2013 Holiday Shopping: Top 5 Popular Botany Books

9 11 2013

Check all the book recommendations here!

The following books released this year cover botany. They are suitable for lay readers and school students. Not in any order. Blurbs are taken from the official book description. Note that featuring a book here does not necessarily mean I agree with its contents. I will gladly do full book reviews if requested.

The Kingdom of Fungi
Petersen; $20.00 Hardcover
k9969 The fungi realm has been called the “hidden kingdom,” a mysterious world populated by microscopic spores, gigantic mushrooms and toadstools, and a host of other multicellular organisms ranging widely in color, size, and shape. The Kingdom of Fungi provides an intimate look at the world’s astonishing variety of fungi species, from cup fungi and lichens to truffles and tooth fungi, clubs and corals, and jelly fungi and puffballs. This beautifully illustrated book features more than 800 stunning color photographs as well as a concise text that describes the biology and ecology of fungi, fungal morphology, where fungi grow, and human interactions with and uses of fungi.
My comment: Fungi are nowhere near plants, but I bow to idiotic disciplinary tradition here.

Ginkgo: The Tree That Time Forgot
Crane; $29.41 Hardcover
9780300187519 Inspired by the historic ginkgo that has thrived in London’s Kew Gardens since the 1760s, renowned botanist Peter Crane explores the history of the ginkgo from its mysterious origin through its proliferation, drastic decline, and ultimate resurgence. Crane also highlights the cultural and social significance of the ginkgo: its medicinal and nutritional uses, its power as a source of artistic and religious inspiration, and its importance as one of the world’s most popular street trees. Readers of this book will be drawn to the nearest ginkgo, where they can experience firsthand the timeless beauty of the oldest tree on Earth.

Early Events in Monocot Evolution
Wilkin, Mayo (eds.); $89.10 Hardcover
9781107012769 Tracing the evolution of one of the most ancient major branches of flowering plants, this is a wide-ranging survey of state-of-the-art research on the early clades of the monocot phylogenetic tree. It explores a series of broad but linked themes, providing for the first time a detailed and coherent view of the taxa of the early monocot lineages, how they diversified and their importance in monocots as a whole. Featuring contributions from leaders in the field, the chapters trace the evolution of the monocots from largely aquatic ancestors. Topics covered include the rapidly advancing field of monocot fossils, aquatic adaptations in pollen and anther structure and pollination strategies and floral developmental morphology. The book also presents a new plastid sequence analysis of early monocots and a review of monocot phylogeny as a whole, placing in an evolutionary context a plant group of major ecological, economic and horticultural importance.
My comment: This one is definitely university-level stuff, but I’ve found that this is a topic that interests many people, so I’m putting it here and hoping that the interested parties will be able to get through it.

Cannabis: Evolution and Ethnobotany
Clarke, Merlin; $85.50 Hardcover
9780520270480_p0_v1_s260x420 Cannabis: Evolution and Ethnobotany is a comprehensive, interdisciplinary exploration of the natural origins and early evolution of this famous plant, highlighting its historic role in the development of human societies. Cannabis has long been prized for the strong and durable fiber in its stalks, its edible and oil-rich seeds, and the psychoactive and medicinal compounds produced by its female flowers. The culturally valuable and often irreplaceable goods derived from Cannabis deeply influenced the commercial, medical, ritual, and religious practices of cultures throughout the ages, and human desire for these commodities directed the evolution of the plant toward its contemporary varieties. As interest in Cannabis grows and public debate over its many uses rises, this book will help us understand why humanity continues to rely on this plant and adapts it to suit our needs.
My comment: Over two years later, and my Cannabis post still brings in hate mail and death threats. If only its wonderful mellowing effects can switch off instinctive psychologically-induced foaming at the mouth. I hope I can refer these people to this book from now on.

Botany: A Junior Book for Schools
Yapp; $22.24 Paperback
61qq2lIsdoL First published in 1927 as the third edition of a 1923 original, this popular book by Professor R. H. Yapp is a well-illustrated and easy-to-read introduction to botany. The text includes detailed botanical drawings and suggestions for simple practical experiments to be performed by the reader; as Yapp explains in his guide, ‘this book is intended to help you find things out for yourself, not merely to tell you what other people have found out’. This book will be of value to anyone with an interest in botany or in the history of botanical education.
My comment: I experimented with using this book in teaching botany to high school students… and it worked surprisingly well, if you know where to update the text.





2013 Holiday Shopping: Top 5 Academic Botany Books

9 11 2013

Check all the book recommendations here!

The following books released this year cover botany. They are suitable as textbooks. Not in any order. Blurbs are taken from the official book description. Note that featuring a book here does not necessarily mean I agree with its contents. I will gladly do full book reviews if requested.

