Tag Archives: Botany

The trees have it…

Image: Stefan Laube/Wikimedia Commons.

Image: Stefan Laube/Wikimedia Commons.

Trees, those magnificent, organic, large – sometimes huge – woody constructions continue to fascinate and inspire all who stop, stand and stare up (and up, and up…) at them. So here’s a selection of tree-based items to maintain – or maybe even initiate? – the phenomenon of arborifascination. But first a question: why did the three-toed sloth come down from the trees?

Answer: to defecate! Sloths are considered to be amongst the most, well, er, slothful of animals that, anecdotally, spend most of their time in trees, doing ‘not a lot’, apart from eating tree leaves [they are arboreal herbivores, after all; Tree Use No. (TUN) 1]. However, not only is this descent to the ground energy-consuming, it also exposes the sloth to potential predators; so why would they risk it? Work by Jonathan Pauli et al. may have the answer to this otherwise inexplicable behaviour. Three-toed sloths* harbour moths, inorganic nitrogen (N) and algae (e.g. green algae Trichophilus spp.) within their fur. The lipid-rich algae are eaten by the sloths and presumably supplement their diet of leaves. By leaving the tree for defecation, the fur-residing moths are transported to their oviposition (egg-laying) sites in sloth dung, which subsequently facilitates further moth colonisation of sloth fur. Since those moths are ‘portals for nutrients’, levels of inorganic N (potentially from moth excreta) in sloth fur increase, which in turn fuels algal growth. As the researchers conclude, ‘these linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle’. Wow! I will never look at a three-toed sloth in quite the same way again.

Also challenging perceived wisdom is work by Marc Ancrenaz et al. Traditionally, orangutans (the world’s largest arboreal mammal) are assumed to be obligate arborealists, swinging seemingly effortlessly from tree to tree (TUN 2) as they navigate their lofty aerial neighbourhood. However, observations of terrestrial activity by these primates in the wild begs the question, why? Hitherto this activity was considered to be a response to habitat disturbance, but Ancrenaz et al. found no difference in instances of this behaviour in disturbed versus non-disturbed areas. They therefore propose that terrestrial locomotion is part of the Bornean orangutan’s natural behavioural repertoire and may increase their ability to cope with at least smaller-scale forest fragmentation, and to cross moderately open spaces in mosaic landscapes. So, it seems that even orangutans can have a bit too much of the ‘high life’ at times.

Finally, a terrestrial–aquatic organism that’s going up in the world. Reviewing evidence of tree-climbing activity in extant crocodilians (crocodiles and alligators), Vladimir Dinets et al. suggest it is much more widespread than previously considered and ‘might have multiple functions’, e.g. as an alternative site for thermoregulation (TUN 4), or increased detectability of prey (TUN 5). So, there you have it, ‘tons’ of alternative tree uses! Trees, helping to make the world an even more amazing place.


* Two-toed sloths don’t go in for this more energetic activity – and have lower densities of moths, lower N levels and reduced algal biomass in their fur…

Colourfully cunning cryptoflorigraphic conundrum

Image: From the ‘Voynich manuscript’.

Image: From the ‘Voynich manuscript’.

Botany is not without its mysteries. And one that’s previously eluded solution for 600 years or so is that of the so-called Voynich manuscript, an illustrated codex (a book made up of a number of sheets) consisting of about 240 pages, hand-written in an unknown writing system. Carbon-dated to the early 15th century, there are nevertheless suggestions that it might not be an ancient language but a hoax. And, despite containing many images of plants and other biological entities, its message and purpose has remained obscure (although an imaginative botanical interpretation is that it might represent a mediaeval plant physiology treatise). However, Stephen Bax, Professor of Applied Linguistics at the University of Bedfordshire (UK) has now claimed to have begun to decipher the manuscript’s text.

