Thursday, April 12, 2018

Gene Editing - A Comment By Bill Gates

I have made remarks here on my blog about CRISPR gene technology as well as a few posts on gene editing and its relevance to modern agriculture and science in general.  I think it is a marvellous technology tool with enormous potential for variety improvement in agriculture.

A recent post highlighted the fact that the USDA has concluded that using CRISPR gene editing is not the same as creating GMO varieties - as no transgenic change occurs.  This allows a less ardous pathway to commercial use for new products developed through this technology, as they are not GMOs.

The comment below by Bill Gates [the one from Microsoft!] might have more clout than me, but he is a strong supporter of genetic improvements across a wide field and now has close contact with eminent researchers  through heading the Bill and Melinda Gates Foundation which supports international research and development.  And he supports CRISPR work generally.

It is worth reading..........

link below:

https://www.foreignaffairs.com/articles/2018-04-10/gene-editing-good?cid=nlc-emc-paywall-free-reading-bill-gates-a-20180411

Monday, April 09, 2018

IP Protection Includes Seeds

The US has made much of the loss of intellectual property to China in recent years.  And in agriculture this includes new varieties and the seeds of those new varieties.

A recent court case has highlighted a new variety that seems to have been on its way to China.......but was detected at the US border.

Sobering reading.

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Chinese Scientist Sentenced to 10 Years in Prison for Rice-Smuggling Plot

The researcher stole genetically modified seeds and planned to give them to a crop research institute in China, the US Justice Department says.
By Ashley Yeager | April 5, 2018
FLICKR, BLOGTREPRENEURChinese scientist Weiqiang Zang was sentenced yesterday (April 4) to 121 months in federal prison for conspiring to steal genetically modified rice seeds from Ventria Bioscience while working at its Kansas-based facility. Zhang planned to give the seeds to a research institute in China, according to a statementfrom the US Justice Department.
“Weiqiang Zhang betrayed his employer by unlawfully providing its proprietary rice seeds to representatives of a Chinese crop institute,” Acting Assistant Attorney General Cronan says in the statement. The “sentence demonstrates the significant consequences awaiting those who would steal trade secrets from American companies.”
Zhang, who has a master’s degree in agriculture from Shengyang Agricultural University in China and a doctorate from Louisiana State University, worked as a rice breeder at Ventria Bioscience. The company develops rice seeds that are genetically reprogrammed to produce human serum albumin, a protein found in blood, or lactoferrin, an iron-binding protein found in human milk. The proteins are then extracted for use as therapeutics.  
According to trial evidence, Zhang stole hundreds of the company’s rice seeds and stored them at his home in Manhattan, Kansas. In the summer of 2013, visitors from a crop research institute in China came to Zhang’s home, and Zhang also took them to tour research facilities in Iowa, Missouri, and Ohio. When the visitors returned home in August 2013, US Customs and Border Protection officers found seeds, including ones belonging to Ventria, in their luggage. Last February, Zhang was convicted of one count of conspiracy to steal trade secrets, one count of conspiracy to commit interstate transportation of stolen property, and one count of interstate transportation of stolen property.
“Ventria invested years of research and tens of millions of dollars to create a new and beneficial product,” says US Attorney McAllister in statement. “It is vital that we protect such intellectual property from theft and exploitation by foreign interests.”

Friday, April 06, 2018

Organic Fertilisers - Contamination with Microplastics Common - Take Care

Users like to belive thay are being positive for the environment by using waste organics that have been converted to organic fertilisers -small pellets or even as bagged compost or by the trailer load.

Recent studies however, confirm the presence of considerable amounts of microplastics in many of the organic fertilisers used around the world.  Most work has been conducted in Europe and North America, but it is highly likely the situation will be broadly similar in Australasia.

While some effort - or even a big effort- is made to eliminate plastics in the original waste stream, it is rarely totally successful, and they get broken up in processing eventually being in the final product as microplastic pieces [ defined as <5mm font="" in="" size="">

There is a lot of discussion about microplastics in both fresh and marine waters, and land contamination is also of  concern.

