Under our feet, in the soil, is a wealth of microbial activity. Just like humans have different metabolisms and food choices, so do those microbes. In fact, microbes play an important role in making nutrients available to plants.
A recent review paper from Xinda Lu and his team looks at different roles that various soil microbes have in soil's nitrogen cycle. Lu is a researcher at Massachusetts Institute of Technology.
According to Lu, "Soil microbes catalyze most of the transformations of soil nitrogen into plant-usable forms. Diverse microbes use different processes - and sometimes work together. Knowing the various styles of soil microbes, and linking microbes to specific soil processes, can be important knowledge for farmers."
Modern nitrogen fertilizers are applied in the form of ammonium. Through a biological process called nitrification, soil microbes convert ammonium to nitrates that plants can absorb. In order to be efficient at this process, microbes need oxygen. Researchers are studying nitrification because it can be linked to greenhouse gases and loss of fertilizer.
Although microbiologists have been studying the nitrogen cycle for over a century, not all steps were well understood. New microorganisms have recently been identified. A type of prokaryote (single-celled organism) called archaea has also been playing a role in nitrification.
Archaea are not technically soil bacteria, due to their structure. These are newly a newly classified group that really do some amazing things. There are many more archaea that contribute to nitrification in some soils than there are bacteria responsible for the same activity. Including the role of archaea in nitrification has broadened the understanding of scientists and researchers.
Researchers reviewed various studies of soil nitrification. This included the abundance of microbes in soil in relation to various environmental factors. Soil pH, temperature and the ratio of soil carbon to soil nitrogen were all compared to the number of microbes in each soil sample. Soil depth and other factors also influence microbe abundance.
Previous studies have shown, for example, that nitrification archaea are more abundant than bacteria in warmer temperatures. Other microbes thrive in lower temperatures.
Soil pH also influences how active soil microbes are in the nitrification process. Soil bacteria Nitrospira were more dominant in acidic soils, including forests and farm fields.
Researchers have also studied how various microbes "talk" to each other. This keeps the nitrification process running smoothly. Various mechanisms have been proposed, including cell signaling. The presence of nitric oxide in soils may enhance interactions between microbes.
Soil scientists are sure they have not found all the microbes that contribute to the vast array of services soils provide. Just as astronomers discover new stars in the sky as tools advance, so will soil microbiologists find new soil microbes. Some may be involved in nitrification.
Collecting and cataloging the type, abundance and location of soil microbes will continue to advance the knowledge we have about the soil nitrogen cycle.
Crenarchaeota are involved with nitrification in the soil. Here's a cell of this group infected by virus STSV1 observed under microscopy.
While domestication of plants has yielded bigger crops, the process has often had a negative effect on plant microbiomes, making domesticated plants more dependent on fertilizer and other soil amendments than their wild relatives.
In an effort to make crops more productive and sustainable, researchers recommend reintroduction of genes from the wild relatives of commercial crops that restore domesticated plants' ability to interact with beneficial soil microbes.
Thousands of years ago, people harvested small wild plants for food. Eventually, they selectively cultivated the largest ones until the plump cereals, legumes, and fruit we know today evolved. But through millennia of human tending, many cultivated plants lost some ability to interact with soil microbes that provide necessary nutrients. This has made some domesticated plants more dependent on fertilizer, one of the world's largest sources of nitrogen and phosphorous pollution and a product that consumes fossil fuels to produce.
"I was surprised how completely hidden these changes can be," said Joel Sachs, a professor of biology at UC Riverside and senior author of a paper published today in Trends in Ecology and Evolution. "We're so focused on above ground traits that we've been able to massively reshape plants while ignoring a suite of other characteristics and have inadvertently bred plants with degraded capacity to gain benefits from microbes."
Bacteria and fungi form intimate associations with plant roots that can dramatically improve plant growth. These microbes help break down soil elements like phosphorous and nitrogen that the plants absorb through their roots. The microbes also get resources from the plants in a mutually beneficial, or symbiotic, relationship. When fertilizer or other soil amendments make nutrients freely available, plants have less need to interact with microbes.
Sachs and first author Stephanie Porter of Washington State University, Vancouver, reviewed 120 studies of microbial symbiosis in plants and concluded that many types of domesticated plants show a degraded capacity to form symbiotic communities with soil microbes.
"The message of our paper is that domestication has hidden costs," Sachs said. "When plants are selected for a small handful of traits like making a bigger seed or faster growth, you can lose a lot of important traits relating to microbes along the way."
This evolutionary loss has turned into a loss for the environment as well.
Excess nitrogen and phosphorous from fertilizer can leach from fields into waterways, leading to algae overgrowth, low oxygen levels, and dead zones. Nitrogen oxide from fertilizer enters the atmosphere, contributing to air pollution. Fossil fuels are also consumed to manufacture fertilizers.
Some companies have begun selling nitrogen-fixing bacteria as soil amendments to make agriculture more sustainable, but Sachs said these amendments don't work well because some domesticated plants can no longer pick up those beneficial microbes from the soil.
"If we're going to fix these problems, we need to figure out which traits have been lost and which useful traits have been maintained in the wild relative," Sachs said. "Then breed the wild and domesticated together to recover those traits."
We will dive into the fascinating world of bees – managed and wild - and learn about the current research to keep them healthy from leading experts in the field. You will also get an opportunity to tell us your concerns about bees and pest management in agriculture and discuss how we can shape the future of CA agriculture together.
Apr 8, 2020 09:00 AM in Pacific Time (US and Canada)
From Integrated Pest Management to Integrated Pest and Pollinator Management: An update on current research on pollinator health
(April 8, 2020 from 9:00 to 11:30 am)
We will dive into the fascinating world of bees—managed and wild—and learn about the current research to keep them healthy. You will also get an opportunity to ask questions and tell us your concerns about bees and pest management in agriculture.