Progress is slow, but amongst the first few words to have been revealed are juniper, taurus, coriander, Centaurea, chiron, hellebore, Nigella sativa, kesar and cotton. A confident Bax declared, ‘… my research shows conclusively that the manuscript is not a hoax, as some have claimed, and is probably a treatise on nature, perhaps in a Near Eastern or Asian language’. Clearly, some way to go before we have a final, complete version, and can use it as a set text in plant physiology classes (so don’t throw out Taiz & Zeiger’s Plant Physiology just yet!). But another ancient manuscript whose purpose is more obvious is the Tractatus de Herbis (‘Treatise on Medicinal Plants), a manual of materia medica [‘a Latin medical term for the body of collected knowledge about the therapeutic properties of any substance used for healing (i.e., medicines)’] compiled during the 15th century. This tome has been reproduced in a limited edition facsimile replica of 987 copies (price available ‘on request’, though I suspect that if you’ve got to ask how much it is, you can’t afford it…). This limited edition is accompanied by a full-colour commentary volume by Alain Touwaide,Research Associate of the Department of Botany at the Smithsonian National Museum of Natural History, USA and Scientific Director of the Institute for the Preservation of Medical Traditions at the Smithsonian in Washington, DC (USA).

[If you want to view the Voynich manuscript – for free! – it is available on-line. Even if the majority of the words are elusive, the images are quite wondrous… For more Voynich images and interpretations – e.g. putative plant identifications – Ellie Velinska’s blog is worth a visit  – Ed.]

So what ARE the 7 most important plants?

A while back Annals Editor Pat Heslop-Harrison was asking what ten plants should botanists know about. I’ve taken it a bit further with a Buzzfeed post on the 7 Plants That Changed Your Life.

I’ve tried to pick seven plants with global consequences, but I’m not entirely happy with the list. The seven plant limit means I’ve missed out a lot of important plants. For example, there are no marine plants on the list. Nothing that really address important evolutionary steps that plants made, so no mosses or ferns,

So what plants would you add to the list and why? I’d be interested to see if our readers could compile another list of another seven plants that would be equally good, or better.

Leave your suggestions below, or at Buzzfeed or on our Facebook page.

An explosive mix: C4, C3, C2 and CCM

Image: Ninghui Shi/Wikimedia Commons.

Image: Ninghui Shi/Wikimedia Commons.

As if the task of explaining the details of the ‘normal’ C3 Calvin Cycle of photosynthesis (P/S) to our students isn’t hard enough, we also need to appraise them of C4 P/S  – with its spatial separation of initial CO2 fixation into organic acids in mesophyll cells and its subsequent release and re-fixation via the enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase)  into the photosynthetic Calvin Cycle proper within bundle sheath cells*. As testing and trying as that is, nature always has to go one ‘better’, and ‘spoil’ things. So, the fin-de-millennial recognition of a variant of this C4 P/S in which initial CO2 fixation into 4-carbon acids and its subsequent release and re-fixation into the Calvin Cycle of C3 P/S takes place within a single cell is kind of unwelcome (no matter how fascinating it is!). Well, anyway, it exists – in such higher plants as Suaeda (Borszczowia) aralocaspica, Bienertia cycloptera, B. sinuspersici and B. kavirense, all in the Chenopodiaceae (now within the Amaranthaceae) – so we need to get over it, and try and understand it. And that’s what Samantha Stutz et al. have been doing. Although these plants perform spatial separation of the two CO2 fixation events within a single mesophyll cell, they do so using two distinct – dimorphic – chloroplasts. Already known is that light is necessary for development of the dimorphic chloroplasts in cotyledons in B. aralocaspica. In the dark they only have a single structural plastid type (which expresses Rubisco): light induces formation of dimorphic chloroplasts from the single plastid pool, and structural polarization leads to the single-cell C4 syndrome. The aim of Stutz et al.’s study was to determine how growth under limited light affects leaf structure, biochemistry and efficiency of the single-cell CO2-concentrating mechanism. Overall, the team found that the fully developed single-cell C4 system in B. sinuspersici is robust when grown under ‘moderate light’. Where might this sort of work be going? Well, whilst it is interesting for its own sake – the pure pursuit of knowledge – it has a more applied dimension too. Central to all of this single-cell photosynthetic biology and biochemistry is the concept of CCM, carbon-concentrating mechanisms, whereby levels of CO2 are increased in the vicinity of Rubisco so that it favours photosynthesis – CO2-fixation – over photorespiration (so-called C2 photosynthesis) which uses O2 as substrate and consequently reduces photosynthetic efficiency. Well, in bids to replicate some of the greater photosynthetic efficiency of C4 plants (largely by virtue of their diverse CCMs…), an attractive notion is to engineer various forms of CCM into C3 crop plants. This approach is exemplified in the work of Mitsue Miyao et al., where they attempted to exploit enzymes of the facultative C4 aquatic plant Hydrilla verticillata (which engages in single-cell C4 P/S) to convert rice from its typical C3 P/S into a single-cell C4 photosynthesiser. Although they didn’t achieve their goal (and it’s good to know that ‘negative’ results can still be published!), their article is an interesting and soul-bearing account of the lessons learned in this work. As we continue our quest for that elusive boost in photosynthetic yield, we’ll no doubt continue to exploit any biochemical variant on the photosynthetic theme that nature displays. Which begs the question: how many more variants exist amongst the 325,000 species of flowering plants (let alone all the algae and other members of the plant kingdom)? Seems like we need more plant anatomists, plant biochemists, plant physiologists – as well as plant taxonomists (see my last post on this blog) – after all!


