Tag Archives: Plant Biology

Timeless inner beauty…

Image: P. Cuttings’ personal archive.

Image: P. Cuttings’ personal archive.

When trying to appreciate something, it’s often remarked that it is the ‘inner beauty’ that’s important. In which case the plant cell biologists who probe the details within cells (and often illuminate them in all their glorious pin-point precision and fluorescent beauty with immunofluorescent techniques*) must not only, as scientists, be seekers of truth (for is it not writ, in scientia veritas?)  but also be true searchers after beauty. And if something’s really beautiful/true then it has a quality that transcends normal, mortal values and should be permanent. Is that correct? Well, the palaeopteridophytological work of Benjamin Bomfleur et al. may just be the definitive proof of that notion of transcendental permanence. Using language unusual for a serious, sober, scientific article, they describe the fossilised stem of a royal fern (family: Osmundaceae) in Lahar deposits (of putative Early Jurassic – Pliensbachian – date; 189.6–183 million years ago) from Korsaröd in Scania (southern Sweden) as having cellular details that are ‘exquisitely preserved’. Amongst the sub-cellular features discernible are parenchyma cells in the pith and cortex that show preserved membrane-bound cytoplasm, cytosol granules and putative amyloplasts (starch-bearing bodies). Furthermore, most cells contain interphase nuclei with conspicuous nucleoli! And – even more remarkably? – Supplementary Fig. S6 shows detail that is interpreted as signs of necrosis and programmed cell death(!). Whilst more importance is attached by the authors to the fact that the genome size of these reputed ‘living fossils’ has remained unchanged over at least 180 million years (and is understandably viewed as a ‘paramount example of evolutionary stasis’), the degree of internal preservation of cell contents is so good (see Figs S4 and S6 in the paper’s supplementary material!) I’m sure many extant workers could only hope to emulate such faithful preservation in their current work! So, not only is a thing of beauty a joy, it is a joy… forever (or 180 million years at least – long enough for you?). Somebody should write a poem about that!

* For a scientific haiku poem about this, may I humbly suggest the following? Page 15 at the Art Science Movement’s website.


[For an award-winning science journalist’s take on Bomfleur et al.’s Science paper, see Jennifer Frazer’s blog. Full-text of the paper – with supplementary pages – appears to be available in front of a paywall via the DiVA portal. And with apologies to our readers for the shameless self-advertisement by Mr P. Cuttings for his ‘poem’! – Ed.]

Better together…

Image: pixabay.com.

Image: pixabay.com.

No, this is not a belated bit of biased support for the Scottish referendum on independence from England  (which was rejected by those who voted and thereby prevented the United Kingdom becoming the anagrammatically amusing Untied Kingdom…). Rather, it is recognition that – at least in nature – sometimes things do work better when two partners co-operate rather than work against each other. Take for example the reef-building corals – an intimate mutualistic symbiosis between a unicellular alga, a dinoflagellate and an animal, the coral polyp. Put very simply, the alga provides much of the polyp’s food requirements by dint of its photosynthesis, which ultimately allows it to make the massive coral reefs. Although warm-water coral reefs are the basis of extremely rich and biodiverse ecosystems, they are nutritionally poor. This ‘nutrient paradox’ – originally recognised by Charles Darwin (is there any branch of biology that doesn’t have a contribution from this venerable Victorian?) – has traditionally been presumed to be due to very tight cycling/recycling of nutrients within the ecosystem (and the abundance of mutualistic symbioses therein, amongst other factors…). However, a new twist to this nutrient tale has recently been proposed by Orr Shapiro et al. They have revealed that, far from being static structures dependent upon the vagaries of currents to bring nutrients to them and remove waste products, the coral polyp actively generates micro-currents and eddies that promote nutrient inflow and exchange of materials. Using externally located cilia, these miniature structures whip up ‘vortical flows’ immediately adjacent to the epidermal surface, which reduces the exchange-limiting boundary layer at that site thereby facilitating mass transport between coral and the ocean. And in the way of all good discoveries, there are potential spin-offs to other areas of study. In this instance the team posits that investigation of these surface-situated cilia could be used as an alternative to the study of more-inaccessible, internalized cilia, e.g. those in the airways of animals. Thus, there may be unpredictable benefits for biomedicine from this photosynthetically dependent marine mutualism (I know, plants lighting up the path for others to follow – again!!). I’ve oftentimes wondered what the polyp brought to this relationship – aside from providing a chalky castle for the enslaved, hard-working alga. Well, I guess we now know, and it’s reassuring to discover (finally…?) that this intriguing symbiosis is much more mutual than we might previously have imagined.


