Guest post: Not alive, but deadly

By David Parrish

Illustration of the structure of a coronavirus particle. Centers for Disease Control and Prevention (CDC); Public domain.

The “novel coronavirus” has many of us cringing at every sniffle, cough, and sneeze we hear (or utter). Anxiety levels are high and justifiably so. Perhaps shedding some light on viruses can help us deal less anxiously with this new one. The old Irish proverb comes to mind: “better the devil you know.”

Viruses inhabit an interesting space in the field of biology. Only a few thousand have been named (versus more than a million species of plants, animals, and fungi), but viruses are likely the most abundant form that biologists study. Here’s the logic. Humans are subject to infection by many different viruses, most of which infect only us, and the same appears to be true for every species of animal, plant, fungus, and bacterium. Accordingly, we can reason that viruses are the most abundant things biologists study.

However, most biologists do not consider viruses to be truly alive. Since the 19^th century, biologists have agreed that living things are made of cells – the complex building blocks of life. Viruses are not cellular. They are quite simple, made of DNA or RNA, a few proteins, and (sometimes) oily substances. They do not carry out the biochemistry associated with life. Antibiotics (the name means “against life” or “not fit for life”) are not effective against viruses exactly because viruses do nothing that an antibiotic can attack.

But viruses do some things that make them seem to be alive. They act a lot like bacteria and fungi in their ability to invade organisms, cause diseases, reproduce, disperse, and then repeat the cycle. It is an act, though, not really life. Living microbes that cause diseases (bacteria and fungi) generally grow and make more of themselves in cavities or on cell surfaces of their “hosts” (victims). They live outside of the hosts’ cells and cause diseases by multiplying, producing toxins, or other effects. By contrast, viruses enter a host cell, unpack their DNA or RNA, commandeer the cell’s metabolic machinery, and cause new virus parts to be made. The parts self-assemble and the resulting viruses can disperse and repeat the process. In essence, a virus is a non-living, stripped-down, nano-robot-like, biochemical assembly that invades cells and hijacks them to make more viruses.

In animals, if a virus invades cells lining air passages, the symptoms will be respiratory – from colds to bronchitis to pneumonia. Several different human viruses attack liver cells and can cause hepatitis. Some viruses can turn genetic switches in infected organs and cause cells to divide malignantly. The human papillomavirus (HPV) is a well-studied virus known to cause cancer, and HPV vaccines have been shown to be quite effective in preventing both HPV infections and associated cancers.

Where does a novel coronavirus – or any new virus – come from? How does a fatal disease like Covid-19 suddenly appear? Unfortunately, a never-before-seen virus with lethal potential can be produced in just one viral generation. The genes (DNA or RNA) that viruses carry are subject to mutation and new combinations. Pieces of DNA from host cells can be picked up by the virus, potentially making it more easily spread, more lethal, or both. In this way, viruses evolve to produce new forms just as living things do.

In another cruel twist, a host cell may be invaded simultaneously by two different viruses and forced to make parts for both. As those parts are self-assembling, mixtures of the two viruses may form. And those hybrids may have unique disease properties. Many virologists suspect that the virus causing Covid-19 resulted from this kind of mashup between something as innocuous as a common cold coronavirus and a coronavirus from a bat. Such cross-species viral hybrids seem inevitable in a world with ever increasing numbers of people and our continual encroachment on other animals’ territory. Both science and common sense are needed in this area.

Virologists, epidemiologists, and physicians still have much to learn about Covid-19 and the virus that causes it, but I am cautiously optimistic that the science being brought to bear on this new scourge will get us past it. And the hope is the knowledge gained will make us better prepared for scourges yet to come.

About the author: After earning his PhD in plant science from Cornell, Parrish joined the faculty of Virginia Tech’s College of Agriculture and Life Sciences, where he taught crop ecology and environmental science. His research interests spanned seed physiology, sustainable cropping systems, and biological sources for renewable energy. In his book, “The Gyroscope of Life” (Pocahontas Press, June 2020), Parrish brings biological studies to the curious non-scientist in an accessible and relevant way, inspiring readers to consider the world around us in a new light.

 

Bloom by Ruth Kassinger

The first things I think of when I hear the word “algae” are the microscopic green cells that were the ancestors of land plants. Reading Bloom by Ruth Kassinger was a powerful reminder that algae are so much more than this. The term “algae” actually describes a diverse collection of lifeforms ranging from single-celled diatoms to kelp and other seaweeds*. In the book, the author explores the origins of algae, their modern uses in food and other products, and the emerging algae-based technologies that may help us save the planet in future.

