How you can help Guam's dying gagu

Caused by bacterial wilt and wetwood bacteria, droplets of ooze often form in declining ironwood trees.

Courtesy of Elizabeth Hahn

Editor’s note: This is the first in a two-part series about plant diseases on Guam and Micronesia.What happened to the huge, lush, towering, 100-year-plus gagu, or ironwood trees, that commonly dotted the island’s landscape at the University of Guam, Tiyan, Windward Hills Country Club golf course and elsewhere?

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Andersen Air Force Base’s Palm Tree Golf Course won an environmental innovation award for its handling of the coconut rhinoceros beetle.

Known by its scientific name Casuarina equisetifolia, ironwood trees are tightly integrated into Guam’s environment and local culture.

It is a hardy, pioneer, salt-resistant tree that occurs on the island’s main soil types: limestone, volcanic, and coral sand. It is propagated for windbreaks, erosion control, and urban landscapes.

Because C. equisetifolia is the dominant tree species on many of the sandy beaches of the Mariana Islands, it has become an important perching tree for the white-collared kingfisher (Halcyon chloris), the Mariana fruit-dove (Ptilinopus roseicapilla), and the white fairy tern (Gygis alba), which commonly lays eggs in the trees.

 There’s a fungus among us

It has been continually propagated since the 1600s. Due to its buoyant cones, it likely floated to Guam’s sandy beaches thousands of years ago on currents from the central Indo-Pacific coastline.From these cones, seeds were shed and grew into trees. Over time, ironwood became one of Guam’s prominent members of the halophytic (sea-salt adapted) vegetation type.Based on what we now know, Guam’s healthiest trees tend to occur in natural areas, near the coastline and in areas not prone to drought.Cocos Island and Ritidian are just a few of the places where healthy coastal stands of ironwood can still be found.

How you can help Guam's dying gagu

Huge, healthy ironwood trees still dominate the shoreline of Ritidian Point in northern Guam.

Courtesy of Elizabeth Hahn

Farmer seeks help

In 2002, local grower Bernard Watson contacted University of Guam professor Robert Schlub about a group of five ironwood trees in one of his windbreaks that exhibited symptoms of rapid yellowing and death. Death occurred within a few weeks of symptom onset.This was totally unexpected because the trees in question were only 10 years old.Cross-sections of these trees exhibited areas of wetwood that were dark, water-infused, and radiated from their centers. Droplets of bacterial ooze appeared inside and outside the wetwood stained areas.Also appearing on Watson’s farm in 2002 were trees with the same cross-sectional symptoms but this time it was accompanied by thinning foliage and a much slower lethal decline.

 How to manage plant diseases

This latter condition was quickly discovered in other areas of Guam and was coined “ironwood tree decline” by Schlub and Zelalem Mersha, a former UOG post-doctoral fellow now working as a Virginia State University research and extension plant pathologist.Unraveling the cause or causes of IWTD would become a major focus of Schlub’s work at the University of Guam for the next two decades.In the course of the investigation, the Guam team would join forces with researchers from institutes in California, Georgia, Florida, Hawaii, Louisiana, South Africa, China and Australia.Many possible causes of IWTD have been eliminated by the team over the years.

Links to the disease

Age was ruled out as an IWTD contributor, when trees of varying ages began dying in areas where decline was most severe. The failure to find a correlation between the presence of beetles or nematodes (microscopic worms) ruled them out as causing IWTD.The normal appearance of tree buds and young foliage eliminated the likelihood of viruses being involved.Seeing no link between typhoon damage and decline in tree surveys in 2008 and 2009, Typhoons Paka in 1997 or Pongsona in 2002 were eliminated as causing Guam’s ‘sick’ trees.

 Plant diseases to watch for in the rainy season

Over time, five things were consistently linked to IWTD: The presence of termites on the side of trees. The occurrence of wood-rot fungi at the base of trees.The exposure of trees to harmful landscaping practices and the presence of bacterial ooze in tree cross-sections caused, namely the bacteria that causes wetwood and the bacteria that causes bacterial wilt.Bacterial wilt is caused by bacteria within the Ralstonia solanacearum species complex.