Presenters: Dr. Boris Baer and Dr. Quinn McFrederick
Panelists: Dr. Monique Rivera and Dr. Barbara Bar-Imhoof
Please take the pre-webinar survey – this will help us understand more about what future workshops/webinars should include.
2.5 CEUs (other) from the California DPR are approved. To obtain the CEUs you have to participate in the entire webinar. Register at https://ucanr.zoom.us/webinar/register/WN_ZwOHzICaRxi9NGkgvNT5Pg
UC Ag Experts Talk: Citricola Scale
(April 8, 2020 from 3:00 to 4:00 pm)
Dr. Elizabeth Grafton-Cardwell will discuss the key stages of citricola scale and how they damage citrus, weather trends that help reduce citricola scale, chemical control choices and their relative efficacy, coverage, and timing of treatments, and monitoring for resistance and methods to manage resistance.
1.0 CEU (other) from the California DPR and CCA is approved. Register at https://ucanr.zoom.us/webinar/register/WN_1_rXqm40SZ6Gm7PXWCdXtA
Recordings of the past webinars are available on UC IPM YouTube channel
CE hours are NOT available for recorded webinars.
Dr. Elizabeth Grafton-Cardwell will discuss the key stages of citricola scale and how they damage citrus, weather trends that help reduce citricola scale, chemical control choices and their relative efficacy, coverage and timing of treatments, and monitoring for resistance and methods to manage resistance.
April 8, 2020, 3 PM
This is part of the series of 1-hour webinars, designed for growers and Pest Control Advisers, will highlight various pest management and horticultural topics for citrus and avocados. During each session, a UC Expert on the subject will make a presentation and entertain write-in questions via chat during and/or after the presentation.
- Invasive shot hole borers in avocado by Akif Eskalen (May 2020)
- Vertebrate pests by Roger Baldwin (June 2020)
- Ants in citrus by Mark Hoddle (July 2020)
- Use of plant growth regulators on citrus by Ashraf El-kereamy (August 2020)
Register for the Citricola Scale webinar (April 8, 2020)
How plants sound the alarm about danger. Hormones are more complex than previously thought. Understanding their roles and interactions may ultimately result in better plant protection practices
Team led by Salk scientists provides a detailed picture of how plant hormones communicate through gene regulation
LA JOLLA—Just like humans and other animals, plants have hormones. One role of plant hormones is to perceive trouble—whether an insect attack, drought or intense heat or cold—and then signal to the rest of the plant to respond.
A multicenter team led by current and former investigators from the Salk Institute is reporting new details about how plants respond to a hormone called jasmonic acid, or jasmonate. The findings, which were published in Nature Plants on March 13, 2020, reveal a complex communication network. This knowledge could help researchers, such as members of Salk's Harnessing Plants Initiative, develop crops that are hardier and more able to withstand assault, especially in an era of rapid climate change.
“This research gives us a really detailed picture of how this hormone, jasmonic acid, acts at many different levels,” says Professor Joseph Ecker, co-corresponding author and Howard Hughes Medical Institute investigator. “It enables us to understand how environmental information and developmental information is processed, and how it ensures proper growth and development.”
The plant used in the study was Arabidopsis thaliana, a small flowering plant in the mustard family. Because its genome has been well characterized, this plant is a popular model system. Scientists can take what they learn in A. thaliana and apply it to other plants, including those grown for food. Jasmonic acid is found not only in A. thaliana but throughout the plant kingdom.
“Jasmonic acid is particularly important for a plant's defense response against fungi and insects,” says co-first author Mark Zander, a staff researcher in Ecker's lab. “We wanted to precisely understand what happens after jasmonic acid is perceived by the plant. Which genes are activated and deactivated, which proteins are produced and which factors are in control of these well-orchestrated cellular processes?”
The researchers started with plant seeds grown in petri dishes. They kept the seeds in the dark for three days to mimic the first few days of a seed's life, when it is still underground. “We know this growth stage is super important,” says co-first author and co-corresponding author Mathew Lewsey, an associate professor at La Trobe University in Melbourne, Australia, who previously worked in Ecker's lab. The first few days in the soil are a challenging time for seedlings, as they face attacks from insects and fungi. “If your seeds don't germinate and successfully emerge from the soil, then you will have no crop,” Lewsey adds.
After three days, the plants were exposed to jasmonic acid. The researchers then extracted the DNA and proteins from the plant cells and employed specific antibodies against their proteins of interest to capture the exact genomic location of these regulators. By using various computational approaches, the team was then able to identify genes that are important for the plant's response to jasmonic acid and, moreover, for the cellular cross-communication with other plant hormone pathways.
Two genes that rose to the top in their degree of importance across the system were MYC2 and MYC3. These genes code for proteins that are transcription factors, which means that they regulate the activity of many other genes—or thousands of other genes in this case.
“In the past, the MYC genes and other transcription factors have been studied in a very linear fashion,” Lewsey explains. “Scientists look at how one gene is connected to the next gene, and the next one, and so on. This method is inherently slow because there are a lot of genes and lots of connections. What we've done here is to create a framework by which we can analyze many genes at once.”
“By deciphering all of these gene networks and subnetworks, it helps us to understand the architecture of the whole system,” Zander says. “We now have this very comprehensive picture of which genes are turned on and off during a plant's defense response. With the availability of CRISPR gene editing, these kinds of details can be useful for breeding crops that are able to better withstand attacks from pests.”
Another noteworthy aspect of this work is that all of the data from the research has been made available on Salk's website. Researchers can use the site to search for more information about genes they study and find ways to target them.