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.

 

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.

The rules of spacing

Guest post by Luke Simon

I was at a Christmas party in conversation with a local engineer who, hearing I design food forests, wanted to pick my brain on apple trees. He had six trees in two rows of three, well spaced in his backyard. He was throwing out terms about the mainstream organic sprays he was using, and framed his questions expecting me to know some super organic spray, or spray regimen, that would fix his problems of pests and low vigor in general. I don’t think he expected the answer I gave: ‘What’s planted around the trees?’

We often think of the rules of spacing as rules for keeping other plants away from each other. In practice I find the lines blur between species, and enters a much more broad science: it’s what should be included near the plant, as well as what shouldn’t. Between these two aspects, you make or break the majority of fruit tree problems.

The lines often blur between species because, let’s face it, plants don’t grow in a vacuum and always have something growing up against them. In this guy’s case, his trees were planted right into his lawn. They were in competition with the grass.

Looking at their history, grass and trees are in most cases nemesis of one another. Trees make forest; but grass needs open space. The setting in most yards of trees with grass between is quite artificial, and only exists because we keep the grass mowed. In any other situation, trees would take over.

The prairies are the kingdom of grass, and these occured because of rain shadows, or areas where circumstances such as the Rocky Mountain range messed with the winds that carry rain, creating droughts in one part of the year, and near flooding in another. Trees don’t like that, because most have relatively shallow roots, as much as 80 percent residing in the top three feet of soil depending on the kind and its conditions; but prairie plants, such as the grasses, and Nitrogen fixers like Senna hebecarpa, put roots down unusually deep, so reach the water table whether rain comes or not.

An experiment showing the root growth of Red Delicious apple tree two years after planting.

Have you ever wondered as you pass woods how the trees survive so close? If you were planting an oak tree in your yard that would someday reach a hundred foot tall, can you imagine the spacing recommendations? They would be over fifty feet apart. Most yards couldn’t fit more than one tree. But in the woods they stand on top of each other, growing for hundreds of years, happy, and healthy.

Studies have shown that trees can grow their roots deep into the ground, but prefer to keep their roots higher in the soil if possible. There is more organic matter, hence nutrients and water, in this layer. If there isn’t, trees will try to put in the work to grow deeper. This is a lot more work, and certainly isn’t their first choice.

What trees really prefer is building networks in which they share and preserve resources. For instance, trees have what is called hydraulic redistibution, which is a fancy term for moving water not only up for their own use, but back down into the soil for storage, and horizontally to other plants. Peter Wholleben, in his book The Hidden Life of Trees recalls his surprise when he found a ring of roots from a beech tree that must have been cut down well over a century beforehand, but still had green, living roots showing above ground. It had no leaves, and the stump was gone. As he explained, citing various studies, the living trees around this ancient (should be dead) tree were feeding it sugars made in their leaves, keeping it alive. Likely, they got some kind of kickback from the extended root system because it allowed them access to more resources.

This is in ancient, established forests, so conditions aren’t quite the same for our young transplants. We can get some similar effects by growing fruit trees in more open settings, or riparian zones. These are zones similar to fencerows and overgrown fields where grasses are just converting to trees. These zones are iconically untidy and wild; but skillful gardeners know the elements of these zones, like clay in a potters hand, have the best potential to form the most beautiful, lush gardens.

Riparian zones have many layers, with notably high numbers of low growing herbaceous and woody shrubs, many of which are nitrogen fixers. The quickest way to simulate this ecology is making ‘guilds’ of plants right around your fruit trees. Here is my manual of bed building for info on quickly clearing grass without tillage. Plan on expanding these plantings every year until the beds around your trees meet. If the tree is older, and larger, the bed should extend at least a couple feet beyond its drip line.

An example guild. 1. Fruit tree 2. Comfrey 3. Siberian Peashrub 4. Amorpha fruticosa 5. Japanese Wineraspberry 6. Honeyberry 7. Blueberry 8. Turkish Rocket 9. Crambe cordifolia 10. Stepping stones, (or in this case, stepping logs). The green base is a ground cover of mint.

Any guild should include at least 2 woody nitrogen fixing plants, about 5 plants that do not fix nitrogen but can be cut for mulch, such as comfrey, or a groundcover of something like mint, then several fruiting shrubs like raspberry or honeyberry, and some perennial vegetables.

This is the best method if you already have fruit trees in the ground, like our engineer friend. If you’re just planning your food forest, Robert Hart, the father of the northern food forests, recommended planting full size or standard fruit trees at recommended spacing for their size, in rows like any orchard, but then semi standard or medium trees, then dwarf trees, then shrubs, then herbaceous plants, then vines to climb and fill in the cracks between them.

I’d recommend mulching as much as you can, and planting that area with a complete planting like this. The space should be completly filled with plants, and will establish faster with less work overall.

This system gives quite attractive results that are increasingly less cost and labor than serial applications of even organic, clay-based sprays, pyrethrums and neems, let alone harsher chemicals. There is work later on, but this is of course debatable, because its mostly harvests of fruit. Sounds like pleasant work to me.

This article was originally published on Mortal Tree on 24th February 2017.

About the author: Luke Simon is garden manager for Simon Certified Organic Family Farm, and on his own time a permanent edible landscape designer in Ohio, United States. He is the author of PASSIVE Gardening and Mastering the Growing Edge. Follow him on his blog, Mortal Tree, and his Instagram @mortal_tree.

 

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.

