Tag Archives: Biodiversity

Host specificity in vascular epiphytes: a review of methodology, empirical evidence and potential mechanisms

A considerable number of plants depend on structural support by other plants. To understand their diversity and ecology, it is essential to know how strongly potential host species differ in their suitability as hosts. A new review in AoB PLANTS by Wagner et al. focuses on vascular epiphytes, i.e. structurally dependent plants that do not parasitize their hosts. Despite a longstanding interest in the topic, knowledge on the strength of their host specificity is still scanty. This is arguably due to conceptual confusion, but also because of the large complexity of the study system, which makes quantifying host specificity in the field rather challenging. The authors conclude that future research should use a more comprehensive approach by (i) determining the relative importance of various potential mechanisms acting locally and (ii) testing several proposed hypotheses regarding the relative strength of host specificity in different habitats and among different groups of structurally dependent flora.

Half measures don’t work when restoring marine forests

Would you recognise a desert if it was covered in water? What I mean by that is if somewhere that should be covered in forest were barren and empty, would you notice? A paper in PLOS One outlines why it matters.

Seaweeds (macroalgae) are the “trees” of the oceans, providing habitat structure, food and shelter for other marine organisms…

Kelp forest

Forest-like kelp at San Diego aquarium. Photo Swandieve/sxc.hu

It’s easy to overlook the importance of marine plants if you’re not a scuba diver. From the shore one patch of sea looks much the same as another. Obviously if you’re underwater then things look different. Towards Restoration of Missing Underwater Forests by Campbell et al. is a paper looking at the missing forests of Phyllospora comosa, a brown algae that should be found of the coast of Sydney.

The seaweed disappeared with increasing pollution from the city but, despite an increase in water quality, the forests have not returned. Why?

Campbell and her team transplanted Phyllospora into sites at Long Bay and Cape Banks near Sydney. They observed the algae to see how they survived. They also watched plants at the donor sites for comparison. The results were mixed.

They did well at Long Bay. Better than well, in fact. They were reproducing better than the control sites, which suggests that the only reason there weren’t Phyllospora at Long Bay is that there weren’t any. That’s tautological, but obviously in nature you get new Phyllospora from older Phyllospora. A colonisation effort in Long Bay would get the re-establishment of the seaweed started.

Things did not go so well at Cape Banks. Here Phyllospora did much worse than at Long Bay or the original populations. What this did see were that the transplanted algae were short and had a lot of bite marks from fish. What they suggest here is that the reason there isn’t Phyllospora on site is because there isn’t enough. Small colonies are suitable for snacking, but because they’re so small all the plants get damaged. A larger area might be so large that not all the plants suffer and that leaves enough for reproduction of the next generation.

They also found the new plants were concentrated in, or at the edge of the adult population. That suggests that the lone colonist plant will not flourish by itself, what matters isn’t just the plant but the whole community.

What I particularly liked about this paper is that there’s a classic example of scientists being scientists in it.

The disappearance of Phyllospora from reefs in Sydney coincided with a peak in high volume, near-shore sewage outfall discharges along the metropolitan coastline during the 1970s and 1980s (Coleman et al. 2008). Although causation has not been formally established, embryos of this species are particularly susceptible to pollutants commonly found in sewage, to the extent that they are used as a test species in standard ecotoxicological assessments.

They’re susceptible to pollutants. There were pollutants in the area, but that’s a correlation, not a proven causation. A causal link between pollution and the demise of the algae would be extremely convenient for anyone wanting to argue now is the time to restore the forests, and it’s not a ridiculous leap to make, but they still point out that it’s still not fully proven.

Correlation does not mean causation.

Image by Randall Munroe CC BY-NC.

What the paper shows is an example of discontinuity in ecosystems. The results show that it’s not simply a question of degree of forestation, but that you either have enough Phyllospora to make a viable forest system or you don’t. The amount you need might vary from place to place, but spending half the money isn’t going to give you half the result.

It’s also something that requires close examination. For plants that you don’t see from the shore, it’s easy not miss them when they’re gone. There are knock-on effects in how the loss of habitat affects other organisms. but that might appear a long way from the site where the root problem is.


The Kelp Forest at an aquarium in San Diego. Photo © Swandieve/sxc.hu
Correlation. Image by Randall Munroe. This image licensed under a Creative Commons by-nc licence.

Asking the right question

Image: Joaquim Alves Gaspar and Tony Wills/Wikimedia Commons.