Trees decline in 13 years

We now know that Guam’s wilt pathogen strain is the same one that has been killing trees in China and India for decades.One of the team’s most recent projects included a resurvey of 200 trees that were part of a survey of 1,427 conducted in 2008-09. The project was funded by the McIntire-Stennis Cooperative Forestry Research Program (project GUA932, accession no. 1017908), under the U.S. Department of Agriculture’s National Institute of Food and Agriculture.The results suggest that the decline of Guam’s ironwood trees that began in 2002 is continuing to this day, and that trees with severe wilt symptoms or that are nearly dead have high bacterial wilt infection levels.From the data, it is reasonable to expect that half the trees that appear healthy today in areas of decline such as at the University of Guam campus or Fort Soledad will begin showing symptoms of decline over the next 13 years and that trees already suffering from IWTD will likely be dead or nearly dead within the same time period.

Foliage thinning is one of the ominous signs that this ironwood tree on the University of Guam campus is suffering from decline.

Courtesy of Elizabeth Hahn

How you can help

Several steps have been taken to reduce the impact of IWTD.Hundreds of trees from various countries have been planted to add new genes to Guam’s tree population through cross-pollination.Some of these trees have been used to establish new ironwood windbreaks and others have been used as replacement trees in windbreaks with high levels of decline.Professionals and the general public are now being advised to reduce lawnmower and weed-trimmer damage to roots and the base of trees as a means to reduce infection and spread of fungi and bacteria.

To reduce transmission of Ralstonia and wetwood bacterial ooze when pruning, individuals are instructed to disinfect all tools.

How you can help Guam's dying gagu

Huge, healthy ironwood trees still dominate the shoreline of Ritidian Point in northern Guam.

Courtesy of Elizabeth Hahn

The public is also being advised to remove severely declined trees as a means to protect nearby healthy trees.Planting healthy, young trees of different varieties or hosts is the quickest way to restore areas with high decline.

Robert L. Schlub is a plant pathology professor and extension specialist, and Elizabeth Hahn and Julia Delorm are extension associates with the Cooperative Extension Service at the University of Guam’s College of Natural and Applied Sciences.

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Brazil: Bacterium combats coffee rust

Posted in Bacteria, Biological control, Fungi, Plant Pathogens on December 26, 2022| Leave a Comment »

DECEMBER 20, 2022

Researchers analyze performance of bacterium in combating coffee rust

by Ricardo Muniz, FAPESP

Researchers analyze performance of bacterium in combating coffee rust
The research is part basic science, investigating the bacterium’s resilience in a hostile environment—coffee leaves—and part biotech, seeing whether the bacterium inhibits the development of a pathogen. Credit: Jorge Mondego/IAC

A new study has analyzed the potential of a bacterium for biological control of the fungus Hemileia vastatrix, which causes coffee rust, a major challenge for Brazilian coffee growers. An article on the study is published in the journal BMC Microbiology.

The symptoms of coffee rust are yellow spots like burn marks on the leaves of the plant. The disease impairs photosynthesis, making foliage wither and preventing bean-producing cherries from growing until the tree resembles a skeleton. It is typically controlled by the use of copper-based pesticides, which can have adverse effects on the environment.

“This was a basic science study, in which we set out to understand the behavior of bacteria that inhabit the leaves of coffee trees. First of all, there are several compounds that are harmful to bacteria and can be used to attack them,” said Jorge Maurício Costa Mondego, last author of the article.

“Second, leaves are environments that undergo significant environmental pressures, such as sunlight and rain. We wanted to understand how bacteria that live on coffee leaves can withstand both the compounds produced by the coffee plant and the stresses of rain and sun,” he said.

Besides this basic science front, the study also addressed applied science challenges. The researchers decided to find out whether bacteria that inhabit coffee leaves can combat the fungus that causes coffee rust. The first step consisted of identifying the expressed sequence tags (ESTs) of Coffea arabica and C. canephora produced by the Brazilian Coffee Genome Project (Projeto Genoma EST-Café).