* That’s C4 P/S as opposed to CAM (Crassulacean acid metabolism), which is also a version of C4 P/S but which involves temporal separation of the same two carbon-fixation events in plants such as pineapple, cacti and agave. However, CAM is hardly ever referred to as C4 P/S because the all-powerful Zea Supremacy lobby has commandeered the term for that spatially separated C4 version found in plants such as maize… but don’t get me started on that!


[Intriguingly, and in addition to its dimorphic chloroplasts, Suaeda aralocaspica has dimorphic seeds, which exhibit distinct differences in dormancy and germination characteristics. Now, they say that things come in threes, so what’s the third dimorphy about this iconic species…? – Ed.]

Cause for optimism (maybe not…)

Image: Wikimedia Commons.

Image: Wikimedia Commons.

As an ‘old-fashioned’ botanist my heart was gladdened to see that Number 1 in the ‘Top 10 most viewed Plant Science research articles in 2013’ from Frontiers in Plant Science was one that dealt with fundamental botany of the taxonomic kind. The paper in question was entitled ‘Angiosperm-like pollen and Afropollis from the Middle Triassic (Anisian) of the Germanic Basin (Northern Switzerland)’ and was written by Peter Hochuli and Susanne Feist-Burkhardt. Whilst that recognition may engender a feel-good view that plant taxonomy is doing rather well, Quentin Wheeler’s timely New Phytologist Commentary, ‘Are reports of the death of taxonomy an exaggeration?’, offers a more cautious interpretation. Commenting upon an article by Daniel Bebber et al., he concludes that plant taxonomy (though one suspects taxonomy of all biota fares as badly) is still in desperate need of greater attention – in terms of people to undertake the work and appropriate funding – as befits its importance to a true appreciation of the planet’s biodiversity and the inter-relationships between living things. Sadly, this state of affairs is unlikely to be helped by news that the Royal Botanic Gardens at Kew (London, UK) – one of the world’s premier centres of plant taxonomic endeavour – is in the midst of a funding crisis. Indeed, the situation is apparently so bad that ‘about 125 jobs could be cut as… Kew… faces a £5m shortfall in revenue in the coming financial year’. This must be particularly concerning since it comes shortly after news that visitor numbers to Kew increased by 29% last year compared to 2012. And this bad news on the plant taxonomy front is echoed in the USA where ‘too few scientists are being trained in agriculture areas of science’. So, there’s an insufficiency of people to grow the new crops that aren’t being identified because of the dearth of plant taxonomists. Where will it all end..?

[If you’re not put off by the precarious state of life as a taxonomist and want a little bit more of a career insight, then you could do much worse that read Elisabeth Pain’s ‘Science Careers’ article.  And for a welcome boost to publicising the plight of the endangered species known as Taxonomus non-vulgaris var. biologicus, see Tim Entwisle’s news article in The Guardian – Ed.]

One of a kind…

Image: Scott Zona/Wikimedia Commons.

Image: Scott Zona/Wikimedia Commons.