Image: Joaquim Alves Gaspar and Tony Wills/Wikimedia Commons.

Often answers to the simplest questions are the most insightful. Take for instance the perfectly reasonable query, ‘why are there so many kinds of plants?’. This fascinating question is pondered by Professor Fred Essig (University of South Florida, USA) in his guest blog entry at Biology Online, a site that claims to provide answers to all your biology questions. I won’t give away the answer, but taking a niche-based approach Essig provides a thoughtful response that can be used by all should the same question come up in your own teaching. Cheers, Fred!

[However, one still can’t help wondering if 10,000 species of grass is too many… especially as they all look the same (or so my students tell me…) – Ed.]

An update on grass-free lawns

We blogged earlier this year about Lionel Smith’s project developing grass-free lawns. He’s uploaded a long video revisiting one of his lawns a couple of years after planting.

It looks like his research is a big success. If you’re even remotely interested, then it’s an excellent idea to visit his blog to see more photos. Apart from the benefits for biodiversity, the lawn is itself is a thing of beauty.

A lawn without grass?

It’s a common complaint that ‘plant-blindness’ means people overlook botany, but even botanists could miss how peculiar lawns are. Lionel Smith hasn’t. He’s working on Grass-free lawns, and I only found out about his blog at the weekend.

You know what a lawn is, it’s a patch of grass mowed to be short. But it doesn’t have to be. For example a chamomile lawn doesn’t have grass. Lionel Smith is experimenting to see exactly what you can do with grass-free lawns.

Aesthetically the lawn at Avondale is very interesting. My first reaction was that it looked more like a patchwork flowerbed. However, the photo Smith took after the second mowing is that it is definitely a lawn. But what is it that makes it a lawn?

A grass-free lawn at Avondale Park

A grass-free lawn at Avondale Park, Kensington. Photo by kind permission of Lionel Smith.

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Reed Control

Beaver lodge Phragmites australis (the common reed) is widespread though not native in many regions of the World, including North America. Phragmites-dominated habitats support many ecosystem services and diverse native and non-native biota.

Studies comparing the density of individuals or the numbers of taxa (species) in reedbeds and alternate habitats show variable results. Reedbeds apparently support fewer individuals or taxa of certain kinds of invertebrates, fishes and birds, such as early life stages of the mummichog, three species of high salt marsh breeding birds, and muskrat, than do alternate habitats. But top-ranked food preferences, and relative density or taxon richness of breeding birds, monophagous herbivores and other groups, are not the only currency by which to judge Phragmites. Other important considerations include the rare species supported by reedbeds; the habitat functions of reedbeds for roosting, escape from predators and shelter from floods and other extreme conditions; the ability of Phragmites to vegetate urban habitats and derelict lands without human inputs; and other non-habitat ecological services provided by Phragmites. Given the severe changes landscapes and biotas resulting from land use, alteration of hydrology and chemistry, and climate change, concepts of the purity of native communities may not be practical for application to abundant, widespread, long-present non-native taxa such as Phragmites. These arguments do not contravene controlling Phragmites where it is clearly a threat to important elements of biodiversity. The use of Phragmites in wastewater management will continue to be important. Phragmites has good potential for bioenergy. The use of Phragmites fibre for paper, insulation and industrial materials should be explored.

A new paper in AoB PLANTS argues that we should look at Phragmites management as optimization: how can we manage to increase and make use of the valuable ecosystem services provided by the plant, while reducing the harm that it causes in certain situations?


Ecosystem services of Phragmites in North America with emphasis on habitat functions. (2013) AoB PLANTS (2013) 5: plt008 doi: 10.1093/aobpla/plt008
Phragmites australis (common reed) is widespread in North America, with native and non-native haplotypes. Many ecologists and wetland managers have considered P. australis a weed with little value to the native biota or human society. I document important ecosystem services of Phragmites including support for many common and rare species of plants and animals. This paper is based on an extensive review of the ecology and natural history literature, discussions with field workers, and observations in 13 US states and one Canadian province during the past 40 years. Phragmites sequesters nutrients, heavy metals and carbon, builds and stabilizes soils, and creates self-maintaining vegetation in urban and industrial areas where many plants do not thrive. These non-habitat ecosystem services are proportional to biomass and productivity. Phragmites was widely used by Native Americans for many purposes; the most important current direct use is for the treatment of wastes. Most of the knowledge of non-habitat ecosystem services is based on studies of P. australis haplotype M (an Old World haplotype). Phragmites also has habitat functions for many organisms. These functions depend on the characteristics of the landscape, habitat, Phragmites stand, species using Phragmites and life history element. The functions that Phragmites provides for many species are optimal at lower levels of Phragmites biomass and extent of stands. Old World Phragmites, contrary to many published statements, as well as North American native Phragmites, provide valuable ecosystem services including products for human use and habitat functions for other organisms. Phragmites stands may need management (e.g. thinning, fragmentation, containment or removal) to create or maintain suitable habitat for desired species of animals and plants.


