Farm & Ranch
[AgriLife Today] Bacteria battle: How one changes appearance, moves away to resist the other
By: Kathleen Phillips
- Writer: Kathleen Phillips, 979-845-2872, ka-phillips@tamu.edu
- Contact: Dr. Paul Straight, 979-845-1012, paul_straight@tamu.edu
COLLEGE STATION — Two types of bacteria found in the soil have enabled scientists at Texas A&M AgriLife Research to get the dirt on how resistance to antibiotics develops along with a separate survival strategy.
The study, published in the journal PLoS Genetics this month, identifies an atypical antibiotic molecule and the way in which the resistance to that molecule arises, including the identity of the genes that are responsible, according to Dr. Paul Straight, AgriLife Research biochemist.
Straight and his doctoral student Reed Stubbendieck observed a species of bacteria changing its appearance and moving away from a drug to avoid being killed.
Straight’s lab on the Texas A&M University campus in College Station in general focuses on understanding how communities of bacteria interact with each other and other microbes.
“Over the past few decades, scientists have come to understand that bacteria aren’t just single individual cells that somehow cause infections or degrade toxins, for example,” Straight said. “In fact, they are populations and communities of many, many cells, whether just a si
Two types of bacteria found in the soil have enabled scientists at Texas A&M AgriLife Research to get the dirt on how resistance to antibiotics develops along with a separate survival strategy. (Texas A&M AgriLife photo by Kathleen Phillips)
ngle species of bacteria or a very diverse community. We are most recently aware of this in terms of the human microbiome. People have more bacteria cells in them than they have human cells.”
Reed Stubbendieck, Texas A&M University graduate student. (Texas A&M AgriLife photo by Kathleen Phillips)
But what has not been fully understood about bacteria and microbes in general, he said, is the way in which they form these types of communities with more than one species.
“It’s both an ecological and a mechanistic bacteriology question,” Straight said. “For nearly 100 years, we’ve known that bacteria can produce molecules that can block the growth of other organisms including other bacteria, and those molecules have been very useful as antibiotics.”
Straight said the common understanding of the usefulness of antibiotics, however, sidestepped the ecological dynamics of the bacteria themselves in how they form communities, and interact with each other.
“We wanted to know what happens when we put two bacterial species together to compete with each other and use that model as a way to identify new molecules, identify pathways, or gene functions, that are required for the bacteria to survive under competitive stress,” he explained. “Identification of interesting new molecules or bacterial mechanisms of control that one might exploit can lead to developing a new antibiotic.”
For this study, Stubbendieck put together two species of non-pathogenic, soil-borne bacteria, Streptomyces and Bacillus subtilis, in different ways in the laboratory. He monitored the bacteria for different patterns in growth, motility and other factors when the organisms were together as opposed to when they were separate.
Stubbendieck noticed that the two bacteria would grow as expected in each colony initially, but over time one of the bacteria colonies would start to destroy the other one.
“It was very visual,” Straight said. “It would cause lysis, meaning that the cells inside the dying colony would be dissolved, leaving a mark of where this had happened.”
Stubbendieck had to identify the molecule or other functions that are responsible for causing the destruction, thus the way in which resistance might emerge.
“The molecule turned out to be very strange. It doesn’t look like any of the familiar antibiotics,” Straight said. “We find it interesting, because its chemical structure suggests it’s probably functioning in a way that is very different from the common antibiotics that are used.”
Stubbendieck also noted that in the region where the cells were destroyed, there developed “little teeny colonies of bacteria” growing, indicating that they’re resistant to the molecule. So he picked a number of those colonies and sequenced the genomes, which found the mutations that cause resistance.
“I put a bunch of the cells with mutant bacterial stains on a petri dish together, and when I came in the next morning and looked in the incubator, I saw a difference between the mutants and the non-mutant strain that was night and day, and we knew we are on to something,” Stubbendieck recalled.
“With two pieces of the puzzle — the molecule itself identified plus a way in which the resistance to that molecule would arise, including the identity of the genes that are responsible for resistance — Reed was able to dissect the pathway of resistance,” Straight said. “And it turns out that in a B. subtilis membrane, proteins work as signaling systems for lots of different things. They can receive signals from the external environment, signals from other bacteria, signals telling them about the status of their cell in a fluctuating environment.
“If something damages a membrane, bacteria have a way of sensing that and then turning on the response,” Straight said.
All of the mutations Stubbendieck identified were in the same gene that encodes for a protein in the membrane that functions like a signaling protein, or it has a partner that it talks to, and all mutations turned on the signaling system. And, because the mutants had proteins that were turned on all the time, the drug that previously would have been effective could no longer kill the bacteria.
Additionally, not only did the researchers see that resistance could emerge that way but also the population of the B. subtilis, the one that’s typically killed by the drug, changed in appearance.