Domestication of Plants in the Old World: The origin and spread of domesticated plants in Southwest Asia, Europe, and the Mediterranean Basin
Zohary, Hopf, Weiss; $51.17 Paperback
41ZO1ISzCaL Domestication of Plants in the Old World reviews and synthesises the information on the origins and domestication of cultivated plants in the Old World, and subsequently the spread of cultivation from southwest Asia into Asia, Europe, and North Africa, from the very earliest beginnings. This book is mainly based on detailed consideration of two lines of evidences: the plant remains found at archaeological sites, and the knowledge that has accumulated about the present-day wild relatives of domesticated plants. This new edition revises and updates previous data and incorporates the most recent findings from molecular biology about the genetic relations between domesticated plants and their wild ancestors, and incorporates extensive new archaeological data about the spread of agriculture within the region. The reference list has been completely updated, as have the list of archaeological sites and the site maps.

Annual Plant Reviews, Volume 45: The Evolution of Plant Form
Ambrose, Purugganan (eds.); $164.95 Hardcover
418flyVxVsL The Evolution of Plant Form, an exciting volume in Wiley-Blackwell’s Annual Plant Reviews, approaches the subject from a diversity of scientific perspectives, bringing together studies of genomics, palaeobotany, developmental genetics and ecological genetics. Written by many of the world’s most widely recognised and respected researchers and drawn together and edited by Professors Barbara Ambrose and Michael Purugganan, this exciting volume is an essential purchase for plant scientists, evolutionary biologists, geneticists, taxonomists, ecologists and population biologists. For libraries in universities and research establishments where biological sciences are studied and taught.

An Introduction to the Study of Algae
Chapman; $35.59 Paperback
9781107644014 Originally published in 1941, this book was written to provide an elementary textbook on phycology suitable for university students and schools including visits to marine biological stations as part of their curriculum. Relatively few types are selected from each algae group; some are described in considerable detail whilst others are mentioned to illustrate the course of development in either the vegetative or reproductive organs. Illustrative figures are included throughout. This book will be of value to anyone with an interest in phycology and the history of science.

Beneficial Plant-microbial Interactions: Ecology and Applications
González, Gonzalez-López (eds.); $119.48 Hardcover
41hzO7nyGUL Beneficial Plant-microbial Interactions: Ecology and Applications provides insight into the mechanisms underlying the interactions of plants and microbes, the ecological relevance and roles of these symbioses, the adaptive mechanisms of plant-associated microorganisms to abiotic stress and their contribution to plant stress tolerance, and the potential of these interactions as tools in agrobiotechnology. A team of authors with wide experience in the area contribute up-to-date reviews in nineteen chapters devoted to different ecological and applied aspects of the rhizobia-legume symbiosis, ecto- and endomycorrhizas, and plant associations with diazotrophic or adiazotrophic plant-growth promoting rhizobacteria. The book is intended for students, researchers and academic faculty members in the field of agrobiotechnology.

Plant Roots: The Hidden Half, Fourth Edition
Eshel, Beeckman (eds.); $176.48 Hardcover
5192Z0sfJ3L The decade since the publication of the third edition of this volume has been an era of great progress in biology in general and the plant sciences in particular. This is especially true with the advancements brought on by the sequencing of whole genomes of model organisms and the development of “omics” techniques. This fourth edition of Plant Roots: The Hidden Half reflects these developments that have transformed not only the field of biology, but also the many facets of root science.





24h blogathon!: Red algae

7 06 2013

Post 21/48 of the blogathon. Nothing witty to say here. Donations at the bottom or on the side. Please? :)

Source: Wikipedia

Source: Wikipedia

The Rhodophyta, vernacularly called the red algae, is a group of around 6000 species of algae, distinguished from other algae by a lack of photosynthetic accessory pigments. They have an alternative system made up of phycobiliproteins, specifically phycocyanin, allophycocyanin, and phycoerythrin. These guidelight energy to the photosynthetic reaction center. The thylakoids of rhodophyte plastids have phycobilisomes attached to them. These are groups of light-harvesting pigments.

On a morphological level, if you want to identify them with a microscope, they’re easy to distinguish. Their cells have no flagella and no centrioles. If you see any alga with no centriole and no flagellum, it is invariably a rhodophyte.

The oldest-known eukaryotic fossil, the 1.2 billion year old Bangiomorpha pubescens (Butterfield, 2000), is possibly a red algal fossil, indicating a very ancient origin (consistent with predictions from molecular studies). Even if it turns out not to be a red alga, the 600 Ma Doushantuo Formation preserves several red algae in typical excellent detail, and even in the regular fossil record, red algae make frequent appearances as coralline algae, whihc are a group of red algae that have a calcareous crust.