“I was the first author, alongside Ramon Vidal, a professor at UNICAMP, of an article in which we compiled the sequences expressed by C. arabica. It was published in 2011. We weren’t yet thinking in terms of metagenomics, but that’s what we did, more or less accidentally,” Mondego said.

Accidental metagenomics

The researchers found sequences they considered contaminating in the midst of the coffee leaf ESTs. “We took these sequences, fed them into the database, and concluded that they appeared to be from Pseudomonas spp, a genus of bacteria.,” Mondego said. “This stimulated the curiosity of our research group, which was led by Gonçalo Pereira, also a professor at UNICAMP. We asked ourselves, ‘What if we’ve done metagenomics without meaning to? Do these bacteria really live on coffee leaves?'”

At the time, Mondego was already a researcher at IAC. A few years later, he was able to join forces with Leandro Pio de Sousa, first author of the article published in BMC Microbiology. Sousa was a student who had a scientific initiation scholarship and now holds a Ph.D. in genetics and molecular biology from UNICAMP.

“I invited Leandro to work with me on this study, which was designed to see if Pseudomonas really does live on coffee leaves. If so, the previous findings would be confirmed. He agreed immediately,” Mondego said.

They isolated bacteria from the coffee leaves and put them in a culture medium. Under ultraviolet light, it is possible to characterize Pseudomonas, which looks purple and can easily be selected in the medium. “We collected the bacteria, extracted their DNA and sequenced one, which we called MN1F,” he said.

They made several interesting discoveries about MN1F, which has a secretion system that reflects its need to survive in a hostile environment full of fungi and other bacteria. “The secretion system produces antibacterial and antifungal compounds. That suggested it could be used for biological control,” Mondego said. They also detected a number of proteins associated with protection against water stress.

The next step entailed physiological experiments, whereby bacteria were cultured in different media to confirm the researchers’ observations regarding the genome. “The biological experiments proved several inferences correct. We showed that the bacterium does indeed have a considerable capacity to withstand strong osmotic pressure, which can be considered analogous to the effects of drought on coffee leaves,” Mondego explained. “Furthermore, MN1F is capable of degrading phenolic compounds that can be harmful to it. It breaks down these compounds from the plant and converts them into material for its own survival.”

The researchers then conducted a battery of tests to find out if MN1F could be used for biological control, preventing or inhibiting the development of H. vastatrix, the fungus that causes coffee rust. The tests took place under greenhouse and laboratory conditions, including an attempt to inhibit in vitro germination of the fungus. In all of the experiments, the bacterium proved capable of inhibiting the development of spores (reproductive units) and mycelium (the filamentous network containing the fungus’s genetic material).

More information: Leandro Pio de Sousa et al, Functional genomics analysis of a phyllospheric Pseudomonas spp with potential for biological control against coffee rust, BMC Microbiology (2022). DOI: 10.1186/s12866-022-02637-4

Journal information: BMC Microbiology 

Provided by FAPESP 

Explore further

Fungus that eats fungus could help coffee farmers

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South Africa: Rodade variety tomato resistant to bacterial wilt

Posted in Bacteria, Host plant resistance on December 23, 2022| Leave a Comment »

Bacterial wilt still threatens crops in tropical and subtropical areas

For tomatoes and more than 200 other plant species, bacterial wilt is an extremely destructive disease. Although some may not show symptoms, they keep the pathogen alive in the soil. The disease is caused by Ralstonia solanacearum, a bacterium found mainly in moist, hot areas.

The first sign of R. solanacearum is plants that start to wilt during the day and recover by nightfall. Later, they remain wilted and die. The disease usually starts in patches and spreads fairly rapidly to neighboring plants. It is almost impossible to control once it takes hold.

Fortunately for farmers, resistant genes are available. However, there are several races of R. solanacearum, with only one occurring in South Africa, namely race 1 biovar 2. It is therefore crucial to choose a tomato variety that has resistance to this race, or it will be ineffective. Varieties with the resistant gene can extend the harvest season into warmer conditions, but when the soil becomes too hot, the gene becomes less effective.