We really do not understand the potential problem with land, and issues when contamnated areas are used for food production.

More below from a recent article which appeared online.
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compostISTOCK, MAERZKIND
The recycling of biological waste from homes and businesses to make fertilizer, either through composting or fertilization, is a source of microplastic pollution, according to a study published today (April 4) in Science Advances. The particles were present despite efforts to sort and sieve out plastic contaminants either before or after the waste was processed, the authors note.


“The recycling of organic waste through composting or fermentation and subsequent application on agricultural land is, in principle, an environmentally sound practice to return nutrients, trace elements, and humus to the soil,” the study authors write. “However, most household and municipal biowaste is contaminated by plastic material.”

See “Plastic Pollutants Pervade Water and Land

Microplastics, which the new study defines as plastic particles smaller than 5 mm, result from the breakdown of plastics, and are pervasive both on land and in the oceans. While the extent of their environmental and health effects is not clear, studies have found they’re detrimental to the health of organisms such as earthworms and rodents, and that they make their way into human food supplies.
In the new study, researchers at the University of Bayreuth in Germany investigated fertilizer produced by a biowaste composting plant (which treats waste aerobically) and a biowaste digester (which uses an anaerobic process). There were fewer than 25 microplastic particles per kilogram in the compost from the first plant, while the freshly-digested fertilizer from the second plant had up to 146 particles per kilogram of the pollutants. By contrast, no microplastics were found in digestate from an agricultural energy crop digester, suggesting that the contamination in the products from the first two plants originated in the homes and businesses that were the source of the waste used.

Tuesday, April 03, 2018

Varieties Developed via CRISPR to be Less Regulated in USA

As CRISPR gene editing only edits the genome and does not insert foreign genetic material from other species the light hand of regulation may be considered as adequate, or does it need more regulation?

So far it seems that less is adequate, which is generally accepted by many involved in new crop and horticulture variety devlopment.

The following article is a brief, but relevant take on the subject from The Scientist online magazine. This attitude is likely to influence other countries regulatory agencies.
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USDA Will Not Regulate CRISPR-Edited Crops

Restrictions will remain on transgenic plants, which contain artificially inserted genes from other species.
By Diana Kwon | April 2, 2018
PIXABAY, ANALOGICUS
The US Department of Agriculture (USDA) will not regulate plants that have been modified through genome editing, according to a statement released last week (March 28) by the agency.
In the announcement, the USDA states that it won’t oversee the use of genetically altered plants, as long as they could have also been developed through traditional breeding methods, such as cross-breeding or selecting for desirable properties. The agency adds that genome editing allows breeders to introduce new traits more precisely, and at a faster rate.
“With this approach, USDA seeks to allow innovation when there is no risk present,” US Secretary of Agriculture Sonny Perdue says in the statement. “Plant breeding innovation holds enormous promise for helping protect crops against drought and diseases while increasing nutritional value and eliminating allergens.” 
MIT Technology Review notes that transgenic crops—plants that contain artificially inserted genes from other species—will still be regulated.

See “The Unregulation of Biotech Crops

This announcement comes as good news to biotech companies using CRISPR to modify plants. According to Wiredthis move will “[shave] years and tens of millions of dollars off the cost of developing a designer plant.”
“Having this consistent position enables smaller companies and academic labs to form this ecosystem of innovation to bring options to consumers,” Federico Tripodi, CEO of Calyxt, a Minnesota-based biotech that has already developed soybeans that produce oil low in trans fats that can be cooked at high heat, tells Wired.  
Whether gene-edited plants require special labeling is still unclear. “Bioengineered foods are defined by containing genetic material that could not otherwise have been conventionally bred or obtained in nature,” Deepti Kulkarni, a former member of the FDA’s Office of Chief Counsel who currently works at Sidley Austin, a corporate law firm in the U.S., tells Wired. “If USDA is construing the language this way, there is some suggestive signaling that these products might not be subject to disclosure.”