References:

Butterfield NJ. 2000. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386-404.

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Donate here!





Fungal questions

20 02 2013

I got some impromptu questions asked of me during a recent classroom visit (ages: 13-14). About fungi, of all things. Here are the four I remember, with my polished answers (with none of the doodles I made in situ).

Why should we bother learning about fungi?

Fungi are extremely important in terrestrial ecosystems, for plenty of reasons. They are prominent decomposers, thus playing a big role in nutrient cycles. Over 90% of plants are symbiotic with fungi, symbioses that are important for growth and fruiting of the plants (Wang & Qiu, 2006); in fact, some have even speculated that fungi managed to become terrestrial by being endophytes in plants (Lewis, 1987). Some of these symbioses turn into parasitism and pathogenicity; the same applies for animals, where fungal pathogens are not uncommon and sometimes of medical importance.

They also serve as prey for myriad animals, from earthworms, to mites and ticks, to vertebrates. Among the invertebrates, there are often specialisations for fungal feeding. For example, some mites have highly-derived mouthparts shaped like stylets, used to pierce through fungal hyphae and suck out the contents. Griffin (1996) shows why this is so: fungi are very nutritious, containing high levels of glycogen and other polysaccharides, glycoproteins and peptidoglycans (up to 44% protein in dry weight!), and low concentrations of cellular DNA an order of magnitude less than what is found in bacteria and other eukaryotes. This nutritiousness has led to many fungi producing potent toxins for defence, collectively termed mycotoxins (this is why you shouldn’t eat any mushroom you haven’t surely identified).

What is the biggest misconception about fungi that you see?

That people use “yeast” to mean a specific taxonomic grouping. Yeast is actually a term used to refer to a specific morph of fungi – it’s not a phylogenetic grouping. Some yeasts are famous for their biotechnological uses (making bread and alcohol), others are known as significant parts of human skin or other flora (Candida, Malassezia) and potential allergens. But if you look at a phylogenetic tree of the fungi, those aren’t all so closely-related.

Also, the continued teaching of fungal biology as botany. This system is extremely antiquated, stemming back from the days when mushrooms were thought to be plants, and is recognised as bad practice by all botanists and teachers. I have no idea why it’s still persisting.

Is it true that fungi are related to animals?

Most likely, yes. Under the Opisthokonta hypothesis, fungi and animals belong to the Opisthokonta, along with diverse protists (Steenkamp & Baldauf, 2004): the choanoflagellates, ichthyosporeans, corallochytreans, nucleariids, and ministeriids. There are few morphological traits that they share, the only prominent one being well-developed flattened or plate-like mitochondrial cristae (Cavalier-Smith & Chao, 2003), although not even that one is universal (Zettler et al., 2001) and is also found in some non-opisthokonts (Sleigh, 1989). However, molecular phylogenies of all kinds overwhlemingly support opisthokont monophyly, and the clade is generally accepted.

Where is the most suprising place to find fungi?

In the oceans – we’re used to mushrooms growing in moist forests, so the idea of fungi growing in the oceans was pretty surprising when I first found out about it. I wrote a blurb about marine fungi here, and I’ve done more reading since that post. It turns out that fungi are important members of coral reefs, playing important roles in the bioerosion critical for setting up the rubble on which corals grow. They’re particularly effective as chemical borers, using organic acids to dissolve the calcareous skeleton. One such microborer is Dodgella, a chytridialid that can dig 40µm deep pits along the circumference of a coral skeleton, greatly reducing its stability (Wisshak, 2006). Marine fungi overall dominate the boring community in cold-water corals (Beuck & Freiwald, 2005).

More impressive is their apparently being able to live in subseafloor basalts (Ivarsson, 2012), but that still technically falls under marine.

References:

Beuck L & Freiwald A. 2005. Bioerosion patterns in a deep-water Lophelia pertusa (Scleractinia) thicket (Propeller Mound, northern Porcupine Seabight). In: Freiwald A & Roberts JM (eds.). Cold-Water Corals and Ecosystems.

Cavalier-Smith T & Chao EE-Y. 2003. Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution. Journal of Molecular Evolution 56, 540-563.

Griffin DH. 1996. Fungal Physiology.

Ivarsson M. 2012. Subseafloor basalts as fungal habitats. Biogeosciences 9, 3625-3635.

Sleigh M. 1989. Protozoa and Other Protists.

Steenkamp ET & Baldauf SL. 2004. Origin and evolution of animals, fungi and their unicellular allies (Opisthokonta). In: Hirt R & Horner D (eds.). Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics.

Wang B & Qiu Y-L. 2006. Phylogenetic distribution and evolution of mycorrhizas in land plants. Mycorrhiza 16, 299-363.