Kassinger strikes a good balance between scientific detail and storytelling so that the text is approachable and not too technical. I especially enjoyed how the text mixes descriptive passages with accounts of the author’s meetings with algae growers, scientists and entrepreneurs. The book is perhaps a bit long winded in places but I don’t think this detracts from the author’s message. I am looking forward to seeing how the technologies and products highlighted in the book develop in the future.

Bloom by Ruth Kassinger
Elliott & Thompson, ISBN: 9781783964413, hardback Jul 2019

(Published in the US under the title Slime by Houghton Mifflin Harcourt in June 2019)

*It is worth noting that there is no generally accepted definition of algae. Traditionally a group of bacteria known as cyanobacteria (also known as blue-green algae) were also considered to be algae, but today many scientists reserve the term “algae” for the non-bacterial species. In Bloom, Kassinger uses the older definition and there is a section on the rise of cyanobacteria.

Toddler-led plant science

Image credit: S. Shailes (CC BY 4.0)

Doesn’t time fly? My little baby is now a walking and talking toddler with a love of books and trains (and anything else on wheels!). Since my last post I have been busy trying to keep up with his ever-changing needs, alongside returning to part-time work and my volunteer role in Girlguiding.

I decided to leave my old job at the end of my maternity leave. I loved working for eLife, but the almost two-hour commute each way to the office no longer seemed compatible with my family life. I now do science writing and editing work on a freelance basis. This suits me really well at the moment as I can work when I like (or should I say when Sprog allows me to!).

I consider myself very fortunate to be able to spend most of my time at home looking after my son. We play games, read books (often the same ones “on repeat”), go for walks, meet friends at toddler groups or in parks, and do all sorts of silly things you don’t usually get to do as an adult (such as running around the dining table or rolling balls down a section of old drainpipe). We also do many jobs around the house together including cooking, gardening and laundry. These jobs take twice as long with my little helper and don’t always go to plan, but that’s all part of the fun, right?

I have to remind myself of these good times when one or more of us are unwell, very tired, or we are just having one of those days where even basic tasks (like getting dressed and out of the house) seem like insurmountable goals.

One of the most rewarding things about spending so much time with my son and other little people is observing how toddlers explore the world around them, often finding great joy from seemingly simple things. We have herbs growing in our garden and a few months ago I offered Sprog some herb leaves to sniff. He was captivated by the scents coming off the leaves and was keen to sniff the leaves of other plants. Weeks later, while preparing dinner in the kitchen, he picked up some basil we had just washed and sniffed it without any prompting from me.

As my son explores, he accidentally points out things that bring interesting scientific questions to my mind: how do plants produce fragrances? How do strawberries and other fruits change colour as they ripen? Why are there ants and aphids on the same branch of the apple tree? I’m going to try to harness his natural curiosity to help me write some new blog posts. Lead the way, son.

Guest post: Garlic mustard across the pond

 

By Mercedes Harris

CC BY-SA 3.0

Spring has finally sprung, and forests are coming to life again. Green leaves are starting to emerge along with the first colorful flowers of the season. But not all green is good. Odds are that much of the green you’re seeing this spring comes from non-native plants, especially in residential communities. At first glance, these “pretty” invaders may not appear destructive, but take a closer look and a different picture emerges.

Invasive species are non-native organisms whose introduction causes environmental or economic harm. An invasive herbaceous plant native to Europe and Asia called garlic mustard (Alliaria petiolata) spreads across North American forests causing multiple problems. Its presence inhibits the survival of butterflies, stops the growth of tree seedlings, and minimizes food sources for mammals. How does a 100 cm plant cause so much havoc?

Figure 1: Garlic mustard sightings in the United States reported to Early Detection and Distribution Mapping System (EDDMapS) 

Garlic mustard uses a variety of techniques to persist for years once introduced into new areas. Fast growth, chemical compounds that make it bitter tasting to herbivores, a cryptic rosette plant form, and hefty seed production all give garlic mustard an advantage over native wildflowers, shrubs, and tree seedlings. Garlic mustard grows quicker and taller than native plants crowding the space on the forest floor. Its chemical compounds are toxic to native butterflies and cut off the supportive fungi networks necessary for native tree seedling growth. It has a two-year growing season consisting of a basal rosette during the first year’s growth, which can go unnoticed in this form, but over-winters and bears flashy flowers in the early spring of the second growth year.