Biodiversity and conservation of heathlands (Invited Review)

Biodiversity and conservation of heathlands (Invited Review)

Biodiversity and conservation of heathlands (Invited Review)

Heathlands are human-shaped habitats that have a strong cultural and natural value, adding substantially to many ecosystem services such as food and water supply, carbon sequestration, recreation and biodiversity conservation. Fagúndez reviews the specific response of heathland ecosystems to the main drivers of biodiversity loss, which include land-use changes, pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. These drivers have generally been treated separately, but their complex interactions demand a more integrated approach in order to predict habitat response to future scenarios.

A salty tale of life on the road

Dipsacus fullonum In the UK, when it snows we panic. Over two million tonnes of salt are spread onto the UK roads each year. At the same time, roadside verges are rapidly becoming life-giving arteries in the countryside, linking habitats and acting as vital corridors for wildlife to thrive on. They also represent a remnant of our native grassland which has suffered catastrophic losses over the last century (Plantlife Read Verge Campaign). Apart from a few seaside species, wild flowers don’t like salt – not even a teaspoonful, let alone two million tonnes a year.

Teasels are an important species for wildlife, visited by bees when they are in flower and birds when carrying seed. The brown seeds from the spiny flower-head of the teasel is a favourite food of goldfinches in winter. And teasels don’t like salt. Writing in AoB PLANTS, Beaton and Dudley examine the salt tolerance observed in roadside populations of the common teasel (Dipsacus fullonum L. subsp. sylvestris) and discuss how this plant responds to new and challenging environments.

Beaton, L.L., and Dudley, S.A. (2013) Tolerance of roadside and oldfield populations of Dipsacus fullonum subsp. sylvestris (Dipsacaceae) to salt and low osmotic potentials during germination. AoB Plants. 5: plt001 doi: 10.1093/aobpla/plt001
Plants inhabiting degraded habitats must contend with stressful environments. However, their ability to adapt may be constrained by available genetic variation and genetic correlations between traits. Here, we examine the correlation between salt and drought tolerance in germinating seeds from contrasting populations of common teasel (Dipsacus fullonum subsp. sylvestris) growing on roadsides that experience high salinity due to de-icing salts, or growing in an old field site, remote from roadsides and free of salinity stress. We examined the contribution of drought and salinity tolerance to the tolerance of roadside conditions in seedlings from five maternal families from three roadside and three old field populations. Germination and early growth were compared under high salinity, low water potential set at −0.5 MPa with solutions of polyethylene glycol 8000, sodium chloride or vermiculite wetted to −0.5 MPa with distilled water. Root length and the emergence of cotyledons (where appropriate) were used as a measure of performance. Maternal families from roadside populations displayed greater tolerance of both high salinity and drought than families from old field populations. However, no maternal family possessed tolerance to both drought and salinity. Salt and drought tolerance during germination were not correlated, indicating that they are separate traits in this species.


Banking on future food security

The last great plant hunt - Kew Publishing

The last great plant hunt - Kew Publishing

Carolyn Fry, Sue Seddon and Gail Vines’ The last great plant hunt (2011, published by Kew Publishing at £25.00 in hardback) is difficult to categorise. Certainly, The Last Great Plant Hunt [hereafter referred to as LGPH] is an unashamed advertisement for – and celebration of – the admirably optimistic and forward-looking achievement that is the UK-based Millennium Seed Bank (MSB), and is written by a trio who have/had strong connections with the Royal Botanic Gardens (Kew, UK) that manages the facility at Wakehurst Place in Sussex (UK). But it is much more than that.