The resistant gene for race 1 biovar 2 was developed at the Agricultural Research Council station in Mbombela, and the resistant variety is named Rodade. This gene is used by other countries for our strain of the pathogen, and was hailed as a major breakthrough at the time.

Source: farmersweekly.co.za

Publication date: Thu 22 Dec 2022

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Pathogen effector characterization for a devastating plant disease

Posted in Bacteria, Plant Pathogens on December 5, 2022| Leave a Comment »

Secretion secrets revealed: Pathogen effector characterization for a devastating plant disease

Date:November 22, 2022Source:American Phytopathological Society

Summary:A recent study has discovered and characterized secreted proteins from the pathogen Candidatus Liberibacter solanacearum. These proteins, called effectors, offer clues into the manipulation tactics this bacterium uses to subdue its plant host. The study found that these effectors can be present in both the plant and insect host.Share:

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Sometimes the most niche plant pathogens pack the greatest punch. Such is the case for the Florida citrus industry, which has seen a 70% decline in its orange production since the introduction of Huanglongbing (citrus greening) in 2005. This disease is caused by the bacteria Candidatus Liberibacter asiaticus, which spreads via a flying insect — unlike most bacterial plant pathogens. When the insect feeds on the sugary sap of a plant, it deposits the bacteria into the veins of the plant, directly into the phloem, which allows the bacteria to follow this transport highway throughout the plant.

A close relative of the citrus greening pathogen, Candidatus Liberibacter solanacearum (CLso), is a newly emerging pathogen of tomato and potato. As this bacterium cannot survive outside of its hosts, very little is known about it, including how it causes disease. A recent study led by Paola Reyes Caldas, of the University of California, Davis, has discovered and characterized secreted proteins from the pathogen CLso. These proteins, called effectors, offer clues into the manipulation tactics this bacterium uses to subdue its plant host.

Newly published in Molecular Plant-Microbe Interactions, the study found that these effectors can be present in both the plant and insect host. Once inside the plant, these effectors can target various parts of the cell such as the iconic chloroplast, which are critical for the plant to perform photosynthesis. Additionally, these effectors are mobile in that they can travel from one plant cell to another. Corresponding author Gitta Coaker comments, “These effectors can also move from cell to cell, which could explain how Liberibacter can manipulate the plant while remaining restricted to the phloem. Unlike effectors from culturable leaf colonizing bacteria, the majority of Liberibacter effectors do not suppress plant immune responses, indicating that they possess unique activities.”

Whether these unique activities alter the phloem environment or insect attractiveness to facilitate pathogen spread remains to be seen, but this research offers an exciting starting point to unravelling this complex disease. Once targets of these effectors are identified, genetically engineering these important crops to prevent manipulation could be a fruitful solution to managing these diseases.

Story Source:

Materials provided by American Phytopathological Society. Note: Content may be edited for style and length.

Journal Reference:

  1. Paola A. Reyes Caldas, Jie Zhu, Andrew Breakspear, Shree P. Thapa, Tania Y. Toruño, Laura M. Perilla-Henao, Clare Casteel, Christine R. Faulkner, Gitta Coaker. Effectors from a Bacterial Vector-Borne Pathogen Exhibit Diverse Subcellular Localization, Expression Profiles, and Manipulation of Plant Defense. Molecular Plant-Microbe Interactions®, 2022; DOI: 10.1094/MPMI-05-22-0114-R

Cite This Page:

American Phytopathological Society. “Secretion secrets revealed: Pathogen effector characterization for a devastating plant disease.” ScienceDaily. ScienceDaily, 22 November 2022. <www.sciencedaily.com/releases/2022/11/221122125304.htm>.