Wisshak M. 2006. High-Latitude Bioerosion: The Kosterfjord Experiment.

Zettler LAA, Nerad TA, O’Kelly CJ & Sogin ML. 2001. The Nucleariid Amoebae: More Protists at the Animal-Fungal Boundary. The Journal of Eukaryotic Microbiology 48, 293-297.





Daily Factoid: Some insects parasitise plants

13 02 2013

In a brilliant bit of parasitism, galling insects drill into plants and affect their metabolism and development in such a way that galls form. The exact molecular mechanisms for this are still largely unknown, but what is known is that these galls are highly-advantageous for the insects. They can take various forms, from being mere modifications of the plant’s nutrient production (inducing greater protein and sugar production for the insect to feed on), to being local growths of nutrient-rich plant tissues on which the insect can munch, to full-blown houses for the insect to live in.

Other insects are leaf-miners, and some of these insects also have the ability to modify the plant’s development. Next autumn, observe the trees with yellow leaves about to drop off. Some of them might have green “islands” on them – areas that are still photosynthetically active even though the rest of the leaf is ageing and dying.

Biochemical analyses of both leaf mines and galls show higher levels of cytokinins, plant hormones that inhibit ageing, maintain chlorophyll, and enhance nutrient release. In other words, the green mined areas are much more nutritious than the rest of the leaf. Like galls, they’re induced by the leaf-mining insects to get an easy source of food – and at a critical time of the year, right before winter.

What’s as interesting as this modification of plant structure by parasitic insects (which is, in principle, similar to behavioural modifications by animal parasites), many studies suggest that the involved cytokinins are not of plant origin, but injected directly by the insects. Going even deeper, the cytokinins injected by the insects aren’t produced by the insects, but by bacterial symbionts. Draw that on a flowchart to see how cool this is: it’s a triple-layered interaction that’s been most likely moulded by millions of years of coevolution.

Further Reading:

General:

The evolution and adaptive significance of the leaf-mining habit

Geometrical Games between a Host and a Parasitoid

Cytokinins and insect galls

Galls:

Manipulation of the phenolic chemistry of willows by gall-inducing sawflies

Mines:

Are green islands red herrings? Significance of green islands in plant interactions with pathogens and pests

Cytokinins:

Extracellular Invertase Is an Essential Component of Cytokinin-Mediated Delay of Senescence

Pathological hormone imbalances





Top Research of 2012: Botany

29 12 2012

Jump to: Arthropods; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

My top 10 picks for botanical research this year. I’m not a botanist, and although I am fascinated by plant physiology, I’m not intellectually able to keep up with that research. So I only really follow plant evolution, palaeobotany, and plant-arthropod interactions; I have tried to make the list more varied though. Picks and rankings are subjective, based on a master list of 17 papers. [OA] indicates an open-access paper.


10. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. [OA]

charophyta

Land plants (Embryophyta) are highly-specialised streptophyte green algae. Of the other streptophyte groups, three are variably recovered as the sister group to the land plants, the results depending on the genes and methods used, and none ending up with truly rigorous support: the Charales, the Coleochaetales, and the Zygnematales (pond scum). The Charales (stoneworts) are the ones commonly depicted in textbooks and have always gained the most support. This paper may change our view on things: it uses a large dataset of 160 phylogenetically-significant genes, and gets perfect support values for a Zygnematales+Embryophyta clade. This has numerous implications, chief of which is that multicellularity is a convergent land plant innovation rather than a condition inherited from an ancestor (as would be the scenario if Charales are the sister).


9. Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges.

This paper studies the molecular basis for UV light detection (280-320 nm) in plants, by looking at the reactions of UVR8, a photoreceptor known to react to UV light. Christie et al. went classical in this paper: they used crystallographic methods to elucidate UVR8′s structure, best summarised as a doughnut; then they used targeted mutations to find out how the protein works. When inert, it’s found as a dimer: two doughnuts connected by bridges. When UV light shines on the plant, these bridges break due to electrons getting excited. The single doughnut then binds to another protein, COP1, to complete the reaction.


8. Phylogenetic niche conservatism in C4 grasses.

c4

I’ve written an overview of C4 photosynthesis, so refer to that post for necessary background. This paper analyses various traits in grasses of the Chloridoideae and Panicoideae, grasses in which C4 photosynthesis is dominant (in the phylogeny above, yellow indicates C3, all other colours are types of C4). It finds that the evolution of these traits, as well as ecological preferences, are determined not by the evolution of C4 photosynthesis, but by phylogeny. In other words, it’s the ancestry that counts. This in turn has implications about how we should treat C4 photosynthesis: there is a tendency to lump C4 plants together as one functional group, regardless of phylogeny. This finding says we are better off sticking to phylogenetic lumping, since there is clear niche conservatism: C4 photosynthesis doesn’t determine the ecology of these plants. Ancestry does, and C4 photosynthesis just tags along.