These articles have been going long enough(!) to be able now to report a successful outcome to a research project whose initiation was announced in a former news item entitled ‘Old meets new’. The project is the elucidation of the genome of Amborella trichopoda. “Amborella is a monotypic genus of rare understory [sic! What ever happened to understorEy??? - Ed.] shrubs or small trees endemic to… New Caledonia”.

Not only is this plant rare and monotypic – truly ‘one of a kind’! – but it is also probably the living – extant – flowering plant [angiosperm] that is closest evolutionarily to the earliest true first member of the angiosperm plant group, and may therefore be “the last survivor of a lineage that branched off during the dynasty’s earliest days, before the rest of the 350,000 or so angiosperm species diversified”. Given Amborella’s exalted status (which “represents the equivalent of the duck-billed platypus in mammals”), it is hoped that understanding its genetics will shed light on the evolution of the angiosperms as a whole. Indeed, the University of Bonn’s Dietmar Quandt is reported as describing Amborella as a more worthy model organism than Arabidopsis(!!!).

Since the angiosperms are probably the most ‘successful’ of all the groups in the Plant Kingdom (‘the land plants’, the Plantae), hopes are understandably high that unravelling the genome of Amborella – reported by the aptly named Amborella Genome Project – will lead to the identification of “the molecular basis of biological innovations that contributed to their geologically near-instantaneous rise to ecological dominance”. And accompanying the main nuclear genome article, Danny Rice et al. report on Amborella’s mitochondrial genome (mitochondria have some of their own DNA additional to that located in the nucleus) and find that numerous genes were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. So, as ancient as it is, Amborella was still prepared to ‘learn’ from the experiences of even older land plants – mosses – and plant-like algae (which are in a different kingdom entirely to the land plants, the Protista). Adopt and adapt: a life lesson for all living things, I suggest.

[For more on this fascinating story, visit the home of the Amborella genome database. And if you still need some ‘proper’ botany (after all this genomery), you need look no further than Paula Rudall and Emma Knowles’ paper examining ultrastructure of stomatal development in early-divergent angiosperms (including Amborella…).  Notwithstanding all of this understandable present-day excitement, I can’t help but think that the importance of Amborella was foretold many decades ago, as "popular-in-the-mid-1970s" British-based pop band Fox seemingly declared: "things can get much better, under your Amborella…". Indeed! So, arabidopsis had better watch out! – Ed.]

Why Botany is Important #epso2014

Society of Biology calls for investment in plant science This week guest author Charlie Haynes is AoB Blog’s roving reporter at the EPSO/FESPB plant biology Europe conference. This post is his pre-conference manifesto.


On the first day of the EPSO/FESPB plant biology Europe conference it’s worth considering why botany is important.

Like many others whilst studying GCSE and A Level biology I found the botanical themed part of the syllabus dull and uninteresting. I arrived at university to find myself surrounded by those with similar experiences in their schools. Not one person I met during my first year of Biological Sciences at Leicester said they wanted to be a professional botanist. Luckily I turned up to all of my lectures and found myself interested and maybe even enjoying some of the botany and ecology modules that I was initially less than thrilled about taking. But there are serious emerging issues in plant science and ecology that need more talent.

  • A burgeoning world population needs ever greater crop yields as people become increasingly affluent and demand a higher quality and quantity of food produce.
  • Climate change is increasing the incidence of severe weather conditions such as droughts and heavy rains. Some climate models show that with a temperature rise of 2 degrees Celsius by 2050 will lower wheat yields by an average of 50%.
  • Despite large scale agricultural enterprises, an estimated 50% of world food production is from small small farmers. Many of these are subsistence farmers. The average Vietnamese farm is approximately 340 times smaller than the average US farm. New innovative strategies need to help these farmers use this space effectively.
  • Disease can still strike harvests dead in their tracks destroying livelihoods and causing skyrocketing food prices.
  • With more individuals demanding a western style lifestyle, the need for fresh water is also climbing. A potato has a water footprint of 25 litres. A hamburger has a water footprint of an estimated 2400 litres. But we live on a planet where only 2.5% of all water is fresh water and much of this is trapped at the polar ice caps. Developing plants capable of reducing their water footprint is vital in some chronically dry regions.
  • Nutritional deficits and diseases account for millions of deaths and over 2 billion are malnourished. Not only does the total number of calories produced need to increase, but there also needs to be an increase in global dietary variance and quality.