[A video of this phenomenon can be seen on YouTube. The irony of internalization of the dinoflagellate symbiont – which, as its name implies, usually has flagella (two in this case, like much bigger versions of cilia)  – within the coral polyp and its consequential loss of its flagella on the one hand, and the importance of the polyp’s cilia (pale imitations of flagella?) in and to this relationship on the other, is not lost on Mr P. Cuttings. And this item gives a whole new meaning to the phrase ‘on the lash’ because cilium is Latin for eye-lash… – Ed.]

Thirsty? Then suck on a stone!

Golden gypsum crystals

Golden Gypsum Crystals from Winnipeg. Image: Rob Lavinsky/Wikimedia Commons

Whilst it is claimed that only the taxman can get blood out of a stone, it seems that some plants can abstract water from stone-like minerals.

Arguably, ahead of light, water is the most important abiotic factor that plants need and obtain from the environment. Although water is essential to plant life, it is not always available in sufficient amounts, and plants have evolved many adaptations that enable them to cope with water-limited environments – e.g. xerophytes in extremely arid areas, and halophytes in saline habitats. One strategy that was hitherto unrecognised is the extraordinary (I don’t think that’s too strong a word to use) ability of some plants to obtain large parts of their life-giving and -sustaining water from a mineral in the soil.

Analysing the isotopic composition of xylem sap in the rock rose Helianthemum squamatum, Sara Palacio et al. showed that it was similar to that of the water of crystallization in gypsum – CaSO4.2H2O, an inorganic mineral common in the plant’s environment. And, significantly, the composition of the water in the xylem differed from that of free water – i.e. that which is freely available within the soil (albeit in short supply!), the more usually assumed water source for plants. This therefore provided strong evidence that the plants were using the mineral as a water source – especially in the summer months when it accounted for 70–90% of the water used by these shallow-rooted plants.

Several other ‘coexisting shallow-rooted, sub-shrub species’ (the gypsum-specialist Lepidium subulatum – a gypsophyte – and the ‘non-specialists’ Linum suffruticosum and Helianthemum syriacum) behaved in an isotopically similar way to H. squamatum, suggesting that this phenomenon may be a widespread strategy of water-extraction by plants in this environment.

Although it is as yet unclear how the plants get hold of the water from this unusual source, it is suggested that high temperatures in the environment may cause the water to evaporate from the mineral when it can then be acquired by the plant.

Whilst this is a neat enough solution (pun recognised, but not intended!) for life on Earth, the authors conclude that ‘given the widespread occurrence of gypsum in dry lands throughout the Earth and in Mars, these results may have important implications for arid land reclamation and exobiology’. So, botanical research that may truly be ‘out of this world’!

[Intrigued by these intriguing gypsophytes? Then why not indulge your interest and read more of Sara Palacio et al.’s research in ‘Plants living on gypsum: beyond the specialist model’? – Ed.]

Brilliant bird-brained bryophyte diaspore diaspora…

many mosses

Ernst Haeckel, Kunstformen der Natur. Leipzig and Vienna: Verlag des Bibliographischen Instituts, 1904.
Pin for later

There is an ancient and time-honoured association – maybe co-evolution even – between birds and flowering plants, e.g. in respect of pollination and dispersal of the fruits/seeds of the latter by the former. Now, at the other end of the evolutionary spectrum of the Plant Kingdom, is news of another avian–Plantae link-up as Lily Lewis et al. present evidence for long-distance transport of bryophyte ‘bits-and-pieces’ in the plumage of transequatorial migrant birds.

Bryophytes – a general term that embraces mosses, liverworts and hornworts – are so-styled ‘lower plants’ that have occupied the planet for megamillennia and have many important ecological roles. But, like the other members of the Plant Kingdom, bryophytes are essentially immobile and fixed to one location. This poses problems to any enterprising moss, etc., that wants to boldly go, seek out, occupy and colonise new areas, in order to command resources and help to ensure its survival in the dog-eat-dog jungle that is the natural world.

However, evolution has equipped these cryptogams with a phase of the life cycle that is potentially mobile, the spore stage. Transfer of those spores away from the parent plant – and their subsequent germination, establishment and development into individual bryophyte plants – reduces competition for resources between parent and offspring, and extends the area occupied by that species.