It produces high volumes of seeds to spread across landscapes; from roadsides to backyards, pastures to wetlands, hillsides, and prairies. Left unchecked, this plant forms dense populations wherever it goes. One single plant can produce anywhere from 350-7,900 seeds!

So, what can we do about this rapidly spreading herbaceous threat? Land managers commonly use two options, and neither is perfect. First, they can apply herbicide routinely. But this comes with the risk of applying herbicide onto surrounding native plants too. Second, managers can put hours and hours of manual labor into removing existing plants by hand, but garlic mustard has a large root that, if left behind, will regenerate next year.

Paul Henjum (public domain)

While land managers are still adjusting methods of garlic mustard removal and eradication, there are some things that everyone can do to limit the spread of garlic mustard and other invasive species. 1) When hiking, remain on marked trail ways to avoid spreading plant seeds. 2) In invaded areas, check shoes and clothing for seeds and remove them before leaving parks and trails. 3) Do not pick the flowers or open the seed pods as this will increase the seed dispersal range. 4) If spotted, report sightings of populations to land owners, or online invasive species detection databases such as EDDMapS.org.

About the author: Mercedes Harris is a recent graduate from the University of Massachusetts Amherst where she received a master’s degree in environmental conservation. She’s a biologist turned plant ecologist because the zoology courses always filled up too quickly during enrollment but the plant courses turned out to be great.

References:

EDDMapS. 2018. Early Detection & Distribution Mapping System. The University of Georgia – Center for Invasive Species and Ecosystem Health. Available online at http://www.eddmaps.org/; last accessed May 31, 2018.

How a virus gives back to its host

 

Image by F_A (CC BY 2.0)

A study by UK scientists has shown that tomato plants infected with a virus are more attractive to bumblebees than healthy plants. Why would a plant virus want to change the behaviour of bumblebees?

The virus in question – cucumber mosaic virus (CMV) – can infect many different species of plant including tomatoes and a model plant called Arabidopsis thaliana. In tomatoes it causes many symptoms including yellowing, mottling, leaf distortion and can reduce the yield of seeds. As a result there is pressure for populations of plants to evolve better defences against the virus. Since CMV can only multiply within plant cells you might expect that, over time, CMV might become less common, but this doesn’t appear to be the case. One way the virus might be able to combat this problem is to compensate for the decrease in seed production in infected plants by encouraging pollinators, such as bumblebees, to visit the flowers.

Bumblebees fertilise tomato flowers by a process called buzz pollination, in which sounds produced by the bees shake the flowers to release pollen. Although tomato flowers can fertilise themselves without help from the bumblebees, buzz pollination makes the process more efficient and also leads to the transfer of pollen between flowers. Volatile compounds (molecules that easily become gases) released from the plants may help to guide the bees to the flowers. CMV infection can change the mix of volatile compounds that plants produce, but it was not clear whether this changes the behaviour of the bees.

Simon Groen, Sanjie Jiang, Alex Murphy, Nik Cunniffe et al. found that the bees are more attracted to the volatiles produced by CMV-infected tomato plants than those produced by healthy, uninfected plants. In the absence of buzz pollination, CMV-infected plants produce fewer seeds than healthy plants. However, mathematical modeling indicates that, in the “wild”, the bee’s preference for virus-infected flowers may help to compensate for this so that CMV-infected plants may produce more seeds than uninfected plants. Further experiments in A. thaliana suggest that molecules of micro ribonucleic acid (or miRNA for short) produced by the plants might regulate the mix of volatiles that plants produce.

These findings suggest that in some environments it may be in a virus’ interest to help its host plant by making the plant more attractive to bumblebees or other pollinators. Bumblebees are important pollinators for many crop plants so these findings may help us to develop new ways to increase crop yields in the future.

Reference: Groen SC, Jiang S, M, Murphy AM, Cunniffe N, Westwood JH, Davey MP, Bruce TJA,  Caulfield JA, Furzer O, Reed A, Robinson SI, Miller E, Davis CN, Pickett JA, Whitney HM,  Glover BJ, Carr JP. 2016. Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts? PLOS Pathogens http://dx.doi.org/10.1371/journal.ppat.1005790

Bramble: friend or foe?