Have I missed anything else blindingly obviously that screams a need for plant science in the 21st century?

If so please let me know in the comments below, I would love to hear from you!


Spotlight on macronutrients (…and finally): Magnesium and a food fight…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Whilst incorporation of essential elements into the body of the plant is undoubtedly important for and to the wellbeing of the plant, their presence in those green organisms constitutes a major source of elements that are also essential for animals that ingest plant matter. Consequently, plants provide an important source of elemental nutrition for us, whether by their direct consumption or via our feasting on the animals that ultimately feed on the plants. And different plants differ in their ability to provide those all-important nutrients.

Take for example, quinoaChenopodium quinoa – a so-called ‘pseudocereal’ that originated in the Andean region of South America.  A 185 g serving of cooked quinoa provides 29.6% of your RDA (recommended dietary allowance, now largely replaced by RDI – reference daily intake, ‘the daily intake level of a nutrient that is considered to be sufficient to meet the requirements of 97–98% of healthy individuals in every demographic in the United States’) of Mg. [Aha, the Mg connection – eventually…! – Ed.] Although this is not as high as, say, seeds of pumpkin, where a serving a third of that of quinoa provides 47.7% of Mg’s RDI, or spinach, which provides about the same RDI for Mg in an equivalent serving  (although with about a seventh of the calories) and is in the same family as quinoa (the Amaranthaceae), quinoa is pretty good. Plus, that same serving of quinoa can also provide high levels of other essential nutrients – 58.5% manganese (Mn), 40.1% phosphorus (P), 40% copper (Cu), and 18.3% zinc (Zn). Given these fairly fascinating food facts it is perhaps no surprise that quinoa – despite its 4000 years history of cultivation and consumption in places today known as Ecuador, Bolivia, Columbia and Peru – has been widely touted as a ‘newly discovered, up-and-coming’ food. So much so that – apparently (well, it somehow passed me by…) – 2013 was the United Nations’ International Year of Quinoa. But this ‘must-have’ food status is not without its problems,  and there are concerns that increased demand for quinoa has pushed up prices to the detriment of those people who traditionally used the crop as a staple of their diet in places like Bolivia.  When will this little planet of ours be free of battles over food?

[For a more in-depth nutrient analysis of quinoa, visit the George Mateljan Foundation’s website.  But, you might want to wait because – allegedly – Ethiopian tef  is set to overtake quinoa as the next ‘super grain’. Despite quinoa not really being a grain,  and tef producing probably the smallest grain in the world – you need approximately 150 of them to match the weight of a single grain of wheat  (and the apparent irony of Ethiopia feeding the rest of the world has not gone unnoticed). But flour produced from tef, unlike wheat, is gluten-free and suitable for those who suffer from coeliac disease, a digestive condition where a person has an adverse reaction to gluten, which symptoms include diarrhoea, abdominal pain, weight loss and feeling tired all the time  – Ed.]

Spotlight on macronutrients: Touchy-feely calcium…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Most essential plant nutrients exert their roles when integrated into organic compounds and macromolecular structures – e.g. nitrogen and sulphur (see previous blog items on those macronutrients). Others – such as magnesium (Mg) – may also act in their ionic form as ‘enzyme activators’. But calcium (Ca)  is almost in a class of its own as it acts – amongst other things! – as a so-called ‘second messenger’,  and participates in many processes of plant growth and development. As a second messenger, levels of Ca2+ in the cytoplasm vary dramatically in response to many environmental and developmental stimuli, which subsequently trigger different physiological responses.  Such a role for Ca is also relevant to interactions between plants and other organisms, as demonstrated by Lehcen Benikhlef et al. in the case of microbial attack.  However, their work goes even further than that because they showed that light ‘mechanical sweeping’ of leaves of arabidopsis led to development of a strong resistance to Botrytis cinerea (a necrotophic fungus that attacks plants and causes ‘grey mould’). This was preceded by a rapid change in Ca concentration and a release of ROS (reactive oxygen species),  and was accompanied by ‘changes in cuticle permeability, induction of the expression of genes typically associated with mechanical stress and release of biologically active diffusates from the surface’. OK, so, it’s a bit more than just Ca, but what a fascinating chain of events. Maybe we should all be handling our plants more often to encourage them to develop pathogen resistance. After all, they do talk of ‘healing hands’