7. A critical transition in leaf evolution facilitated the Cretaceous angiosperm revolution. [OA]

veins

This paper presents a cool hypothesis for a contributing factor to the great angiosperm radiation of the Cretaceous: leaf vein density (Dv in the above diagram) as a key feature. This is an observation in the fossil record, that the density of the veins increases in two bursts, once in the initial angiosperm radiation (100 Ma) and another time at 65 Ma to reach today’s levels. The greater vein density leads to vastly improved gas exchange rates, which would have provided them with a distinct advantage as the CO2 levels decreased in the Cretaceous, allowing them to more easily outcompete the conifers and other land plants.


6. Widespread impact of horizontal gene transfer on plant colonization of land. [OA]

hgt

This genomic analysis of a moss, Physcomitrella patens, finds that it has 57 nuclear gene families by horizontal gene transfer from bacteria, fungi, or viruses. 18 of them are inherited ancestrally; 18 of them are recent acquisitions; and 15 of them are also found in more derived land plants, passed on from the last common ancestor with mosses. To put these numbers into perspective, the functions of the acquired genes are essential, involved in defence and stress tolerance, hormone biosynthesis, and even DNA repair. The picture painted by these facts is one of a harsh environment that early land plants had to colonise, in which UV radiation was rampant and the ground was inhospitable; these genes enabled the early mosses to survive by helping DNA stability in early mosses (later plants got yellow pollen, the yellow pigment serving as a UV shield), and numerous stress tolerance mechanisms and development helpers to keep them surviving in the harsh environment.


5. Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior.

This is some pretty cool research from an ecological and from a plant-insect interaction perspective. The study finds that plant defence systems can be synchronised with insect feeding times; at least it is so in the case of the caterpillar of Trichoplusia ni and the Arabidopsis weed this experiment was done on. The synchronisation is achieved not by detecting the caterpillar, but by circadian rhythms – when raised on the same day/night cycle, the plant’s defence system will adjust to be active at the same time as the caterpillar is active. When circadian mechanisms are interrupted or the hormone jasmonate’s production is deficient, then the synchronisation gets thrown off and the plant experiences much higher herbivory levels and are thus at a physiological disadvantage. I’m interested in seeing how this plays out in nature with day-active vs. night-active insects.


4. Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants.

This paper reports the draft nuclear genome of the basal glaucophyte alga Cyanophora paradoxa. The most significant result is evidence for the monophyly of the Plantae, as even the untypical plastid of the glaucophytes appears to be homologous with that of the rhodophytes and green algae (together, these three groups make up the Plantae). The data gathered from the genome says that 274 of the alga’s proteins were transferred from endosymbiotic cyanobacteria, and that 444 gene families were transferred by horizontal gene transfer from other bacteria. Many of these proteins and genes are involved in photosynthesis and associated processes, as well as plastid integration, meaning that we now have more light shone on how built-in photosynthesis in plants first evolved.


3. Oldest known mosses discovered in Mississippian (late Visean) strata of Germany.

Mosses are expected to be one of the earliest plants to have evolved on land, but their early fossil record has been severely lacking because of their very low preservation potential. This paper describes the oldest mosses to date, which grew in the tropical forests of the German Carboniferous. Older ones are still to be expected, but their lack is merely an example of an expected inadequacy in the fossil record.


2. Underground leaves of Philcoxia trap and digest nematodes.

I admittedly include this so high up because of the coolness factor, but it does bring up deeper issues. But first, the cool stuff: the plant has sticky leaves that grow underground. Nematodes stick to them, and the plant digests them. In other words, this is a carnivorous plant, and it uses a completely novel way to capture its food. The deeper ecological and evolutionary issue to be brought up is about how such a unique strategy can evolve.The plant grows in a region with one of the poorest soils of the world, the Brazilian Cerrado. So it could be that the evolution of carnivory is instigated by soil nutrient deficiencies, and so they eat animals in order to get those critical nutrients.


1. Rise to dominance of angiosperm pioneers in European Cretaceous environments.

This paper reviews the early record of angiosperm fossils from Europe to propose a temporal framework for their megadiversification in the Cretaceous in which they outcompeted the conifers and other land plants. The scenario Coiffard et al. synchs up with the view from the North American record, so it can be viewed as reliable. The scenario has three bursts of diversification into new habitats. From the abstract: “(i) Barremian (ca. 130–125 Ma) freshwater lake-related wetlands; (ii) Aptian–Albian (ca. 125–100 Ma) understory floodplains (excluding levees and back swamps); and (iii) Cenomanian–Campanian (ca. 100–84 Ma) natural levees, back swamps, and coastal swamps.”