“It had morphological shapes and structures to it, which suggested that this organism had undergone a really profound change. That allowed it not only to be resistant to this drug, which causes lysis, but also to move as a population of bacteria across the agar surface in a petri dish,” Straight said.
“This shows a way that organisms can interact with each other in a competitive, dynamic environment that’s very different from the way we typically think about antibiotics,” he added. “It is not just a simple, one-way street of a molecule that’s produced and causes growth inhibition of the pathogen, and the pathogen can become resistant and that might be a problem for health reasons. What we’re seeing here are molecules that can function like an antibiotic and cause something like lysis, or cell death. And the organisms can use not just one resistance function but a combination of responses as a way of circumventing a competitive crisis.”
“This helps scientists build a much more mechanistically detailed picture of the competitive dynamics between bacteria, which helps us understand what happens in soil or inside a human intestine,” Straight added. “It helps us start to get a better image to work from when we talk about the role of microbes in the environment and the way competitive interactions structure microbial communities; how something becomes resistant and therefore how we might control that.”
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Farm & Ranch
Grazing North Texas – American Lotus
Farmers and ranchers are in a very close partnership with Mother Nature. If we really pay attention, she presents us some interesting scenarios.
For example, though they are totally different types of plants, water lilies and prickly pear have a lot in common. They both have strikingly beautiful flowers, both plants are edible, both of them are invaders into their respective habitats, and too much of either one can be an obstacle that we have to deal with.
Many north Texas ranches rely on excavated ponds for livestock water. Any time a pond contains a significant amount of shallow water so that sunlight reaches the bottom, some type of pond weed will develop. The plant family that includes water lilies and lotuses is a common invader in our livestock water.
Water lilies and lotuses are in the same plant family but they are two separate genera. There are easy ways to tell them apart:
• A primary difference is that water lily leaves commonly float on the surface, but lotus leaves can grow above the water line.
• Water lily leaves and flowers are thick and waxy, while lotus leaves and flowers are thin and papery.
• Water lily leaves have a distinct notch in the leaf, while lotus leaves are more rounded.
• Water lily flower petals are pointed, and lotus petals are more rounded.
The photos attached to this writing are from Clay County, and this plant is common across north Texas. American lotus is adapted to a wide area, from Honduras north through Mexico and across the eastern US and into Canada.
American lotus is a perennial, and it is cold tolerant and heat tolerant. It can grow in any pond or slow moving stream that contains shallow water areas. It prefers water with a depth of about 12 inches. Germination can occur from the large lotus seeds. Tubers, or roots, are established in the mud, and long slender stems extend upward. Leaves and flowers are both emergent in that they grow above the water line.
Lotus flowers are fragrant, and yellowish white with rich gold centers. They open in the morning and close by late afternoon, then open again the next day.
Lotus is an edible plant and has a history as a food source. The large tuberous roots, the size of a human arm, were baked like sweet potatoes. The leaves were eaten like spinach, and the large seeds were ground into flour. Stems taste somewhat like beets and were usually peeled before being eaten.
There is a large world-wide industry of cultivating lilies and lotuses in water gardens. According to Dr. Jerry Parsons, Professor and Extension Horticulturist with Texas A&M AgriLife Extension, cultivation of these plants dates back as early as ancient Egypt. Today, anyone with determination and a little money can have a water garden.
In 2011, the 82nd Texas Legislature designated the water lily “Texas Dawn” as the official Texas State Water Lily. Texas Dawn is a hybrid developed by Texas resident Kenneth Landon, a world-renowned expert in the field of water lilies and the director of the International Water Lily collection in San Angelo.
Ducks and other wildlife utilize the large acorn like seeds of American lotus, and submerged portions of all aquatic plants provide some form of wetland habitat. Many of us have tried to pull a bass out of a group of water lilies or lotuses, and I’m sure others have had better luck than I did. Although there can certainly be benefits to lilies, lotuses, and other aquatic plants, they can also infest ponds to the extent that the pond is not functioning correctly.
So, while the rest of the world works hard to grow these plants, ranchers sometimes need to control populations in their stock ponds. Once it gets a foot hold, American lotus can spread aggressively in wetland areas.
The primary issue that encourages American lotus, and most other water weeds, is shallow water. Look closely at a good livestock pond and you will find that the deeper water is basically free of infestation. Any pond will have a certain amount of shallow water that encourages water weed growth, depending upon the terrain at the pond site and how the pond was constructed. Some ranchers who enjoy and utilize wetland habitat may prefer to have ponds with significant shallow water area.
Almost all livestock ponds have a certain life expectancy. Siltation, or movement of soil into the pond bottom through rainfall runoff, is a natural occurrence. How fast siltation occurs into each pond, and how deep the pond was to start with, determines the length of time that the pond will contain adequate depth for dependable water for livestock.