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Florida, USA: Relationship Between the HLB Bacterium and Trees

Posted in Bacteria, Plant Pathogens on December 5, 2022| Leave a Comment »

Unraveling the Relationship Between the HLB Bacterium and Trees

 DECEMBER 2, 2022 HLB MANAGEMENT,  RESEARCH

At the heart of the HLB threatening the Florida citrus industry is a complex exchange between the citrus tree and an insidious bacterium.

bacterium
Photo courtesy of UF/IFAS photography

University of Florida Institute of Food and Agricultural Sciences (UF/IFAS) researchers continue to study the bacterium that causes HLB. They are learning more about how it works within the citrus tree in an effort to find viable solutions for growers.

In a new paper, Amit Levy, assistant professor of plant pathology, and first author Chiara Bernardini, a post-doctoral researcher, have discovered some new ways that the bacteria interact with a citrus tree’s natural defenses. Their findings shed light on the complexity of the disease path within the tree and what it means for scientists looking to mitigate its deadly impact.

Levy and Bernardini discovered how the bacteria and citrus tree engage in a “back-and-forth” reactionary relationship. Levy and others showed that once infected with the Candidatus Liberibacter asiaticus (CLas) bacterium, the tree’s defense system starts to generate callose in the phloem. Callose is a material that essentially “plugs” the phloem and generates something called reactive oxygen species (ROS).

In plants, ROS is involved in a plant’s defense systems and impacts a plant’s tolerance to various types of stress. Presence of a pathogen like CLas can increase ROS production to a negative effect and eventually cause cell death.

Levy’s research found that the CLas bacteria responded to the generation of callose and ROS by actually reducing them, allowing bacteria to once again replicate and transport throughout the tree.

This back-and-forth repetitive relationship of callose plugging and ROS accumulation ­— and then their elimination by Clas — is a complicated one and replicates an immune response competition between hosts and pathogens found in many other diseases.

Citrus varieties that maintain a fine balance between callose and ROS generation and then elimination without either side gaining “control” may be more inclined to continue to produce fruit over many years.

“This research demonstrates the complicated, intertwined relationship between the HLB bacteria and the tree’s immune defense system,” Levy said. “The fact that CLas developed mechanisms to suppress the immunity tells us that the plant immunity is critical to stop the bacteria. The HLB disease is about both the pathogen and the immune response, and their interaction. It is a fine balance.”

Learning more about how and when to stop this back-and-forth relationship and how it varies among different citrus varieties may bring scientists closer to finding sustainable solutions to fighting HLB.

Levy’s research appears in the July issue of Plant Physiology.

Source: UF/IFAS

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Florida, USA: It’s hard to manage bacterial spot in tomatoes

Posted in Bacteria, Crop protection, Plant Pathogens on November 20, 2022| Leave a Comment »

Florida researchers get funding to help tomato growers and breeders fight bacterial spot

“It’s really hard to manage this disease”

Florida scientists received a grant to investigate strategies to control bacterial spot in tomatoes. The disease creates major challenges for commercial production throughout Florida and across the United States.

Bacterial spot first affects the leaves of the plant, developing black spots the size of shotgun pellets. Then the leaves blacken and ultimately drop. The fruit is still edible but can develop little blisters, making them practically unmarketable.

The plant pathogen that causes bacterial spot in the southeast is called Xanthomonas euvesicatoria pv. perforans. The “pv.” abbreviation stands for “pathovar” and is used to designate a specialized group of bacteria with the same or similar characteristics within a species.


Courtesy UF/IFAS

Gary Vallad, professor of Plant Pathology at the University of Florida’s Gulf Coast Research and Education Center in Balm, said the pathogen has been problematic for the tomato industry since the early 1990s because it has developed a tolerance to copper-based pesticides, typically used for managing bacterial diseases.

“This pretty much limited the usefulness of copper, and without using other types of antibiotics, which we don’t use in the field, it’s really hard to manage this disease,” he said.

Hard to peel, hard to process
Other variations of the bacteria can also cause really large lesions, “which makes the tomato hard to peel mechanically, so processors don’t like that either, so that becomes a loss for them as well,” Vallad said.

That means the tomatoes can’t be canned or used for products like ketchup. There’s much that is unknown about the pathogen, Vallad said.

“A lot of that has been limited by our ability to differentiate strains of the bacterium. So, there’s been a lot of recent advances in our tools to be able to discriminate between different species based on sequencing of the pathogen’s genome,” he said.