Jump to: Arthropods; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

Zoology





C4 Photosynthesis

2 11 2012

C4 plants are plants that undergo a specialised extrametabolic pathway, the C4 cycle, in which CO2 is transferred from mesophyll cells to a special ring of bundle sheath cells by a pump. CO2 gets dissolved by carbonic anhydrase, forming bicarbonate, which is then fixed with phosphoenolpyruvate carboxylase into C4 oxaloacetic acid (hence the name), which is then converted to malate. This diffuses to the bundle sheath ring through plasmodesmata, where the CO2 is set free by decarboxylases, including the all-important RuBisCo (Hatch, 1987). Regular C3 photosynthesis occurs, but under the locally very high CO2 concentrations 3-8x higher than other area of the leaf.

The net result is a minimisation of CO2 loss through photorespiration, a reduction in use of stomata leading to less water loss through transpiration, and a much higher rate of photosynthesis, at the cost of substantial energy needed to drive the CO2 pump, energy acquired from sunlight. C4 plants are also more efficient in using nitrogen, since they need to use less enzymes to maintain their higher photosynthetic rates (Pearcy & Ehleringer, 1984).

In practical ecological terms, what those advantages bring is either an ability to grow faster than C3 plants, or an ability to grow in more challenging environments than C3 plants (Hatch, 1987).

The reason why C4 photosynthesis works is the evolutionary history of C3 enzymes, especially the main one, RuBisCo. RuBisCo evolved back in the times when the atmosphere contained very little oxygen and 100x more CO2 than today (Rye et al., 1995). Therefore, all that C4 photosynthesis does is recreate that atmosphere very locally around the enzyme so that it acts in the environment it evolved to be optimal in, namely an atmosphere with very high CO2 and low O2, so that the competitive inhibition of RuBisCo by O2 is eliminated. For those with engineering experience, C4 photosynthesis works just like a supercharged combustion engine.

Although only 3% of vascular plant species undergo C4 photosynthesis, those plants are responsible for almost a quarter of the photosynthesis that happens on land (Lloyd & Farquhar, 1994). Its evolution is therefore quite an important development not only from a physiological perspective, but also from an ecological one.

C4 metabolism evolved convergently from regular C3 photosynthesis in over 45 land plant families, both monocot and dicot (Sage, 2004), as a result of the steady depletion atmospheric CO2 levels between 40-15 Ma (Edwards & Smith, 2010). This reduction in CO2 levels led to inefficiency in carbon uptake in land plants, especially those in warm and arid landscapes (most C4 plants are grasses), providing a strong selective pressure to reduce photorespiration, and by the Pliocene, C4 grasslands had displaced C3 grasslands in lower latitudes. Tropical grasslands and savannahs are dominated by C4 plants, as are many breakfast tables (Sorghum, maize, and sugarcane are all C4). At higher latitudes, the cost of driving the CO2 pump outweighs the gains: the C4 vs. C3 biogeographical dominance has a threshold defined by temperature (Ehleringer et al., 1997), with C4 plants dominating in warm temperatures and C3s in cold temperatures (the distinction also applies with altitudinal gradients). Other important factors influencing distribution are moisture/precipitation and light intensity.

Water plays a large role in the distributional patterns of C4 and C3 plants. C3 plants dominate in low latitude rainforests because of the abundance of water: C4 plants may be very efficient, but that doesn’t hold a candle to the high growth rates achieveable by C3 plants when environmental variables are ideal, e.g. when there is an overabundance of water. (THanks to Don Strong in the comments for pointing this out!)

There are no novel enzymes involved in C4 photosynthesis, it is all achieved using cooption of pre-existing enzymes and changes in their expression patterns causing the enzymes to accumulate to various levels in the mesophyll and bundle sheath cells. These changes are pretty complicated considering that they involve 20-30 unlinked genes (Wyrich et al., 1998) – it’s remarkable that this all evolved convergently so many times. We know of some intermediate species exhibiting some “proto-C4″ characteristics, e.g. several species in the Neurachne, Flaveria, Parthenium, Mollugo, and Alternanthera genera (list just random examples I dug up, there are definitely more!). Xu et al. (2012) show that both C3 and C4 pathways work at the same time in the alga Ulva prolifera.

It’s also worth noting that some unique lineages have managed to make a C4 mechanism that takes place within individual cells rather than in different tissues, see Keeley (1998) for examples.

References:

Edwards EJ & Smith SA. 2010. Phylogenetic analyses reveal the shady history of C4 grasses. PNAS 107, 2532-2537.

Ehleringer JR, Cerling TE & Helliker BR. 1997. C4 photosynthesis, atmospheric CO2, and climate. Oecologia 112, 285-299.