Ponds that develop infestations of water weeds over a large percent of the surface may not have adequate depth to remain a viable water source for livestock during drought periods, especially in western north Texas where evaporation rates are higher.
Mud, or silt, from the pond bottom, can be removed to deepen the water, but this is a very expensive process. It is often more economical to construct a new pond rather than try to remove the silt from an old one. Most of us do not have the funds to continually construct deep water livestock ponds, so we must try to keep existing structures functioning and providing good drinking water for livestock, for as long as we can. Control of pond weeds like American lotus may be necessary, and it can be accomplished.
There is currently no feasible biological control. American lotus can be cut and removed, but this process us usually temporary because lotus can reestablish from seeds and roots.
American lotus can be safely controlled by chemicals. This must be done carefully. If a pond containing a large amount of any pond weeds is treated to remove all of the vegetation, a fish die-off could occur. When the dying weeds decompose, they use up the oxygen in the water and fish can suffocate. If possible, treat only a portion of the area, wait about two weeks, and treat another portion.
Farm & Ranch
The Many Benefits of Rabbit Manure
By Landon Moore
Rabbits offer a lot to the home gardener, and perhaps the most useful of all is their waste. Rabbit manure is likely the single most versatile and valuable fertilizer of any animal manure. It’s a “cold” manure, meaning it can be applied directly to plants in any form without the risk of burning them. In contrast, manure from sheep, horses, cows, and especially poultry must be aged before it’s applied, or it may damage plants. Because rabbit manure doesn’t need to be aged, it retains more of its nutrients and is therefore twice as rich as chicken manure and four times more potent than horse or cow manure. Rabbit manure is safe to apply to soil growing edible crops, has virtually no smell, and contains no harmful seeds. It can be used immediately, or be dried, powdered, made into tea, or turned into worm castings. A single trio of rabbits and their offspring can produce up to two cubic yards of fertilizer per year, along with 100 to 200 pounds of meat.
Rabbit manure is in such high demand as a fertilizer, particularly for roses, that it’s often sold online at a premium price. Some rabbitry owners even charge people to come scoop the manure themselves, paying by the bag. Larger rabbitries might sell by the truckload, but many owners keep it all for their own gardens. You may wonder what makes this little mammal’s excrement so uniquely useful. To understand, we first need to look at the qualities that make it special and then explore its various applications.
To begin with, let’s take a closer look at a rabbit’s biology. Contrary to popular belief, rabbits are not rodents but belong to the order Lagomorpha and family Leporidae, along with hares. All domestic rabbits are domesticated European rabbits (Oryctolagus cuniculus) and are unable to produce fertile offspring with American cottontails. Rabbits are considered “pseudo-ruminants” because they have a single-chambered stomach, but they also have an organ called the cecum, which functions similarly to a rumen and makes up about 40% of their digestive tract. They are crepuscular, meaning they are most active at dawn and dusk, typically feeding in the evening.
Rabbits actually produce two kinds of manure. The familiar dry pellets make up most of their waste, while the other type, known as “cecotropes,” is a moist and smelly substance resembling tiny bunches of grapes. Cecotropes are not fully digested, and because rabbits cannot chew their cud, they reingest the cecotropes as they are excreted. This fermented substance allows the rabbit to absorb more nutrients than it would through initial digestion. While cecotropes are occasionally found in cage trays, the feeding behavior that leads to them is usually only witnessed by the rabbit owner.
The dry pellets are the true manure that most people are familiar with. These small, round, dry pellets have almost no smell when kept dry. When crushed, they break down into a powder resembling tiny grass fragments because, in essence, that’s what they are. Some people crush the pellets before applying them to speed up their absorption into the soil, while others appreciate their “slow-release” feature. Additionally, the manure’s water solubility can be exploited in several ways. Soaking a wheelbarrow full of manure creates a potent sludge that can be easily applied to flat surfaces. If the odor is not an issue, the smell will dissipate once the manure is either dissolved by moisture or dried by the sun. Another method is to make manure tea: fill a cloth bag with manure, seal it, and submerge it in a barrel of water for a few weeks. A simpler method involves placing damp manure at the bottom of a barrel, filling it with water, and letting it sit in the sun for a couple of weeks. Stir occasionally, and you’ll have a powerful liquid fertilizer ready for use.
Domestic rabbits should be fed a modern, pelleted feed, which provides all the nutrients they require. This diet eliminates the risk of noxious seeds being present in the manure, making it safe to apply directly to the lawn, especially during winter. Winter and spring rains will break it down, and by late spring, you’ll have a healthy carpet of turf.