LGPH tells the story of Kew’s MSB – the “most biodiverse building on earth” (p. 93) – whose mission in storing seeds and understanding how to germinate them aims to “provide an insurance policy against imminent and future plant extinctions and to reverse the ongoing degradation of biodiversity by helping communities cultivate plants rather than exploit wild stocks” (p. 34). And it is doing that job rather well. In 2009 the MSB had secured seed from 10% (24,200 spp.) of the world’s flora, 14 months ahead of schedule (!), and under budget(!!). [Although the wisdom in 2007 of placing the billionth seed in the hands of a politician (p. 41) is questionable.] Currently, the MSB aims to have banked 25% of the world’s plant spp (angiosperms and gymnosperms in this context) by 2020; surely, a desperate race against time for the 100,000 spp. that are estimated to be currently facing extinction (p. 76).

Although much of the collected seed is stored safely in the chilled depths of the UK’s Sussex countryside, those carefully catalogued huddled masses have travelled there from every continent, like refugees from some global catastrophe. Accordingly, we have plant profiles of the Red Data-listed Tsodilo daisy of Botswana, ‘endangered in Lebanon’ Syrian bear’s breeches, and Berkshire (UK)’s critically endangered starfruit, along side insights into the Useful Plants Project (p. 152) – which helps local communities store and propagate their own particularly useful plants – operating in places as far-flung as Mali and Mexico. Accompanying the plants’ own stories are those of the people involved in their collection or use: The people dimension to the story is as important as the plants’. In some respects LGPH’s seed-collector’s tales are reminiscent of the exploits of the great plant hunters of the 18th, 19th and early 20th Centuries – notables such as Joseph Banks, Robert Fortune, Joseph Dalton Hooker, and George Forrest. But the MSB’s mission is arguably more important than those expeditions; its goal is to preserve plant biodiversity for all of humanity, rather than indulge in what may be regarded by some as the much less noble curiosity- and vanity-driven collection of new plants for the gardens of the already rich and famous. But is this really the last great plant hunt? Let’s hope not! There is still more angiosperm – and gymnosperm – diversity to find and preserve/conserve, which will only be possible with the MSB’s international partnerships with organisations in 50 countries such as South Africa, Malawi, Bulgaria, China, Australia, and Chile.

With more than 7 billion people on this planet – all of whom need to be fed – concerns over food security are firmly on the global humanitarian – if not yet the political – agenda. All too often wars, famines, and disease displace large human populations and interrupt the peaceful cultivation of crops, whilst salinisation, and desertification of soils put increasing demands on the agriculturally productive land that remains. Solutions to some of these problems may require development of new crop varieties, many of which will need to be found, or created using a mix of both traditional crop breeding and GM approaches. However, without the underlying genetic variety to work with those plans may be short-lived. So, finding and preserving the genetic diversity of certain crop spp. is an important dimension to the work of the MSB. Whilst the waste hierarchy’s 3 Rs of Reduce, Reuse, and Recycle may be the mantra of the sustainability movement, the 3 Es – Endangered, Endemic, and Economic (pp. 44/5) – is the Leitmotiv of seed conservation, and helps to direct the MSB’s seed collecting efforts. But is this subterranean seed storage in sleepy Sussex a case of putting all one’s egg in one basket? Hopefully, not; several similar depositories exist throughout the world, and the book does make a nod in their direction (e.g. probably the coolest one of them all in the Arctic archipelago of Svalbard, whose single mention is on p. 38), so the risk is somewhat spread. But I do wonder how safe such installations are – whether it be from terrorist – or extraterrestrial – attack, natural disasters (such as earthquake, tsunami…), or something as mundane as a power cut so that the freezers fail.

LGPH contains some of the most sumptuous illustrations I’ve seen in a botanical book for some time (exemplified in the 2-page spread entitled ‘Nature’s life-giving works of art’ on pp. 14-15. and the far-too-blue seeds of traveller’s palm on pp. 114/5). The book is arranged as numerous short items – typically only 2 pp. long, and which are easy to read – spread over 6 chapters covering such topics as conserving wild plants on a global scale, in search of the world’s seeds, and breathing life into degraded ecosystems. The abundant ‘amazing plant facts’, ‘amazing seed facts’, and ‘conservation facts’ scattered throughout the book help to keep it highly readable, informative, and interesting. LPGH also contains a wealth of other facts about seed biology, biodiversity, endangered floras and botanising in some of the world’s most challenging environments, and provides an interesting focus around which to base teaching sessions. And the global dimension of those short snippets of information also serves to underline the fact that the MSB is not just Kew’s story, it is everybody’s story.

In summary, The Last Great Plant Hunt is part glossy PR marketing brochure, part textbook, part blueprint for global survival, part Guinness book of seed-related facts, part adventure story, part heart-warming tale of international co-operation and optimism, part gazetteer, and part coffee-table book; and the whole is greater than the sum of its parts.