Consequently, exploiting agents that can contribute to wide-ranging dispersal of those spores represents a considerable boost to aspirations of territorial gain for an ambitious ‘lower plant’. But reliance on spores to spread the species can be risky; e.g. if the bryophyte taxon concerned is dioicous and it either doesn’t travel along with another spore that gives rise to, or to a place that already contains, the corresponding male/female gametophyte in the new neighbourhood. Which is why Lewis et al.’s work is of considerable interest because – and despite the headline in Scientific American’s news item on the subject – the bird-assisted moss migration is not really about spores, but diaspores.

Although a diaspore (or ‘disseminule’) can be defined as ‘a reproductive plant part, such as a seed, fruit, or spore, that is modified for dispersal’, the definition is usually broadened to include any plant part that could result in the establishment of a new individual. Thus, it includes not only bryophyte spores, but also fragments of established plants, too.

Sampling the plumage of bird species in their Arctic breeding grounds – prior to their South Pole-ward migration – the team found examples of diaspores not only of bryophytes, but also of green algae/cyanobacteria, and fungi. The presence of these putative propagules amongst bird feathers thus seems to establish this phenomenon as another instance of ectozoochory (transport of plant – and algae/fungi/bacteria! – propagation units on the external surface of an animal).

But just because these passengers may be present at the start of the journey doesn’t necessarily mean that they arrive at the carrier’s destination, which in some cases – such as the red phalarope and the semipalmated sandpiper – is the southernmost tip of South America; e.g. could the disseminules be consumed during preening as a sort of in-flight snack by the birds…?

And – as the investigators recognise – even if diaspores arrive, this doesn’t demonstrate that they are viable and could become established in the new home. But it’s another step towards unlocking the mystery of how the disparate bipolar distributions of certain taxa of bryophytes, etc. could be established and maintained. Whether this counts as ‘blue-skies’ research I’m not sure, but it’s a topic that’s certainly got legs and could well take off!

[And if you’re interested in seeing of some of the pre-publication comments on the bryophyte paper, they can be found online. And for more on the world of moss, I recommend Jessica M. Budke’s blog site. – Ed.]

M people and the ‘B’ word…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

No, this is not an item about M People, an ‘English house music band which formed in 1990 and achieved success throughout most of the 1990s’, nor about using profane language… Anyway, how would any of that be relevant to a straitlaced, sober, serious botanical news round-up that is the hallmark of a P. Cuttings item? It is about the phenomenon (I don’t think that’s too strong a word) known as ‘Dr M’. If you’ve not encountered this gentleman, then you should – we can probably all learn a little from him in our eternal quest to big-up botany and help to enthuse the next generation of plant biologists (or, at least, attempt to engender plant appreciation into the citizens of tomorrow). Dr M is the moniker of Dr Jonathan Mitchley, botanist and plant ecologist who goes WILD about teaching plant identification at the University of Reading (UK), and also acts as an ecological consultant with RSK Ltd. Looking like one imagines the Peter Pan of phytology should look like, his grinning visage beams botanical radiance upon all who chance upon his various web-based antics. His enthusiasm for all things verdant seems boundless and is evident in his varied offerings, such as his blogvideo-based plant ID quizzes and his YouTube-tastic Poaceae song. Maybe all of his outputs may not be to everyone’s taste, but they’re worth a look – you are highly likely to find something you can ‘borrow’ to enhance your own teaching of botany. In any event it’s really uplifting to see Dr M and ‘his people’ having so much botanical fun! As Dr M himself is wont to say, ‘Rock on, Botanists!!!’ Indeed (!).


[The true diehards amongst you might like to consider the extended-play, blooper-enhanced version of the Poaceae song on YouTube. Right, now what is the collective noun for a group of botanists? Answers, on a postcard-sized sheet of herbarium paper, please to… And in breaking news – well it was when this piece was penned – Dr M is now Associate Professor of Field Botany at the University of Reading – Ed.]

New plant journal

Image: Wikimedia Commons.

Image: Wikimedia Commons.