Rabbit manure’s nutrient content varies depending on factors like storage, age, and diet, but it generally contains around 2% nitrogen (N), 1.3% phosphorus (P), and 1.2% potassium (K). The Oregon Extension Service gives a range of 3-4.8% nitrogen, 1.5-2.8% phosphorus, and 1-1.3% potassium. Even at the lower end of the scale, rabbit manure has higher nitrogen content than poultry manure and twice the nitrogen content of cattle manure. One reason rabbit manure doesn’t burn plants is due to the biology of birds, which lack bladders and produce more ammonia in their waste. In contrast, rabbits release ammonia in their urine, which is why their manure may have a stronger odor.
Because of its balanced nitrogen-to-phosphorus ratio, rabbit manure promotes a wider variety of species in the same application area. Applying it directly to heavy clay soils will improve them quickly, especially when combined with other organic matter. It can also improve sandy soils by adding texture and helping them retain moisture. Anyone raising rabbits will have a steady supply of manure, as they are efficient producers. A small herd of 17 animals, including their litters, can produce about one ton of manure annually.
Beyond fertilizing, rabbit manure has several other uses. It is considered the best food for earthworms and can be combined with moisture-holding bedding like peat moss, shredded paper, or hay taken from used nestboxes. Many rabbitries (including my own) keep worm beds right under the cages. The resulting castings are rich in nutrients and can be used as-is or incorporated into soil amendments. A couple of feet of manure under a foot of soil in a hotbox can generate enough warmth to start and grow seeds, even in cold climates like Vermont.
In Europe and Asia, the rabbit meat industry is a billion-dollar market. While the Czech Republic leads in per capita consumption (over 8 pounds per person annually), China is the leading producer of rabbit meat. A recent study in China examined the effects of replacing peat moss in seed-starting soil with rabbit manure. The study found no significant difference in germination rates and noted that the manure provided increased nutrients for seedlings. The ideal ratios for seed-starting soil were found to be one-third manure, one-third perlite, and one-third vermiculite, or half manure and half perlite.
Rabbit manure is often overlooked as a nuisance, but as we can see, it’s an incredibly versatile soil conditioner, excellent fertilizer, ideal food for earthworms, and a superior seed-starting medium. Anyone raising rabbits should consider this another benefit, in addition to having a home meat supply, exhibition livestock, or pets.
Farm & Ranch
Leopold’s Legacy: The Five Tools That Shaped Conservation
By Raenne Santos
Known as the father of wildlife management, Aldo Leopold’s teachings reshaped our understanding of conservation and our role in nature. His philosophy, rooted in ethics, ecology, and action, emerged in response to the environmental degradation of the early 20th century in the American West. Overgrazed pastures, eroding soils, and changing wildlife populations revealed the consequences of treating natural resources as limitless.
Recognizing these challenges, Leopold theorized a transformative approach to land stewardship, emphasizing that the land is not merely a commodity, but a community in which we all belong. His works, A Sand County Almanac and Land Ethic, are still referenced to this day by modern conservationists. In Land Ethic, he introduced a practical framework for wildlife management known as the Five Tools of Wildlife Management, which offers land stewards a structured approach to maintaining and restoring ecological balance.
Symbolizing brush management, the axe is one of Leopold’s tools for controlling invasive species, shaping habitats, and mitigating wildfire risks. By selectively removing vegetation, land managers can enhance biodiversity, create open spaces for native species, and maintain healthy ecosystems.
Representing grazing animals, the cow (when used properly) mimics the natural disturbances once provided by bison. Grazing animals promote healthy ecosystems by aiding in nutrient cycling and soil disturbance. Responsible grazing practices prevent overuse and contribute to sustainable land management.
The plow signifies mechanical disturbance and soil preparation, crucial for habitat restoration and agricultural productivity. Used strategically, it aids in cultivating crops and creating conditions favorable to wildlife. However, misuse can lead to erosion, requiring careful application in conservation efforts.
Fire, a powerful natural tool, plays a crucial role in maintaining biodiversity and landscape resilience. Land managers use prescribed fire to control invasive species, rejuvenate plant communities, and shape habitats. Fire promotes the natural cycles of ecosystems and supports species diversity.
The final tool, the gun, is used to manage game populations and control predators. During Leopold’s time, unregulated hunting contributed to species extinction and posed threats to others. Today, hunting is strictly managed through game laws and seasonal regulations to ensure sustainable populations.
Leopold’s Five Tools of Wildlife Management continue to influence conservation practices today. While techniques have evolved, the fundamental principles remain the same—balancing human involvement with ecological processes to sustain healthy ecosystems. His approach emphasizes the importance of working with nature rather than against it. By embracing ethical land stewardship, modern conservationists honor Leopold’s vision, ensuring that future generations inherit thriving landscapes.
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