Tuesday, March 27, 2018

Smart Water Management Matters

'Nature-based solutions' key to water management: UN report - World Water Day 22 March.


Wednesday, 21 March, 2018

Adobestock 102784556
Nature-based solutions can play an important role in improving the supply and quality of water and reducing the impact of natural disasters, according to the 2018 edition of the United Nations World Water Development Report.
Presented at the 8th World Water Forum this week by UNESCO Director-General Audrey Azoulay and UN-Water Chair Gilbert Houngbo, the study argues that reservoirs, irrigation canals and water treatment plants are not the only water management instruments at our disposal.
In 1986, the State of Rajasthan (India) experienced one of the worst droughts in its history. Over the following years, an NGO worked alongside local communities to set up water harvesting structures and regenerate soils and forests in the region. This led to a 30% increase in forest cover, groundwater levels rose by several metres and cropland productivity improved.
These measures are examples of the nature-based solutions (NBS) advocated by the latest edition of the report, ‘Nature-based Solutions for Water’. It recognises water not as an isolated element, but as an integral part of a complex natural process that involves evaporation, precipitation and the absorption of water through the soil. The presence and extent of vegetation cover across grasslands, wetlands and forests influences the water cycle and can be the focus for actions to improve the quantity and quality of available water.
“We need new solutions in managing water resources so as to meet emerging challenges to water security caused by population growth and climate change,” said Azoulay. “If we do nothing, some 5 billion people will be living in areas with poor access to water by 2050. This report proposes solutions that are based on nature to manage water better. This is a major task all of us need to accomplish together responsibly so as to avoid water-related conflicts.”
“For too long, the world has turned first to human-built, or ‘grey’, infrastructure to improve water management,” Houngbo said in the foreword of the report. “In so doing, it has often brushed aside traditional and Indigenous knowledge that embraces greener approaches. Three years into the 2030 Agenda for Sustainable Development, it is time for us to re-examine nature-based solutions (NBS) to help achieve water management objectives.”

Focusing on ‘environmental engineering’

So-called ‘green’ infrastructure, as opposed to traditional ‘grey’ infrastructure, focuses on preserving the functions of ecosystems, both natural and built, and environmental engineering rather than civil engineering to improve the management of water resources. This has multiple applications in agriculture, the greatest consumer of water by far. Green infrastructure can help reduce pressures on land use while limiting pollution, soil erosion and water requirements by contributing to the development of more effective and economic irrigation systems, for example.
Thus, the System of Rice Intensification, originally introduced in Madagascar, helps restore the hydrological and ecological functioning of soils rather than using new crop varieties or chemical products. It enables savings of 25 to 50% in water requirements and 80 to 90% in seeds while raising paddy output by 25 to 50%, depending on the region in which it is implemented.
It is estimated that agricultural production could be increased by about 20% worldwide if greener water management practices were used. One study cited by the report reviewed agricultural development projects in 57 low-income countries and found that using water more efficiently, combined with reductions in the use of pesticides and improvements in soil cover, increased average crop yields by 79%.
Green solutions have also shown great potential in urban areas. While vegetated walls and roof gardens are perhaps the most recognisable examples, others include measures to recycle and harvest water, water retention hollows to recharge groundwater and the protection of watersheds that supply urban areas. New York City has been protecting its three largest watersheds since the late 1990s. Disposing of the largest unfiltered water supply in the USA, the city now saves more than US$300 million yearly on water treatment and maintenance costs.
Faced with an ever-increasing demand for water, countries and municipalities are showing a growing interest in green solutions. China, for example, recently initiated a project called ‘Sponge City’ to improve water availability in urban settlements. By 2020, it will build 16 pilot Sponge Cities across the country. The goal is to recycle 70% of rainwater through greater soil permeation, retention and storage, water purification and the restoration of adjacent wetlands.