It just had to happen, but we didn’t know it would take nearly 150 years to come to fruition. And fruition is an apt word because the creation of a new botanical journal has recently been announced by the publishers behind Nature, the world’s premier general science journal. Imaginatively entitled Nature Plants, this new organ is due to be officially published in January 2015 but already has interweb presence with a blog and can be ‘followed’ on such social media as Facebook and Twitter. Its aim is to provide a fully rounded picture of the most accomplished and significant advances in the plant sciences, and will cover ‘all aspects of plants be it their evolution, development or metabolism, their interactions with the environment, or their societal significance’. Furthermore, along with original research, Nature Plants will also deliver ‘Commentaries, Reviews, News and Views’ from across the full range of disciplines concerned with the plant sciences (i.e. a bit like the Annals of Botany…). However, with topics covered in the journal including (deep breath) ‘agronomy, genomics, biochemistry, metabolism, biofuels, metabolomics, biophysics, molecular biology, cell biology, photosynthesis, defence physiology, development, plant–microbe interactions, disease resistance, proteomics ecology, secondary metabolism, economics, sociology, evolution, symbiosis, food security, systems biology, forestry and water use’, I do hope they leave something for other – more established – botanical journals, such as the Annals of Botany!

[Have others heard that the original Nature – in keeping with its soon-to-be somewhat impoverished science coverage – is being retitled Nature Cosmology, Palaentology and Non-botany? Whilst we wish this new venture well, it will be interesting to see if anybody publishes in the new journal because, and despite the undoubted cachet and kudos associated with the word Nature in the article’s citation, it won’t have an Impact Factor (IF) for a few years. Now, who wants to risk having publications on their CV in journals with no IF with potential damage to promotion prospects and career advancement (not that IFs should be used for such purposes – see e.g. EASE statement on inappropriate use of Impact Factors? Just saying. – Ed.]

Plants, the inside story

Image: Anton Joseph Kerner von Marilaun and Adolf Hansen. Pflanzenleben: Erster Band: Der Bau und die Eigenschaften der Pflanzen. Kurt Stüber, 1913.

Image: Anton Joseph Kerner von Marilaun and Adolf Hansen. Pflanzenleben: Erster Band: Der Bau und die Eigenschaften der Pflanzen. Kurt Stüber, 1913.

As well-read botanists, readers of this blog site are probably quite knowledgeable on the subject of epiphytic plants, which are plants – such as mosses, liverworts, ferns, cacti, orchids and bromeliads – that live on the outer surface of other plants.  However, most of us are probably less familiar with the concept (and reality…) of endophytic plants, which live within the body of other plants. Or, where we’ve heard of the term it is likely to be more in the context of endophytic fungi or bacteria. Strange as it may seem, endophytes can also be found amongst the angiosperms. And, by way of giving a ‘shout-out’ for those curious plants who’ve adopted this most couch-potato of lifestyles, I’m pleased to advise that a new key (plus consideration of the systematics of this worldwide family, a map, and colour photos of most species’ sexual organs…) to the Apodanthaceae (a family of two genera comprising 10 species) has been published by Sidonie Bellot and Susanne Renner

Living as endo-parasites permanently inside trees or shrubs of the families Salicaceae or Fabaceae, these plants emerge only to flower and fruit; consequently the Apodanthaceae is among the least-known families of flowering plants. Since the plants do not carry out any photosynthesis of their own, they are completely dependent upon their host for their nutrition (i.e. they are also holoparasitic). Endophytes, curious organisms(!). However, probably more famous is the equally holoparasitic relative of Apodanthes and Pilostyles, Rafflesia. Notwithstanding the smallness of its vegetative body, R. arnoldii has the honour of producing a flower >100 cm in diameter and weighing up to 10 kg. Amongst its other claims to fame – or should that be infamy? – is the smelliness of the flower’s odour, which is reminiscent of rotting flesh and which has earned it the rather ghoulish appellation of ‘corpse flower’. Furthermore, as well as stealing nutriment from its host, Rafflesia has also famously ‘borrowed’ many genes from the vine within which it resides, by the non-reproductive DNA transmission process known as horizontal transfer of genesSo, and although allegedly named in honour of Sir Thomas Stamford Raffles (both the ‘Father of Singapore’ and the ‘Father of the London Zoo’), this curious case of karyo-kleptomania seems more reminiscent of the antics of one A. J. Raffles, ‘gentleman thief’! And there’s even more bizarre genetic antics with the ‘suggestion’ (scientist’s code ‘for highly likely probability’…) that R. lagascae may be devoid of a chloroplast genome. I don’t know – flowering plants devoid of leaves, roots, shoots and some without chloroplast DNA. Are they really plants? Discuss!

Sugar versus Auxin: which is dominant?