Blackberries change colour from red to black as they ripen. Image by Thomas’ pics (CC BY 2.0 via Flickr)

In England at this time of year, the hedgerows along country lanes are full of delicious fruits called blackberries. Just last week I spent an enjoyable afternoon with friends gorging on blackberries along the route of an old railway line in Norwich (now a footpath and cycleway). The berries are a good source of vitamin C and antioxidants, and are commonly used in desserts and preserves. Although I love collecting and eating blackberries, I have a bit of a love-hate relationship with the plant that produces them, the bramble (Rubus fruticosus agg.).

Rubus fruticosus agg. isn’t a single species, but instead is a group (or aggregate; agg) of around 200-300 very similar species of shrub in the rose family that are very hard to tell apart (1). Like roses, brambles are covered in sharp thorns that help to protect the plant from herbivores (and humans). The thorns also help to make brambles a safe haven for many small birds and other wildlife.

Brambles are pollinated by insects. Image by Roger Bunting (CC BY-NC-ND 2.0 via Flickr)

Brambles grow wild across most of Europe and in the UK they can thrive in most environments (1). The white or pinkish flowers are self-fertile and can still produce seeds even in the absence of fertilization (a process called apomixis) to produce an army of clone plants (2). Furthermore, brambles can produce suckers – new shoots from buds in the roots – which helps them rapidly cover an area of ground. As a result, brambles are often among the first plants to colonise abandoned plots of land. This is great for wildlife and the casual blackberry picker, but it’s not so helpful if you are trying to work on said piece of abandoned land…

When some friends and I took on an allotment this year, our plot had been neglected for a while and contained quite a lot of brambles. We removed a lot of the plants but have left some to be our own personal blackberry patch. Removing brambles is not a fun business as the thorns can cut through clothes (and gardening gloves). For several weeks in the spring my arms and legs were covered in scratches and I often found bramble thorns impaled in my fingers. If you don’t manage to completely remove the whole root, the bramble is quite capable of growing a fresh shoot so we’ve had a few cheeky brambles reappearing in the vegetable beds.

Despite my moaning about brambles I must say that the blackberry crop from the allotment has been great. It is kind of ironic that our most successful crop this year is something we weren’t deliberately growing. All in all, if I had to summarize my relationship with the bramble at the moment, I would say: “it’s complicated”.

 

References:

1) Wikipedia: Blackberry https://en.wikipedia.org/wiki/Blackberry

2) Brambles (Rubus fruticosus) http://www.woodlands.co.uk/blog/flora-and-fauna/brambles-rubus-fructicosus

Image links:

Bramble by Thomas’ pics

Canal: Morse to town 7 June ’11 by Roger Bunting

Lab Girl by Hope Jahren

In Lab Girl, scientist Hope Jahren has cleverly weaves a memoir of her own life with passages about the lives of plants, her scientific passion. From her childhood in a small town in Minnesota to her current position as a Professor at the University of Hawai’i, she gives a candid account that includes some of the adventures, funny incidents, obstacles, and shifts in her scientific thinking that happened along the way. The book is a fascinating window into the life of a gifted, passionate, yet (reassuringly) human scientist. If you haven’t read it yet, then I highly recommend you get your hands on a copy.

If you aren’t convinced by my mini-review, then I suggest you check out this longer review from the NY times.

Tracing the roots of an ancient friendship

 

An AM fungus (yellow) contacts the surface of a plant root. The nuclei of the plant cells are visible as blue spots. Image adapted from ref 3. Credit: Andrea Genre and Mara Novero (CC BY 3.0).

Plants need nutrients to be able to grow. Unfortunately, many of these nutrients can be scarce in the soil and therefore hard to get hold of. To get around this problem, most plants are able to form friendly relationships – known as symbioses – with soil microbes that can provide them with certain nutrients in exchange for sugars.

Today, around 80% of land plants form symbioses with a group of fungi known as arbuscular mycorrhizal (AM) fungi (1). Fossil evidence suggests that this symbiosis first emerged around 450 million years ago. This is around the same time that plants first started to colonise land. The transition from water to the dry and harsh environments on land would have presented many challenges to the early land plants, for example, how to avoid losing too much water. Another challenge would have been how to access essential nutrients that their ancestor (a type of green algae) would have gained directly from the water.