This account of the first 10 years of the MSB’s Project – and its ongoing Partnership – is a great story and deserves to be told. And Fry et al.’s book does it well!
Nigel Chaffey
E-mail: n.chaffey@bathspa.ac.uk

Italian Genetics Societies in Assisi: staple foods and orphan crops via epigenomics and systems biology

Joint meeting of the Italian Genetics Societies Assisi

Joint meeting of the Italian Genetics Societies Assisi

Italian genetic research is in good health: this week I’m at a meeting held in the Cittadella in Assisi with about 500 people and 300 posters. The conferees reflect my own research interest with respect to species: about 80% of the work was on plants, and 80% of that work on crops, making a good start. The posters were all in English, as were the slides, but almost all the talks were in Italian, proving an unusual challenge. Nevertheless, my command of Italian is improving, and I am now fluent with Italian phrases such as “loss of function mutanti” and “next generation sequencing risultati”.

The three Genetics Societies in Italy – AGI, SIBV and SIGA  – put together a programme that nicely flagged the research going on in the country with strong international-level programmes. It was great that many of the top geneticists took part in the meeting, including Roberto Tuberosa, Michele Morgante, Antonio Blanco, Giovanni Giuliano, Roberto Papa or Mariano Rocci, to name just a few from my area. Even better, many only played a supporting role to key laboratory members who showed their own dedication and hard work in their results! This was much appreciated by the strong student representation, many of whom presented their first work at this meeting with its informal and supportive ethos. Not least because of my general familiarity with the work presented and its background (making the language of presentation less of a problem for me), it was particularly valuable to hear the Italian students and post-docs focusing on their contributions to major European and international projects, whether in whole genome sequencing, annotation and functional analysis, or in crop physiology, or animal genetics. The Organizers juggled the difficulty of breadth of coverage with keeping the meeting short and focussed nicely, with plenary and mostly only two parallel sessions. Major sessions were on topical issues such as epigenetics and epigenomics, then genome plasticity, moving on to systems biology. Sadly though, despite coverage of so many crops of special importance in Italy and the involvement of the agricultural genetics society, I failed to notice substantial contributions to discussions or presentations from breeders or seed organizations, the end users of so much of the research discussed.

Thunderstoms, here approaching Assisi, kept us in the conference centre

Thunderstoms, here approaching Assisi, kept us in the conference centre

At a couple of recent conferences, I have helped writing a slightly more balanced report of many talks through Twitter. I’m not going to give any overview of the meeting here – the abstracts are of course helpful – but I can just point to a few pieces of work which I will certainly be discussing with my lab. Next week. It was very exciting to hear and consider the consequences of modern genetic work for the crops of particular importance in Italy: a systematic analysis of transcriptomics through three wine vintages in three different regions, all with same grape variety, Corvina, demonstrated how modern biology is addressing long-standing questions about genotype x environment interactions, agronomy and food production (Dal Santo et al.). Genes involved in transcriptome plasticity can be assigned to vineyards with different agronomic classes and plastic transcriptional drifts impacted metabolic rearrangements depending on microenvironment and growing conditions.

Pre-breakfast viewing avoids the crowds at the posters

Pre-breakfast viewing avoids the crowds at the posters

Several posters addressed the genetics and diversity of Tuber magnatum, the white truffle, and one was even using mitochondrial DNA fingerprinting to identify the oils in paints used by the Renaissance artists of Italy. The next area of genetics research – integrating systems – was well-covered, with A Vigilante showing network analysis approaches for identifying gene associations or functions, and understanding consequences of genome duplication.

I was really pleased to have been part of this meeting, and to have so many valuable discussions. I have a substantial list of people where I want to continue discussions – ranging from needs for cytogenetic textbooks, to systems biology, to alien gene transfer. I hope some of the discussions we had will lead to visits to my lab for periods of joint research too. Of course, the beautiful environment of the Cittadella in Assisi was ideal for the meeting. We could mediate on the impact of genetics in the shadow of St Francis and world’s finest renaissance frescoes, in a small enough venue (the conference represented nearly 15% of the total population of the town) that demanding meditation (translating words of the Cittadella website) was in the framework of informal discussions of molecular genetics.

Back to reality: 77 hours without e-mails and 248 new ones!

Back to reality: 77 hours without e-mails and 248 new ones!