Plant Cuttings

As an essential macronutrient (http://en.wikipedia.org/wiki/Plant_nutrition) calcium participates in many aspects of plant biology, e.g. structural roles in the cell wall, as a counter-cation for anions in the vacuole (see Philip White and Martin Broadley, Annals of Botany92: 487–511, 2003) and as a so-called ‘secondary messenger’, where calcium signals participate in many developmental processes (Jörg Kudla et al., The Plant Cell22: 541–563, 2010). But one function that has passed me by until now is the part it plays in the water-splitting reaction of photosynthesis (http://bit.ly/Xnyxb8). Although all parts of photosynthesis are important, arguably the photolysis of water is the most important reaction in the process since it generates the hydrogen ions (protons) and electrons that participate in the ATP- and NADPH-generating activities of the light-dependent reactions of photosynthesis, which are fundamental to subsequent carbon-fixation in the light-independent stages (‘dark reactions’) of the process. Oh! And this photolysis also releases oxygen that accumulates in the atmosphere, and which is so essential to all aerobic life forms. Whilst I was familiar with the idea that manganese (an essential micronutrient; Robert Hänsch and Ralf Mendel, Current Opinion in Plant Biology12: 259–266, 2009) is a major component of the water-splitting complex, I didn't realise that calcium was too. However, although its presence there was known to others, its role was not (so I don't feel so bad about my state of comparative ignorance …). But work by Emily Tsui et al. has revealed that calcium plays an important supportive role in allowing the manganese to transfer electrons away from the oxygen, thereby facilitating the subsequent production of molecular oxygen (Nature Chemistry5: 293–299, 2013). Fascinating as this is in adding yet another role to the already extensive catalogue of calcium's competencies, it is also hoped that this insight might help in the construction of artificial photosynthesis systems, with promises of renewable, cleaner energy (http://rsc.li/Y9d0o7). New light on an old topic: we like that! Image: Wikimedia Commons. The weather's been so bad in the UK recently that I'm not sure if spring – ‘one of the four conventional temperate seasons, following winter and preceding summer’ (http://en.wikipedia.org/wiki/Spring_%28season%29) – with its attendant promise of life reinvigorated, etc, has actually arrived or not. Let's assume it has, but as we await the long-overdue blossom on the trees, look to the future with some spring-blossom-related items. Ashley Shade et al. have uncovered successional changes in the microbial community associated with blossom of apple (Malus domestica; mBio4: e00602-12). Whilst we may be used to terrestrial successions of land plants taking hundreds of years (http://www.countrysideinfo.co.uk/successn/summary.htm), in keeping with the fast-cycling times of microbes these six-stage apple successions took place during the 7-day lifespan of the studied flowers. This previously unknown floroplane community included a preponderance of members of the Deinococcus–Thermus phylum (http://en.wikipedia.org/wiki/Deinococcus-Thermus; which include many species that are resistant to extreme radiation, as well as several thermophiles: Emma Griffiths and Radhey Gupta, International Microbiology10: 201–208, 2007), and ‘TM7’ a so-called ‘candidate phylum’ (a major lineage of bacteria whose existence is known solely through environmental 16S r(ibosomal)RNA sequences, as to date no species has been grown in the lab; http://en.wikipedia.org/wiki/Candidate_division_TM7). Together with the decoding of its genome (Riccardo Velasco et al., Nature Genetics42: 833–839, 2010), one hope for this unexpected insight into apple floral biology is that it will provide a basis for better disease management of this economically important fruit (http://en.wikipedia.org/wiki/Apple). And hot on the heels of that research, Jonathan Leff and Noah Fierer have used similar techniques – culture-independent 16S rRNA gene pyrosequencing (which ‘by sequencing well-characterized hypervariable regions of genes such as 16S rRNA … sequence data provides … unambiguous and discriminatory information for microbial identification’; http://bit.ly/10MENqr) – to examine the microbiota of 11 store-bought ‘produce types’, which included fruit (yes, apple was one such) and vegetables (including mushrooms; PLoS ONE8: e59310). Demonstrating that the sampled fruit and veg harboured diverse bacterial communities – and the communities on each product were significantly distinct from one another – they conclude that ‘humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation’. Tantalisingly, differentiating between closely related taxa that may have pathogenic and non-pathogenic representatives was not an objective of that study (nor was adding to the discussion as to whether ‘organic’ or ‘conventional’ farmed produce might be ‘safer’ in this regard …). So, an assessment of whether those produce-residing bacterial communities may impact human exposures to potential pathogens is