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Of the plethora of aspects of plant growth and development that the hormone (OK, plant growth regulator…) auxin is implicated in/involved with (e.g. embryo development, leaf formation, phototropism, gravitropism, fruit development, abscission, root initiation and development…), surely one of the most enduring is apical dominance.

Apical dominance is the phenomenon whereby the outgrowth of buds on the side of a shoot is suppressed in favour of growth by the apical bud (hence its name…). Maintenance of this suppression has long been assumed to be due to the production of auxin by the apical bud and its transport down the stem, which effectively keeps the lateral buds in check. Understandably, outgrowth of lateral buds upon removal of the apical bud – and its associated auxin-production and outflow – is a key bit of evidence for the role of auxin in this phenomenon.

Just as you should never (ever…) take anything for granted in science (or anything else), it’s rather satisfying to note that work by Michael Mason et al. – and rather pleasingly from ‘down under’ – has seemingly burst that little bubble of plant physiological certainty.  The primarily Australia-based team show that bud outgrowth following apical bud removal takes place >24 hours before changes in auxin content in the adjacent stem, i.e. ‘initiation of bud growth after shoot tip loss cannot be dependent on apical auxin supply’. However, upon removal of the shoot tip, sugars not only accumulate in axillary buds, but do so within a timeframe that correlates with bud release. Rather than auxin being the main lateral-growth suppressant, the team conclude that enhancement in sugar supply is both necessary and sufficient for suppressed buds to be released from apical dominance. Ah, the sweet smell of success? G’day BrucesSheilas… and ‘possums’ everywhere!

[And if this item has initiated a craving for more sugar-based botanical items, may I recommend Winnie Lin et al.’s Letter investigating nectar secretion and the role of the sugar transporter, aptly named SWEET9? – Ed.]

Dodgy photos dog phytology

Image: Wikimedia Commons.

Image: Wikimedia Commons.

It has oft been claimed that a picture is worth a thousand words. In the case of certain images in Klementina Kakar et al.’s study entitled ‘CLASP-mediated cortical microtubule organization guides PIN polarization axis’ it seems quite clear that many more than a thousand words have been written about them. Why? The normally genteel world of botanical research has been shaken, stirred and shocked to its very core by a retraction of that paper – which purported to identify the molecular machinery that connects the organisation of microtubules to the regulation of the axis of polarisation of auxin-transporting PIN proteins (which membrane-sited molecules are needed for transport of the plant hormone auxin across plasma membranes and thereby help to maintain polarity of growth and development within the plant). Relating as it does to fundamental aspects of plant growth and development and such phenomena as gravitropism, this is an important finding and understandably published in a very high-impact and influential journal. So what’s gone awry? A retraction is, after all, a very serious state of affairs. Well, and in the words of the same four authors of the original paper, ‘after re-examination of this Letter [this is how Nature articles are formally described], concerns with some of the reported data were raised. It was found that two confocal images were near-identical in panels of Figure 3 and two confocal images were re-used in panels of Figure 4, and that some gel images were inappropriately generated by cutting and pasting of non-adjacent bands. Therefore, we feel that the most responsible action is to retract the paper. We sincerely apologize for any adverse consequences that may have resulted from the paper’s publication’. For more on this, visit the various items at the Retraction Watch* website. Fortunately – for those unaware of this from media reports, etc, but who might otherwise come across the article in their literature searches, the PubMed entry for the original Nature paper does make mention of its subsequent retraction, and provides a link to the retraction notice. Although I don’t know if the paper’s retracted status is indicated on all search engines… However, in the scrabble to find appropriate literature to cite in one’s work, one might overlook that notification. Is this therefore a weakness in the otherwise laudable retraction process/system whereby subsequent readers of those papers may not be aware of their retraction? Maybe we need a form of historical revisionism reminiscent of the rewriting of history in George Orwell’s classic novel Nineteen Eighty-Four to expunge such items from the record totally so that they’re never ever found…? Hmm, what would historians of science make of that? Do let us know!

* Retraction Watch is a blog that reports on retractions of scientific papers. Launched in August 2010 it is produced by science writers Ivan Oransky (executive editor of Reuters Health) and Adam Marcus (managing editor of Anesthesiology News).

[For more on the costs associated with retractions, check out Tracy Vence’s commentary at The Scientist.  And with such sobering news, if you are concerned that retractions can unduly affect one’s career, Virginia Gewin has some words of comfort. But, if you want more retraction stories, why not check out last year’s ‘Top 10’? – Ed.]

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…