“We can’t just look at the bacteria and say, ‘this is Bacteria A, and this is Bacteria B.’ This is what we kind of refer to as almost like cryptic species … they all look the same, so we have to actually … use molecular tools to really be able to differentiate between different strains.”

Vallad said he’s now interested in breeding a tomato with more resistance to the bacteria.

“We need to have a better understanding of the composition of that population, so breeders can actually identify resistance within a tomato that will actually cover all the strains or most of the strains,” he said. They also want to trace the movement of the strains throughout tomato production.

“We know different areas we can always find the bacteria, but we don’t know if the bacteria is exactly the same at every point,” Vallad said. “So, we’re trying to understand, to really look at the movement of the of these strains throughout the production system so we can find where in the production system is the best place to manage them.”

Xanthomonas euvesicatoria pv. perforans is also prominent bacterial species threatening tomatoes in the Midwest, Great Lakes, Northeast, and in neighboring areas of Canada, along with Xanthomonas hortorum pv. gardneri.

Thanks to $5.8 million from the National Institute of Food and Agriculture, Vallad and his team of scientists across Florida and the U.S. will spend the next four years identifying and understanding the different strains of the pathogen to help tomato growers and breeders manage the bacterial spot disease more successfully.

“These types of advancements are not just in this particular disease. It’s really impacting a number of plant diseases, animal diseases and human diseases,” Vallad said. “The exact same technology that was used to understand the COVID virus, we’re using to understand this particular pathogen on tomato.

“And this group of pathogens impact a number of other crops, not just tomato … Other Xanthomonas affect almost every crop we grow in the world. There is a Xanthomonas that can cause disease on it. So, understanding this group of organisms, tomato can be used as a model for other researchers for other crops as well.”

For more information:
WUSF News
www.wusf.usf.edu 

Publication date: Fri 4 Nov 2022

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South Africa: A new way to name bacteria

Posted in Bacteria, Identification on November 9, 2022| Leave a Comment »

A new way to name bacteria: 300-year-old system revised thanks to scientific advances

Published: October 27, 2022 10.41am EDT

Author

  1. Stephanus Nicolaas VenterProfessor in Microbiology and Deputy Director of the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria

Disclosure statement

Stephanus Nicolaas Venter receives funding from the National Research Foundation and the Water Research Commission. He is currently a member of the organizing committee of the SeqCode Initiative and a member of the Committee on Systematics of Prokaryotes.

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Prokaryotes are single-celled organisms without nuclei and are commonly known as bacteria. Ichigomaru/Shutterstock

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Nearly 300 years ago the Swedish botanist Carl Linnaeus secured his place in scientific history when he created what’s known as the binomial system. The year was 1737 and, due to the large diversity of plants and animals collected by naturalist explorers in different parts of the world, Linnaeus saw the need to develop a logical system to classify and group this material in a systematic way.

It’s a system that’s stood the test of time – his basic formula is still in use.

The naming convention applies to all biological organisms: plants, animals and bacteria. Each species receives a name consisting of two parts. The genus name is similar to a surname; all species that share this name are closely related. The second name is unique for each species within the genus. This combination creates a unique name for any described organism. Well known examples include Homo sapiens (modern humans) and Escherichia coli (bacteria).

One of the main benefits of assigning universally accepted distinct names is that it helps people, and particularly scientists, to clearly communicate about a specific organism, regardless of language or geographic barriers. Another boon is that unique names link all the available information on a species together. It also helps scientists to understand shared characteristics and relationships between organisms.

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Naming decisions are not made in a vacuum. Although ideas of what species are and how to recognise them have developed over the past 300 years, the naming system as proposed by Linnaeus remained unchanged.

There are “rule books” for the naming of organisms, generally referred to as “codes”. There are different codes for naming animals, plants, algae and fungi, viruses and bacteria. The Botanical Code, which initially also dealt with bacteria, was first developed in 1867 and is revised every six years during the International Botanical Congress. The Bacterial Code was first published as a separate document in 1947 and was updated this year by the International Committee on Systematics of Prokaryotes.