awaited. But, until then, do remember to wash your fruit and veg before eating! Image: Roberta F./Wikimedia Commons. There are only two types of people in the world: those who chew gum, and those who don't. Those who do, say it helps them to concentrate; those who don't, concentrate on denigrating this habit as unpleasant. Chewing gum was originally made of chicle derived from trees of the Manilkara genus in the Sapotaceae (http://en.wikipedia.org/wiki/Chicle), but has now been largely replaced by synthetic ‘gum base’ (Raychelle Burks; Chemical & Engineering News85(32): 36, 2007). Just as other plant-derived substances – illegal or otherwise – have been credited with ‘fuelling creativity’ (http://bit.ly/17hn1zh), etc, so devotees of chewing gum have extolled its virtues. In particular they claim it aids concentration. Well, that view is supported by the work of Kate Morgan et al. (British Journal of Psychology, currently in press), who demonstrate that chewing gum ‘moderates the vigilance decrement’ – i.e. chicle-chompers ‘focused and remembered number sequences better than non-gum chewers’ http://bit.ly/Z3bKBU) – in an auditory test. Furthermore, Lara Tucha and William Simpson showed that in visual tests, beneficial effects on sustained attention were observed at later stages (although chewing – spearmint-flavoured, sugar-free – gum had detrimental effects on sustained attention in earlier stages of the task …; Appetite56: 299–301, 2011). ‘Gum-deniers’, however, will probably point to Michail Kozlov et al.'s study that chewing flavourless gum can interfere with short-term memory (The Quarterly Journal of Experimental Psychology65: 501–513, 2012). So, to chew, or not to chew, that is the question. And certainly one to ruminate on – in both senses of the word (http://bit.ly/XyS0YK)! Image: Jóhann Heiðar Árnason/Wikimedia Commons. Nitrogen (http://en.wikipedia.org/wiki/Nitrogen) is an essential macronutrient (e.g. Frans Maathuis, Current Opinion in Plant Biology12: 250–258, 2009) for plants – i.e. they cannot complete their life cycle without it – and it is needed in relatively large amounts. Although it is abundant in the atmosphere – N2 (‘dinitrogen’) comprises about 80 % of the Earth's invisible gaseous envelope mantle – that molecule cannot be used directly by plants. Instead they rely on oxidation of nitrogen to NO3− – ‘nitrate’ – since that is the form in which most plants absorb the nitrogen they need from the soil. Although some imaginative plants, like legumes, can supplement their nitrogen intake using NH3 produced by symbiotic microbes (that ‘fix’ N2 directly from the atmosphere; http://en.wikipedia.org/wiki/Nitrogen_fixation), I thought that such inorganic N sources were about it as far as root-routed plant N-sources went. Astonishing news then that ‘quaternary ammonium compounds [think inorganic ammonium – NH4+ – but with organic groups replacing each of the four hydrogens; http://bit.ly/10MJdxN] can be abundant in some soils and are taken up as intact molecules by plants’ (Charles Warren; New Phytologist198: 476–485, 2013), because these are organic N-compounds. Warren demonstrates that ‘two ecologically disparate species’ (an understatement if ever there was!) – non-mycorrhizal Banksia oblongifolia (http://en.wikipedia.org/wiki/Banksia_oblongifolia) and mycorrhizal Triticum aestivum (wheat; http://en.wikipedia.org/wiki/Common_wheat) – take up intact molecules of betaine, carnitine and acetyl-carnitine. Two key findings of the study are that ‘the pool of small, nonpeptide organic-N in the soil solution is chemically diverse and not dominated solely by protein amino acids’, and that plants have an ‘even broader palate than is suggested by most of the literature on organic N’(!). I'm grateful to that article for putting me straight on the fact that other soil-sited organic N-sources – such as intact amino acids – can be used by plants as well. All of which suggests one has to be very careful in assessing the N-status of soil as a suitable growing medium for plants – have all possible plant-usable N-sources been considered and quantified? Maybe N is not in such short supply as frequently stated …? Maybe we don't need to add as much expensive N-fertiliser to achieve decent crop yields as purveyors of N-fertiliser might like us to believe …? Certainly, time to update those plant mineral nutrition lecture notes (again …). Image: Wikimedia Commons. Parasitic plants – angiosperms that directly attach to another plant via a haustorium, a modified root that forms a morphological and physiological link between the parasite and host (e.g. Daniel Nickrent and Lytton Musselman; http://bit.ly/16HWRXW) – tend to get a bad press. And it's little surprise with the antics of such villains as Striga (http://en.wikipedia.org/wiki/Striga), the ‘violet vampire’ (http://bit.ly/11IOvhG), which greatly reduces the production of staple foods and commercial crops such as maize, sorghum, millet, rice, sugarcane and cowpea in many African countries, and can cause up to 100 % crop loss. Slightly less devastating and livelihood-threatening is Rhinanthus minor – ‘yellow rattle’ – a