMID: 23258418
Altitudinal gradient; bryophytes; carbon balance; dark respiration; gas-exchange measurements; hepatics; liverworts; mosses; net photosynthesis; photosynthesis-response curves; temperature; tropical rain forest
17.  Plants & people 
Annals of Botany  2012;111(3):vii-ix.
doi:10.1093/aob/mcs280
PMCID: PMC3579438
19.  Functional genomics and evolution of photosynthetic systems 
Annals of Botany  2012;111(3):x-xi.
doi:10.1093/aob/mcs282
PMCID: PMC3579440
20.  Spatio-temporal history of the disjunct family Tecophilaeaceae: a tale involving the colonization of three Mediterranean-type ecosystems 
Annals of Botany  2012;111(3):361-373.
Background and Aims
Tecophilaeaceae (27 species distributed in eight genera) have a disjunct distribution in California, Chile and southern and tropical mainland Africa. Moreover, although the family mainly occurs in arid ecosystems, it has colonized three Mediterranean-type ecosystems. In this study, the spatio-temporal history of the family is examined using DNA sequence data from six plastid regions.
Methods
Modern methods in divergence time estimation (BEAST), diversification (LTT and GeoSSE) and biogeography (LAGRANGE) are applied to infer the evolutionary history of Tecophilaeaceae. To take into account dating and phylogenetic uncertainty, the biogeographical inferences were run over a set of dated Bayesian trees and the analyses were constrained according to palaeogeographical evidence.
Key Results
The analyses showed that the current distribution and diversification of the family were influenced primarily by the break up of Gondwana, separating the family into two main clades, and the establishment of a Mediterranean climate in Chile, coinciding with the radiation of Conanthera. Finally, unlike many other groups, no shifts in diversification rates were observed associated with the dispersals in the Cape region of South Africa.
Conclusions
Although modest in size, Tecophilaeaceae have a complex spatio-temporal history. The family is now most diverse in arid ecosystems in southern Africa, but is expected to have originated in sub-tropical Africa. It has subsequently colonized Mediterranean-type ecosystems in both the Northern and Southern Hemispheres, but well before the onset of the Mediterranean climate in these regions. Only one lineage, genus Conanthera, has apparently diversified to any extent under the impetus of a Mediterranean climate.
doi:10.1093/aob/mcs286
PMCID: PMC3579441  PMID: 23277471
Biogeography; California; Chile; disjunct distribution; Greater Cape region; Mediterranean climate; Tecophilaeaceae
21.  Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth 
Annals of Botany  2012;111(3):375-383.
Background and Aims
Carnivorous plants of the genus Nepenthes possess modified leaves that form pitfall traps in order to capture prey, mainly arthropods, to make additional nutrients available for the plant. These pitchers contain a digestive fluid due to the presence of hydrolytic enzymes. In this study, the composition of the digestive fluid was further analysed with regard to mineral nutrients and low molecular-weight compounds. A potential contribution of microbes to the composition of pitcher fluid was investigated.
Methods
Fluids from closed pitchers were harvested and analysed for mineral nutrients using analytical techniques based on ion-chromatography and inductively coupled plasma–optical emission spectroscopy. Secondary metabolites were identified by a combination of LC-MS and NMR. The presence of bacteria in the pitcher fluid was investigated by PCR of 16S-rRNA genes. Growth analyses of bacteria and yeast were performed in vitro with harvested pitcher fluid and in vivo within pitchers with injected microbes.
Key Results
The pitcher fluid from closed pitchers was found to be primarily an approx. 25-mm KCl solution, which is free of bacteria and unsuitable for microbial growth probably due to the lack of essential mineral nutrients such as phosphate and inorganic nitrogen. The fluid also contained antimicrobial naphthoquinones, plumbagin and 7-methyl-juglone, and defensive proteins such as the thaumatin-like protein. Challenging with bacteria or yeast caused bactericide as well as fungistatic properties in the fluid. Our results reveal that Nepenthes pitcher fluids represent a dynamic system that is able to react to the presence of microbes.