Hatch MD. 1987. C4 photosynthesis: a unique blend of modified biochemistry, anatomy and ultrastructure. Biochimica et Biophysica Acta 895, 81-106.

Keeley JE. 1998. C4 photosynthetic modifications in the evolutionary transition from land to water in aquatic grasses. Oecologia 116, 85-97.

Lloyd J & Farquhar GD. 1994. 13C discrimination during CO2 assimilation by the terrestrial biosphere. Oecologia 99, 201-215.

Pearcy RW & Ehleringer J. 1984. Comparative ecophysiology of C3 and C4 plants. Plant, Cell & Environment 7, 1-13.

Rye R, Kuo PH & Holland HD. 1995. Atmospheric carbon dioxide concentrations before 2.2 billion years ago. Nature 378, 603-605.

Sage RF. 2004. The evolution of C4 photosynthesis. New Phytologist 161, 341-370.

Wyrich R, Dressen U, Brockmann S, Streubel M, Chang C, Qiang D, Paterson AH & Westhoff P. 1998. The molecular basis of C4 photosynthesis in sorghum: isolation, characterization and RFLP mapping of mesophyll- and bundle-sheath-specific cDNAs obtained by differential screening. Plant Molecular Biology 37, 319-335.

Xu J, Fan X, Zhang X, Xu D, Mou S, Cao S, Zheng Z, Miao J & Ye N. 2012. Evidence of Coexistence of C3 and C4 Photosynthetic Pathways in a Green-Tide-Forming Alga, Ulva prolifera. PLoS ONE 7, e37438.





Picocyanobacteria

22 07 2012

This is a guest post by Sophie, written in response to a reader request I am unqualified to fulfil.

Picocyanobateria are cyanobacteria that are less than 3 µm in diameter. Their tiny size makes them significant parts of nutrient cycles: their surface area:volume ratios make them very efficient at nutrient uptake, much more so than larger cells. In lakes, they can contribute up to 80% of the primary production when conditions are suitable (Stockner et al., 2000). In ultraoligotrophic environments, picocyanobacteria dominate, as seen in Lake Superior where picocyanobacteria have radiated in the offshore part of the lake (Ivanikova et al., 2007). Their success in this type of environment is due to advantages in phosphorus use: they can make membranes with less phosphorus than other bacteria (Dyhrman et al., 2009) and they have higher uptake rates of phosphorus due to their ability to hydrolyse dissolved organic phosphorus (Moore et al., 2005).

Picocyanobacteria can be individuals (rods and coccoids) or they can be colonial. Colonies have more than 50 individuals; microcolonies of less than 50 individuals also form. Colonial picocyanobacteria are chroococcal ovoids, rods and cones. The colony can be loose, dense, stalked or filamentous. The arrangement is species-specific, used for identification.

Our knowledge of individual picocyanobacteria is limited. They are in a clade called the Syn/Pro clade with three genera, Synechococcus, Prochlorococcus and Cyanobium. They have higher diversity in marine environments: most strains belong to one lineage and are collected in two genera, Synechococcus and Prochlorococcus (Sánchez-Baracaldo et al., 2005). Freshwater strains are similar to Synechococcus (Weisse, 1993). This summary is not satisfactory because Synechoccus is polyphyletic (Robertson et al., 2001), but this is the state of the art at the moment.

Picocyanobacteria are classified in two types according to the light-harvesting pigment, visible with epifluorescence microscopy: yellow autofluorescing phycoerythrin or red autofluorescing phycocyanin (Wood et al., 1985). The first absorb green light (560 nm), the second absorb orange-red light (625 nm).

Their phylogeny is investigated only with molecular sequences (Steglich et al., 2003). Morphology is useless (Ernst et al., 2003) but molecular sequences are also problematic. Ssu rDNA is not reliable for broad phylogenetic study (Litvaitis, 2002) because it is too conserved. ITS-1 (the spacer between 16S and 23S rDNA) is useful for fingerprinting (Becker et al., 2002) because of its variability, but not good for phylogeny. Pigment genes are tricky because of lateral gene transfer (Dufresne et al., 2008).

Sánchez-Baracaldo et al. (2005) is the largest and most reliable study of cyanobacterial phylogeny, including picocyanobacteria. It is a total evidence analysis with phylogenomics, individual sequences and some morphology. Picocyanobacteria are the second most ancient lineage. By parsimony character reconstruction, the study concludes that the habitus of picocyanobacteria is representative of the first cyanobacteria. It also concludes that cyanobacteria evolved on land or in freshwater, not in the oceans. All together this means that studying freshwater picocyanobacteria is an exciting avenue for future research.