hemiparasite (http://en.wikipedia.org/wiki/Parasitic_plant) on grasses, which is found in Europe, Russia, western Siberia, northern USA and Canada (http://www.kew.org/plants-fungi/Rhinanthus-minor.htm). Whilst it is generally recognised that such plants have major negative impacts on plant community structure via influence on host productivity and competitive ability, James Fisher et al. show that nutrient-rich leaf litter from R. minor has a positive effect on plant community structure (New Phytologist198: 222–231, 2013): ‘critically, in the case of grass and total community biomass, this partially negates biomass reductions caused directly by parasitism’. From sub-terranean to supra-terrestrial community impacts now, with another hemiparasite – mistletoes (http://en.wikipedia.org/wiki/Mistletoe) – and work by David Watson and Matthew Herring (Proceedings of the Royal Socirty, B279: 3853–3860, 2012). Having already been established as ‘keystone resources’ (http://en.wikipedia.org/wiki/Keystone_species) – species providing important resources for a broad range of taxa and determining local diversities in these habitats (Annual Review of Ecology and Systematics32: 219–249, 2001) – Watson and Herring experimentally investigated the role of Australian mistletoes such as Amyema miquelii (Loranthaceae, bog mistletoe; http://en.wikipedia.org/wiki/Amyema_miquelii) in eucalyptus woodland. After 3 years, sites from which mistletoe was removed lost, on average, a fifth of their total species' richness, 26·5 % of woodland-dependent bird species and more than one-third of their woodland-dependent residents. The researchers, from The Institute for Land, Water and Society at Australia's Charles Sturt University (http://www.csu.edu.au/research/ilws/) suggest that ‘nutrient enrichment via litter-fall is the main mechanism whereby the mistletoe promotes species’ richness, driving small-scale heterogeneity in productivity and food availability for woodland animals'. They further propose that this explanation applies to other parasitic plants with high turnover of enriched leaves, and that the community-scale influence of these plants is most apparent in low-productivity systems. I wonder if they had R. minor in mind? Prescience (http://bit.ly/14Z9K1K) is, after all, a virtue (http://en.wikipedia.org/wiki/Patience_Is_A_Virtue; http://bit.ly/Z3haNe)… [In the interests of fairness, it should be stated that Fisher et al. do cite Watson and Herring's paper – Ed.] Image: http://www.flagstaffotos.com.au/ (Creative Commons Attribution). An age-old conundrum is how many beans make five (http://bit.ly/10yXSPN)? Well, one for the 21st century is how many peas make two? The answer is surprising, and it's one, if the ‘pea’ in question is chickpea. Within 11 weeks of each other, two teams have published draft genome sequences of chickpea (Cicer arietinum). Rajeev Varshney et al. report the approximately 738-Mb draft whole genome (Nature Biotechnology31: 240–246, 2013; manuscript received 21 September 2012, accepted 21 December 2012), whereas Mukesh Jain et al. document 520 Mb (70 %; Plant Journal, in press as I write this; manuscript received 6 November 2012, accepted 4 March 2013). Questions of whether an incomplete genome draft is a legitimate draft genome aside, these sequences join the ever-growing list of sequenced plant genomes (http://bit.ly/ZvaA5j). But why two genomes? Well, the two groups have examined different ‘types’ of chickpea: Varshney et al. have tackled ‘kabuli’, Jain et al. have dissected ‘desi’. And this distinction is important because the two varieties have different properties, e.g. ‘kabuli’ types contain higher amounts of dietary fibre, particularly cellulose and hemicellulose (http://bit.ly/12z8IJi). Additionally, ‘desi’ is cultivated mostly in the Indian subcontinent, Ethiopia, Mexico and Iran, whereas ‘kabuli’ is mainly grown in southern Europe, northern Africa, Afghanistan, Pakistan and Chile (http://en.wikipedia.org/wiki/Chickpea). Furthermore, ‘chickpea is the second largest cultivated grain food legume [in the wonderful, but sadly fictional, plant family Fabulaceae] in the world, grown in about 11·5 million hectares mostly by resource poor farmers in the semi-arid tropics. The highly nutritious, drought-tolerant chickpea contributes to income generation and improved livelihoods of smallholder farmers in African countries … and is crucial to the food security in India’ (http://bit.ly/ZcXvrk). So, given the importance of chickpeas, arguably the more genomes – draft or otherwise, complete or not – the better, not least in helping efforts to develop more drought-tolerant forms (Hari Upadhyaya et al., Frontiers in Plant Physiology3: 179). [If all of this ‘genome tussle’ sounds a little familiar, readers might recall the controversy surrounding the ‘two’ genomes of pigeon pea (Cajanus cajan), which was summarised in this column in April 2012 (http://bit.ly/10LbupY). Arguably, no other genomes have caused so much controversy (unless it's Henrietta Lacks'! http://bit.ly/Zve3Rs) – Ed.] Image: Kirti Poddar/Wikimedia Commons.

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