Conclusions
The secreted liquid of closed and freshly opened Nepenthes pitchers is exclusively plant-derived. It is unsuitable to serve as an environment for microbial growth. Thus, Nepenthes plants can avoid and control, at least to some extent, the microbial colonization of their pitfall traps and, thereby, reduce the need to vie with microbes for the prey-derived nutrients.
doi:10.1093/aob/mcs287
PMCID: PMC3579442  PMID: 23264234
Antimicrobial activity; carnivorous plants; defensive proteins; digestive pitcher fluid; naphthoquinones; Nepenthes spp.; mineral nutrients; pitfall traps
22.  Manninotriose is a major carbohydrate in red deadnettle (Lamium purpureum, Lamiaceae) 
Annals of Botany  2012;111(3):385-393.
Background and Aims
There is a great need to search for natural compounds with superior prebiotic, antioxidant and immunostimulatory properties for use in (food) applications. Raffinose family oligosaccharides (RFOs) show such properties. Moreover, they contribute to stress tolerance in plants, acting as putative membrane stabilizers, antioxidants and signalling agents.
Methods
A large-scale soluble carbohydrate screening was performed within the plant kingdom. An unknown compound accumulated to a high extent in early-spring red deadnettle (Lamium purpureum) but not in other RFO plants. The compound was purified and its structure was unravelled with NMR. Organs and organ parts of red deadnettle were carefully dissected and analysed for soluble sugars. Phloem sap content was analysed by a common EDTA-based method.
Key Results
Early-spring red deadnettle stems and roots accumulate high concentrations of the reducing trisaccharide manninotriose (Galα1,6Galα1,6Glc), a derivative of the non-reducing RFO stachyose (Galα1,6Galα1,6Glcα1,2βFru). Detailed soluble carbohydrate analyses on dissected stem and leaf sections, together with phloem sap analyses, strongly suggest that stachyose is the main transport compound, but extensive hydrolysis of stachyose to manninotriose seems to occur along the transport path. Based on the specificities of the observed carbohydrate dynamics, the putative physiological roles of manninotriose in red deadnettle are discussed.
Conclusions
It is demonstrated for the first time that manninotriose is a novel and important player in the RFO metabolism of red dead deadnettle. It is proposed that manninotriose represents a temporary storage carbohydrate in early-spring deadnettle, at the same time perhaps functioning as a membrane protector and/or as an antioxidant in the vicinity of membranes, as recently suggested for other RFOs and fructans. This novel finding urges further research on this peculiar carbohydrate on a broader array of RFO accumulators.
doi:10.1093/aob/mcs288
PMCID: PMC3579443  PMID: 23264235
Lamium purpureum; manninotriose; raffinose; RFO; red deadnettle; stachyose
23.  Light requirements of Australian tropical vs. cool-temperate rainforest tree species show different relationships with seedling growth and functional traits 
Annals of Botany  2012;111(3):479-488.
Background and Aims
A trade-off between shade tolerance and growth in high light is thought to underlie the temporal dynamics of humid forests. On the other hand, it has been suggested that tree species sorting on temperature gradients involves a trade-off between growth rate and cold resistance. Little is known about how these two major trade-offs interact.
Methods
Seedlings of Australian tropical and cool-temperate rainforest trees were grown in glasshouse environments to compare growth versus shade-tolerance trade-offs in these two assemblages. Biomass distribution, photosynthetic capacity and vessel diameters were measured in order to examine the functional correlates of species differences in light requirements and growth rate. Species light requirements were assessed by field estimation of the light compensation point for stem growth.
Results
Light-demanding and shade-tolerant tropical species differed markedly in relative growth rates (RGR), but this trend was less evident among temperate species. This pattern was paralleled by biomass distribution data: specific leaf area (SLA) and leaf area ratio (LAR) of tropical species were significantly positively correlated with compensation points, but not those of cool-temperate species. The relatively slow growth and small SLA and LAR of Tasmanian light-demanders were associated with narrow vessels and low potential sapwood conductivity.
Conclusions
The conservative xylem traits, small LAR and modest RGR of Tasmanian light-demanders are consistent with selection for resistance to freeze–thaw embolism, at the expense of growth rate. Whereas competition for light favours rapid growth in light-demanding trees native to environments with warm, frost-free growing seasons, frost resistance may be an equally important determinant of the fitness of light-demanders in cool-temperate rainforest, as seedlings establishing in large openings are exposed to sub-zero temperatures that can occur throughout most of the year.
doi:10.1093/aob/mcs289
PMCID: PMC3579444  PMID: 23264237
Conduit diameter; Hagen–Poiseuille equation; leaf area ratio; relative growth rate; sapwood conductivity; shade tolerance; vessel diameter; whole-plant compensation point; growth traits; functional traits
24.  The endangered Iris atropurpurea (Iridaceae) in Israel: honey-bees, night-sheltering male bees and female solitary bees as pollinators 
Annals of Botany  2012;111(3):395-407.