The liverworts, hornworts and mosses are thought to be the earliest groups of land plants (2). Since the AM symbiosis is widespread in these groups, it has been suggested that this symbiosis is one of the innovations that helped these primitive plants to survive on land.

Previous studies have identified many plant genes that are needed for AM symbiosis in legumes and other land plants. These genes can be split into two main groups: some are in a signalling pathway needed for the plant and fungus to communicate with each other, and others are activated later to allow the fungus to infect into the roots of the plant. Recently, Pierre-Marc Delaux and colleagues used a technique called phylogenetics to analyse genetic material from many different algae, liverworts, hornworts and mosses with the aim of finding out when the AM symbiosis genes first appeared (2).

Delaux et al. show that these plant genes emerged in stages, starting from before earliest plants colonised land. The signalling pathway genes appeared first, and are present in the algae that are thought to be the closest relatives of land plants, the Charophytes (2). On the other hand, the infection genes appear to be missing from the algae, but are present in the liverworts, hornworts and mosses.

These findings suggest that the algal ancestors of land plants were pre-adapted to interact with fungi. Currently, there is no evidence to suggest that the Charophytes are able to form AM symbioses themselves. Therefore, it is possible the signalling pathway evolved to allow algae to interact with other microbes and was later altered to allow the early land plants to interact with AM fungi.

Reference:

1. Parniske, M. (2008). Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol, 6, 763-75.
(Good review of AM symbiosis, but unfortunately this article is hidden behind a paywall…)
2. Delaux P, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels CJ, Sederoff HW, Stevenson DW, Surek B, Zhang Y, Sussman MR, Dunand C, Morris RJ, Roux C, Wong GK-S, Oldroyd GED, Ané JM. 2015. Algal ancestor of land plants was preadapted for symbiosis. Proceedings of the National Academy of Sciences of the United States of America. 2015, DOI: 10.1073/pnas.1515426112, PMID: 26438870
3. Corradi N, Bonfante P. 2012. The Arbuscular Mycorrhizal Symbiosis: Origin and Evolution of a Beneficial Plant Infection. PLoS Pathog 8(4): e1002600. doi:10.1371/journal.ppat.1002600

The catch-22 of being a carnivorous plant

Guest post by Sonja Dunbar (@PlantSciSonja)

Plants, like any other organism, want to reproduce. The usual way that plants achieve this is known as sexual reproduction, where an egg cell and sperm from two different individuals fuse and then develop into a new plant. However, since plants are generally anchored to one spot, they can’t meet up to reproduce. Instead, they rely on a variety of more indirect methods to transport sperm to other plants. For example, many flowering plants (also known as angiosperms) recruit insect messengers to carry their sperm, safely packaged in pollen grains, from one plant to another. They use colourful, sometimes scented, flowers to attract potential pollinators and often reward them with a sugary drink, nectar, while coating them in the pollen the plant wants them to carry. But what if you are a plant that also eats insects?

Some of the most well-known pollinators; bees and butterflies. Image credit: S. Dunbar

Carnivorous plants obtain nutrients from trapped insects to help them cope with a lack of important nutrients in their environment, such as nitrogen, that they need to grow (1). There are several different trap types, from snap traps, to flypaper traps and pitfall traps. The fact that carnivorous species are found in multiple different plant families suggests this strategy has arisen several times.

On the origin of chloroplasts

Guest post by Joram Schimmeyer

Chloroplasts in plant cells are easily identified under a microscope by their green colour. Image: J. Schimmeyer.

Of all the biological processes found on Earth, photosynthesis could be considered one of the most important. During photosynthesis, the energy from sunlight is used to build up sugars in the cells of plants, algae and some bacteria. These sugars can then be metabolised by the cells or other organisms that feed on them. Also, photosynthesis produces oxygen gas as a by-product, which is needed by most forms of life on earth. Without photosynthesis, life as we know it would not be possible.

In plants and algae, photosynthesis is carried out in tiny compartments inside cells called chloroplasts. This compartment contains a green pigment called chlorophyll, which is used to harvest light energy and is responsible for plants appearing green in colour. Chloroplasts vary greatly in shape and size, but they are all enclosed by two membranes and filled with even more membranes known as the thylakoid membrane system. The key players of photosynthesis are located within these thylakoid membranes; large groups of proteins use the light energy from chlorophyll to convert carbon dioxide form the atmosphere into sugars. The sugars can then be broken down to provide energy to drive growth and other cellular processes.