Thank you

As you may know, my year did not get off to the best start and I’ve been having a bit of a break from blogging.

Thank you to everyone who volunteered to write guest posts during my break. My plea for help with the blog got a much bigger response than I had anticipated and this brightened what was otherwise a very tough time for me. It has been a real treat for me to host articles written by such a variety of different people and covering such different topics. Most of the guest articles are now up but there should be a couple more to come in the next few weeks.

I also want to thank the many other people who spread the word about my hunt for guest bloggers and sent me supportive messages. I feel really lucky to belong to such a supportive online community.

I’m starting to feel the urge to write again so I hope to be able to publish a science post on here in the next week or so. I always enjoy receiving guest posts so please do get in touch if there is something you would like to write about.

An unsustainable trade

Guest post by Isabella Whitworth (@Orchella49).

Roccella gracilis on wool yarn that has been dyed with orchil made from Lasallia pustulata. Image credit: Isabella Whitworth .

Lichens are complex plant-like organisms made up of a fungus and an alga or cyanobacterium that live together in a mutually beneficial relationship (symbiosis). They are often found attached to rocks or trees and species can vary hugely in appearance, from flat, crusty forms to leaf-like growths. Certain species have been used as dyestuffs for millennia, although not all lichens produce dye.

My research into dye lichens was triggered by a chance mention of ‘an archive in the attic’ by local friends. Their forebears were dye manufacturers in nineteenth century Leeds in the UK and the company archive had been passed down three generations. The company’s initial fortunes came from the successful processing of orchil, a dye made from lichens.

Peer mentoring & why you should, too

Guest post by Liz Haswell (@ehaswell)

Image licensed under CC BY-SA 3.0 NY via Google (author not known).

Mentoring programs are believed to be essential to a successful career in science and are considered a critical step in improving the retention of women and under-represented minorities in science, engineering and technology fields*. Traditional mentoring matches a junior or inexperienced person—the mentee—with someone senior or more experienced—the mentor. The topic of today’s post is a different kind of mentoring, which I am calling “peer mentoring**”. In this case, each participant is both a mentor and a mentee. Over the last 15 years, I have been involved in several different peer-mentoring groups, and in every case they have been a powerful source of personal and professional growth. Here, I explain what I mean by peer mentoring, describe my own experiences, and list some suggestions for starting your own group.

One possible format for a peer-mentoring group is laid out in the book Every Other Thursday: Stories and Strategies from Successful Women Scientists. Ellen Daniell describes her experience as part of a group of women faculty—including beloved University of California, San Francisco (UCSF) professors Carol Gross and Christine Guthrie—as they meet every two weeks to set goals and troubleshoot challenges. Though this book is more memoir than instruction manual, it explains in detail how the group members established a rigorous yet supportive framework that helped them to be as productive as possible during their meetings, and how the work they did in “group” improved their personal and professional lives. 

Sudden oak death – a disease as ominous as its name

Guest post by Monica Lewandowski (@MMLewandowski52)

Sudden oak death is a disease that has killed millions of oaks (Quercus spp.) and tanoaks (Notholithocarpus densiflorus) in the western United States. First detected in California in the mid 1990s, it continues to steadily spread through northern California and Oregon forests, with the potential to wreak more havoc in forests and landscapes across the world.

The underlying cause of sudden oak death is a fungal-like organism, Phytophthora ramorum. The spores of P. ramorum are spread by wind, rain and human movement of infected plants. And more bad news – P. ramorum can infect much more than oaks. A strain of P. ramorum that infects larch trees is making headlines in the United Kingdom, where it’s better known as larch tree disease. Several species of trees and shrubs, herbaceous plants and even maidenhair fern are on P. ramorum‘s “host” list (view regulated plant list in the United States). This is a cause for concern as losing one or more key plant species in a forest can lead to dramatic changes for both the flora and fauna of an ecosystem.

Where’s the plant science in beef?

Guest post by Erin Sparks (@ErinSparksPhD)

Four years ago I became a first generation beef farmer. I had just started a postdoc studying the development of plant roots when my husband told me that his parents intended to give us beef cows as a wedding present. Whoa. Wait. What?!?!?! First of all, we live in a very small apartment – where are we going to put cows? Second of all, we know nothing about farming. Fear not fair reader, the good news is that my in-laws keep the cows for us and they are “many”-generation beef farmers so they know what they’re doing. Through their tutelage, I’m slowly becoming a beef farmer. I’ve learned about herd management, breeding, economics and more. Although all aspects of farming fascinate me, I wanted to tell you specifically about how plant science contributes to our farm.

One of Erin’s cows and her new twins. Much like humans, twins are a rarity for bovine. Image credit: E. Sparks

We run a cow-calf operation, which means that we keep a herd of cows (100+ in total) and three bulls on the farm. These animals are bred and their calves are then sold to market. What do these animals eat? Feeding cattle is a basic cost-benefit analysis. If you pay more to feed your animals than the profit you gain, you can’t make a living. Although it is not as simple as that, because beef prices are constantly fluctuating, so you also have to consider market projections. On our farm, we strive to be self-sufficient for feeding our animals. This means we grow over 200 acres of hay that is rolled and stored. In the summer, the animals are grazing in the fields, but come winter, when the fields freeze over, the animals get fed these hay bales. Alternatively, you can raise animals on grain feed, but this is exceedingly more expensive. We save grain feed for the calves after weaning, and to increase growth before selling.