Background and Aims
The coastal plain of Israel hosts the last few remaining populations of the endemic Iris atropurpurea (Iridaceae), a Red List species of high conservation priority. The flowers offer no nectar reward. Here the role of night-sheltering male solitary bees, honey-bees and female solitary bees as pollinators of I. atropurpurea is documented.
Methods
Breeding system, floral longevity, stigma receptivity, visitation rates, pollen loads, pollen deposition and removal and fruit- and seed-set were investigated.
Key Results
The main wild pollinators of this plant are male eucerine bees, and to a lesser extent, but with the potential to transfer pollen, female solitary bees. Honey-bees were found to be frequent diurnal visitors; they removed large quantities of pollen and were as effective as male sheltering bees at pollinating this species. The low density of pollen carried by male solitary bees was attributed to grooming activities, pollen displacement when bees aggregated together in flowers and pollen depletion by honey-bees. In the population free of honey-bee hives, male bees carried significantly more pollen grains on their bodies. Results from pollen analysis and pollen deposited on stigmas suggest that inadequate pollination may be an important factor limiting fruit-set. In the presence of honey-bees, eucerine bees were low removal–low deposition pollinators, whereas honey-bees were high removal–low deposition pollinators, because they removed large amounts into corbiculae and deposited relatively little onto receptive stigmas.
Conclusions
Even though overall, both bee taxa were equally effective pollinators, we suggest that honey-bees have the potential to reduce the amount of pollen available for plant reproduction, and to reduce the amount of resources available to solitary bee communities. The results of this study have potential implications for the conservation of this highly endangered plant species if hives are permitted inside reserves, where the bulk of Oncocyclus iris species are protected.
doi:10.1093/aob/mcs292
PMCID: PMC3579445  PMID: 23275630
Endangered; Iris atropurpurea; pollination; pollinator effectiveness; Apis mellifera; night-sheltering; eucerine bees; solitary bees; pollen removal; pollen deposition; stigma receptivity; pollen viability
25.  Mycorrhizal preference promotes habitat invasion by a native Australian orchid: Microtis media 
Annals of Botany  2012;111(3):409-418.
Background and Aims
Mycorrhizal specialization has been shown to limit recruitment capacity in orchids, but an increasing number of orchids are being documented as invasive or weed-like. The reasons for this proliferation were examined by investigating mycorrhizal fungi and edaphic correlates of Microtis media, an Australian terrestrial orchid that is an aggressive ecosystem and horticultural weed.
Methods
Molecular identification of fungi cultivated from M. media pelotons, symbiotic in vitro M. media seed germination assays, ex situ fungal baiting of M. media and co-occurring orchid taxa (Caladenia arenicola, Pterostylis sanguinea and Diuris magnifica) and soil physical and chemical analyses were undertaken.
Key Results
It was found that: (1) M. media associates with a broad taxonomic spectrum of mycobionts including Piriformospora indica, Sebacina vermifera, Tulasnella calospora and Ceratobasidium sp.; (2) germination efficacy of mycorrhizal isolates was greater for fungi isolated from plants in disturbed than in natural habitats; (3) a higher percentage of M. media seeds germinate than D. magnifica, P. sanguinea or C. arenicola seeds when incubated with soil from M. media roots; and (4) M. media–mycorrhizal fungal associations show an unusual breadth of habitat tolerance, especially for soil phosphorus (P) fertility.
Conclusions
The findings in M. media support the idea that invasive terrestrial orchids may associate with a diversity of fungi that are widespread and common, enhance seed germination in the host plant but not co-occurring orchid species and tolerate a range of habitats. These traits may provide the weedy orchid with a competitive advantage over co-occurring orchid species. If so, invasive orchids are likely to become more broadly distributed and increasingly colonize novel habitats.
doi:10.1093/aob/mcs294
PMCID: PMC3579446  PMID: 23275632
Terrestrial orchid; mycorrhizal fungi; disturbed habitats; south-western Australia; invasive species; Microtis media

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