Spotlight on macronutrients: Stressed-out sulphur…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Amongst its many roles in plants, sulphur (S) is found in two of the 20 standard amino acids that form proteins, namely cysteine and methionine, and is therefore important in crucial cell components such as membranes and enzymes. Sulphur is also present in the organic compounds that give plants such as onion, garlic and mustard their characteristic odours.  Sulphur is generally taken up from the environment by plants as the sulphate ion (SO42–), which is frequently produced by bacterial activity in the soil.  Well, as much as plants need sufficient amounts of S to maintain growth, development and ‘health’, some forms of S in the environment can be damaging. Take for example H2S – hydrogen sulphide, a gas with the ‘characteristic foul odor of rotten eggs’ – which is found naturally in oxygen-poor areas as bacteria metabolise SO42–. Sediment-derived H2S can impact deleteriously on the growth and health of seagrasses  – flowering plants that live a submerged existence and that provide important marine habitats often covering large areas (up to 600 000 km2 of the oceans), which, because of their similarity to terrestrial meadows, are termed seagrass meadows.  In view of the inter-relatedness of marine ecosystems, damage to seagrass stands can have knock-on effects upon such iconic habitats as coral reefs.  Monitoring seagrass health is therefore important. And an important diagnostic technique to assess seagrasses’ well-being has been developed by Kieryn Kilminster et al., and has a S dimension. Outwardly, seagrass that is ‘compromised’ may look healthy, so an internal diagnostic test is needed to indicate its state of health. Such a test was provided when the Dano-Australian team discovered that elemental S accumulated in tissues of the seagrass Halophila ovalis when their environment was stressful. The incorporated sulphur resulted from the plant’s uptake of H2S from the sediment, whose microbial production was in turn an indication that the sediment had become anaerobic, which is a stressful state of affairs for the aerobic seagrasses… Another marine–sulphur–stress dimension has been revealed by Melissa Garren et al. (The ISME Journal in press) for hard corals – those mutualistic symbiotic organisms that comprise an animal coral polyp and an internalised microalga, a zooxanthella. When the coral Pocillopora damicornis was heat-stressed (to 31 oC), concentrations of DMSP (dimethylsulphoniopropionate) in its mucus increased 5-fold and the chemotactic response of the pathogenic bacterium Vibrio coralliilyticus was enhanced. The bacterium appears to be using the DMSP as an ‘infochemical’ to home in on stressed coral hosts, which it subsequently attacks. Vibrio coralliilyticus is associated with many coral diseases and infects them at temperatures above 27 oC. (Nikole Kimes et al., The ISME Journal 6: 835–846, 2012). And what is the relevance of all of this? Think heat-stress, think global warming. Interestingly, DMSP – which is produced by a wide range of marine algae when variously ‘damaged’, not just heat-stressed corals – is the precursor for DMS (dimethylsulphide), which ultimately acts as a nucleating agent for cloud formation in the atmosphere. The clouds can act as reflectors of some of the incoming solar radiation, which would otherwise serve to increase the temperature of the Earth (global warming). Thus, DMS might actually contribute to global cooling (and features in the CLAW Hypothesis), and which DMS may have been formed from DMSP produced by corals as a response to global warming… Nature: she’s complicated(!). For more information on the range of S-compounds in plant biology, see Katharina Gläser et al.’s paper that explores the so-called ‘sulphur metabolome’ of arabidopsis.


[By way of fuelling the debate, Mr Cuttings says that he will continue to spell sulphur with a ‘ph’. He knows the ‘f-spelling’  is the standard form of spelling for this element in ‘chemistry and other technical uses’, but he prefers consistency of spelling, so SULPHUR (NOT sulfur…), please. And anyway, our cousins across the Atlantic pond have won the war and got us all to use ‘program’ for those computer programme things…, so let’s make a principled stand; there’s no ‘f’ in sulphur! – Ed.]