Picocyanobacteria can be health hazards. Their small size allows them to pass through all filters used in water treatment. Toxin-producing (microcystin) picocyanobacteria have been found (Bláha and Marsálek, 1999) and are a potential risk if they bloom in drinking water, as shown by deaths of people in Brazil getting treated with contaminated water (Domingos et al., 1999).

References:

Becker S, Fahrbach M, Börger P & Ernst A. 2002. Quantitative tracing, by Taq nuclease assays, of a Synechococcus ecotype in a highly diversified natural population. Applied Environmental Microbiology 68, 4486-4494.

Bláha L & Marsálek B. 1999. Microcystin production and toxicity of picocyanobacteria as a risk factor for drinking water treatment plants. Algological Studies 92, 95-108.

Domingos P, Rubim RK, Molica RJR, Azevedo SMFO & Carmichael WW. 1999. First report of microcystin production by picoplanktic cyanobacteria isolated from a Northeast Brazilian drinking water supply. Environmental Toxicology 14, 13-35.

Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, Paulsen IT, Tandeau de Marsac N, Wincker P, Dossat C, Ferriera S, Johnson J, Post AP, Hess WR, Partensky F. 2008. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biology 9, R90.

Dyhrman ST, Ammerman JW & van Mooy BAS. 2009. Microbes and the Marine Phosphorus Cycle. Oceanography 20, 110-116.

Ernst A, Becker S, Wollenzien UIA & Postius C. 2003. Ecosystem-dependent adaptive radiations of picocyanobacteria inferred from 16S rRNA and ITS-1 sequence analysis. Microbiology 149, 217-228.

Ivanikova NV, Popels LC, McKay RML & Bullerjahn G. 2007. Lake Superior supports novel clusters of cyanobacterial picoplankton. Applied Environmental Microbiology 73, 4055-4065.

Litvaitis MK. 2002. A molecular test of cyanobacterial phylogeny: inferences from constraint analyses. Hydrobiologia 468, 135-145.

Moore LR, Ostrowski M, Scanlan DJ, Feren K & Sweetsir T. 2005. Ecotypic variation in phosphorus-acquisition mechanisms within marine picocyanobacteria. Aquatic Microbial Ecology 39, 257-269.

Robertson BR, Tezuka N & Watanabe MM. 2001. Phylogenetic analyses of Synechococcus strains (Cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon reveal multiple evolutionary lines and reflect phycobilin content. IJSEM 51, 861-871.

Sánchez-Baracaldo P, Hayes PK & Blank CE. 2005. Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach. Geobiology 3, 145-165.

Steglich C, Post AF & Hess WR. 2003. Analysis of natural populations of Prochlorococcus spp. in the northern Red Sea using phycoerythrin gene sequences. Environmental Microbiology 5, 681-690.

Stockner J, Callieri C & Cronberg G. 2000. Picoplankton and Other Non-Bloom-Forming Cyanobacteria in Lakes. In: Whitton B & Potts M (eds.). The Ecology of Cyanobacteria: Their Diversity in Time and Space.

Weisse T. 1993. Dynamics of autotrophic picoplankton in marine and freshwater ecosystems. Advances in Microbial Ecology 13, 327-370.

Wood AM, Horan PK, Muirhead K, Phinnea DA, Yentsch CM & Waterbury JB. 1985. Discrimination between types of pigments in marine Synechococcus spp. by scanning spectroscopy, epifluorescence microscopy and flow cytometry. Limnology and Oceanography 30, 1303-1315.

Research Blogging necessities :)

P. SÁNCHEZ-BARACALDO, P. K. HAYES, & C. E. BLANK (2005). Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach Geobiology DOI: 10.1111/j.1472-4669.2005.00050.x
Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, Paulsen IT, de Marsac NT, Wincker P, Dossat C, Ferriera S, Johnson J, Post AF, Hess WR, & Partensky F (2008). Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome biology, 9 (5) PMID: 18507822





Using Microalgae to Clean Up Coal Plants

11 01 2012

This is a guest post by Sophie.

In 2009, at least 7994703000 tons (~8 billion tons) of coal were used globally (EIAa), with a resulting 13393577 tons of CO2 released as a result (EIAb) – and that’s not counting countries with no statistics. This makes coal the dirtiest energy source available. Read the rest of this entry »





The Potential of Microalgae for Biofuels: Use of Wastewater

8 12 2011

This is the first guest post, by Sophie. The original manuscript is 12 pages long, and will be split into several posts.

According to Worldmapper data, itself sourced from the World Bank and the United Nations Environment Program, 3937 km³ of freshwater were used globally in the year 2000. Between 1987 and 2003, 325 m³ of freshwater were used domestically per year; 2.4 trillion m³ used agriculturally; and 665 billion m³ industrially. Read the rest of this entry »








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