But the existing code was not enough to deal with advances in technology that have changed how prokaryotes can be studied. So, a new, complementary code has been introduced.

A stable system

If the description of a new species meets all the requirements set out in the rules in the relevant code, the name will be validated – made permanent.

Each new species is also linked to type material: something concrete to compare other individuals against. The type can be represented by museum or herbarium examples, living cultures or even drawings.

But this system doesn’t work well for prokaryotes. These single cell organisms, which don’t have nuclei, are commonly referred to as bacteria (though they also include the Archaea, a group of micro-organisms that are similar to but distinct from bacteria). Prokaryotes are named under the International Code of Nomenclature of Prokaryotes.

Unlike other disciplines’ naming rule books, this code is strict about type material: only a pure culture of the bacterium, available from collections in two different countries, counts as type material. But there’s a problem: most bacteria still can’t be grown in pure culture, on its own in a Petri dish in the laboratory.

Read more: Following a fungus from genes to tree disease: a journey in science

This means that, under the code, they could not be named.

A new initiative, SeqCode, will change the game by allowing DNA sequencing data to serve as the type. I was one of several biologists around the world involved in creating the SeqCode and I believe it is a great achievement.

A formal and stable naming system for all bacteria will help science to unlock the hidden potential of the planet’s biodiversity and to understand their role in the functioning of ecosystems. It will also help scientists to communicate their findings to each other – a big step towards perhaps identifying the next generation of antibiotics or cancer treatment.

Genome sequencing

It’s not known how many prokaryotic species there are – there could be millions or trillions. But so far only around 18,000 have been given permanent (valid) names. The increasing ubiquity of genome sequencing is an opportunity to change this. Rather than having to grow a prokaryotic species in a laboratory to then study and describe its characteristics, biologists can now sequence the organisms’ DNA directly from an environmental sample to obtain a complete or near complete genome. The genome is the DNA blueprint of the bacterium which encodes all the functions the organism will be able to perform.

Read more: Why African scientists are studying the genes of African species, and how they do it

The sequence data is stable enough and adequate to be used to recognise other members belonging to the same species.

In 2018 an international group of bacterial taxonomists and ecologists attended a workshop in the US, funded by the US National Science Foundation, to discuss the future of bacterial taxonomy. The attendees recognised that genome sequencing was a good, scientifically sound way to give many prokaryotes permanent names. This idea was supported by many other microbiologists around the world.

However, a proposal to change the existing code to allow genome sequences as types was not accepted by the International Committee on Systematics of Prokaryotes. With the support of the International Society for Microbial Ecology, some of the meeting attendees began discussing other possibilities.

The idea of an entirely separate code for naming genomically described prokaryotes emerged. Wide consultation followed and, in September 2022, SeqCode – or, to give it its full name, the Code of Nomenclature of Prokaryotes Described from Sequence Data, was launched.

This doesn’t replace the existing code. Bacteria can still be named under the Bacterial Code when a pure culture is available.

It is possible that, in coming years, similar adjustments might be made to – or new codes created for – naming other genomically described micro-organisms such as yeasts and other fungi.

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Taxonomic response of bacterial and fungal populations to biofertilizers

Posted in Bacteria, Biofertilizers, Fungi on November 5, 2022| Leave a Comment »

 Grahame Jackson

PestNet

 Sydney NSW, Australia

 

Taxonomic response of bacterial and fungal populations to biofertilizers applied to soil or substrate in greenhouse-grown cucumber

Nature

Abstract

Reductions in the quality and yield of crops continuously produced in the same location for many years due to annual increases in soil-borne pathogens. Environmentally-friendly methods are needed to produce vegetables sustainably and cost effectively under protective cover. We investigated the impact of biofertilizers on cucumber growth and yield, and changes to populations of soil microorganisms in response to biofertilizer treatments applied to substrate or soil. We observed that some biofertilizers significantly increased cucumber growth and decreased soil-borne pathogens in soil and substrate. Rhizosphere microbial communities in soil and substrate responded differently to different biofertilizers, which also led to significant differences in microbial diversity and taxonomic structure at different times in the growing season. Biofertilizers increase the prospects of re-using substrate for continuously producing high-quality crops cost-effectively from the same soil each year while at the same time controlling soil-borne disease.

Read on: https://www.nature.com/articles/s41598-022-22673-4

 Biofertilizers

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Florida, USA: Managing bacterial spot in tomatoes

Posted in Bacteria on November 4, 2022| Leave a Comment »

Florida researchers get funding to help tomato growers and breeders fight bacterial spot

“It’s really hard to manage this disease”

Florida scientists received a grant to investigate strategies to control bacterial spot in tomatoes. The disease creates major challenges for commercial production throughout Florida and across the United States.

Bacterial spot first affects the leaves of the plant, developing black spots the size of shotgun pellets. Then the leaves blacken and ultimately drop. The fruit is still edible but can develop little blisters, making them practically unmarketable.

The plant pathogen that causes bacterial spot in the southeast is called Xanthomonas euvesicatoria pv. perforans. The “pv.” abbreviation stands for “pathovar” and is used to designate a specialized group of bacteria with the same or similar characteristics within a species.


Courtesy UF/IFAS

Gary Vallad, professor of Plant Pathology at the University of Florida’s Gulf Coast Research and Education Center in Balm, said the pathogen has been problematic for the tomato industry since the early 1990s because it has developed a tolerance to copper-based pesticides, typically used for managing bacterial diseases.

“This pretty much limited the usefulness of copper, and without using other types of antibiotics, which we don’t use in the field, it’s really hard to manage this disease,” he said.

Hard to peel, hard to process
Other variations of the bacteria can also cause really large lesions, “which makes the tomato hard to peel mechanically, so processors don’t like that either, so that becomes a loss for them as well,” Vallad said.

That means the tomatoes can’t be canned or used for products like ketchup. There’s much that is unknown about the pathogen, Vallad said.

“A lot of that has been limited by our ability to differentiate strains of the bacterium. So, there’s been a lot of recent advances in our tools to be able to discriminate between different species based on sequencing of the pathogen’s genome,” he said.

“We can’t just look at the bacteria and say, ‘this is Bacteria A, and this is Bacteria B.’ This is what we kind of refer to as almost like cryptic species … they all look the same, so we have to actually … use molecular tools to really be able to differentiate between different strains.”

Vallad said he’s now interested in breeding a tomato with more resistance to the bacteria.

“We need to have a better understanding of the composition of that population, so breeders can actually identify resistance within a tomato that will actually cover all the strains or most of the strains,” he said. They also want to trace the movement of the strains throughout tomato production.

“We know different areas we can always find the bacteria, but we don’t know if the bacteria is exactly the same at every point,” Vallad said. “So, we’re trying to understand, to really look at the movement of the of these strains throughout the production system so we can find where in the production system is the best place to manage them.”

Xanthomonas euvesicatoria pv. perforans is also prominent bacterial species threatening tomatoes in the Midwest, Great Lakes, Northeast, and in neighboring areas of Canada, along with Xanthomonas hortorum pv. gardneri.

Thanks to $5.8 million from the National Institute of Food and Agriculture, Vallad and his team of scientists across Florida and the U.S. will spend the next four years identifying and understanding the different strains of the pathogen to help tomato growers and breeders manage the bacterial spot disease more successfully.

“These types of advancements are not just in this particular disease. It’s really impacting a number of plant diseases, animal diseases and human diseases,” Vallad said. “The exact same technology that was used to understand the COVID virus, we’re using to understand this particular pathogen on tomato.

“And this group of pathogens impact a number of other crops, not just tomato … Other Xanthomonas affect almost every crop we grow in the world. There is a Xanthomonas that can cause disease on it. So, understanding this group of organisms, tomato can be used as a model for other researchers for other crops as well.”

For more information:
WUSF News
www.wusf.usf.edu 

Publication date: Fri 4 Nov 2022

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