The importance of wetlands

Wetlands only cover about 2.6% of the planet but play a disproportionately large role in hydrology. They directly impact water quality by filtering toxic substances from pesticides, industrial and mining discharges.
There is evidence that wetlands alone can remove 20 to 60% of metals in water and trap 80 to 90% of sediment from runoff. Some countries have even created wetlands to treat industrial wastewater, at least partially. Over recent years, Ukraine, for example, has been experimenting with artificial wetlands to filter some pharmaceutical products from wastewater.
However, ecosystems alone cannot perform to totality of water treatment functions. They cannot filter out all types toxic substances discharged into the water and their capacity has limits. There are tipping points beyond which the negative impacts of contaminant loading on an ecosystem become irreversible, hence the need to recognise thresholds and manage ecosystems accordingly.

Mitigating risks from natural disasters

Wetlands also act as natural barriers that soak up and capture rainwater, limiting soil erosion and the impacts of certain natural disasters such as floods. With climate change, experts predict that there will be an increase in the frequency and intensity of natural disasters.
Some countries have already started taking precautions. For example, Chile announced measures to protect its coastal wetlands after the tsunami of 2010. The State of Louisiana (USA) created the Coastal Protection and Restoration Authority following Hurricane Katrina (2005), whose devastating impact was magnified by the degradation of wetlands in the Mississippi Delta.
Nevertheless, the use of nature-based solutions remains marginal and almost all investments are still channelled to grey infrastructure projects. Yet, to satisfy the ever-growing demand for water, green infrastructure appears to be a promising solution complementing traditional approaches. The authors of the report therefore call for greater balance between the two, especially given that nature-based solutions are best aligned with the Sustainable Development Goals adopted by the United Nations in 2015.
Coordinated by the World Water Assessment Programme of UNESCO, the United Nations World Water Development Report is the fruit of collaboration between the 31 United Nations entities and 39 international partners that comprise UN-Water. Its publication coincides with World Water Day, celebrated every year on 22 March.
Image credit: ©stock.adobe.com/au/Zffoto

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Some thoughtful ideas that should be considered more often, even in Australia.  Unfortunately it often cuts across the old engineering concepts and old ideas are hard to change.  It also tends to have longer time frames to see change and involves more community groups to develop meaningful ideas.


Sunday, March 04, 2018

Neonicotinoids - EU Ban Possible ?

This insecticide class has been under threat for some time mainly due to the damage possibly caused to bees, a valuable component in crop production of broadacre field crops and in horticulture.

In the EU the products cannot be used on major bee activity crops - eg sunflowers, oilseed rape and maize -  now.

But a recent report is advocating a broader approach and a ban across the  EU might be an option that could be considered, at least outdoors.

More rationale discussion is canvassed here -
https://www.scientificamerican.com/article/e-u-expected-to-vote-on-pesticide-ban-after-major-scientific-review/?utm_source=newsletter&utm_medium=email&utm_campaign=sustainability&utm_content=link&utm_term=2018-03-01_featured-this-week

Given the importance of bees in the production of fruit and seed in many species most growers are careful with most insecticides, but problems can arise, and with this class of chemical  the active ingredient does seem to persist and move within the plant.





Friday, March 02, 2018

Eradicating Mosquitoes - Without Trying

Yes, in the world of science there are some things that occur when unexpected.

This has been a fortutious positive effect in which rat eradication on a remote island chain has resulted in eradication of mosquitoes too.

Read more below.  Something very positive!

If only eradicating Asian tiger mosquitoes was always that easy..........but hey, with many populations of rats on islands now highly targetted for eradication, will we see more positive side effects in warmer regions?

Is there a message in this success that could be replicated on some of Australia's offshore islands where this mosquito occurs too, by targetting rats? 

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Paradise Regained: How the Palmyra Atoll Got Rid of Invasive Mosquitoes

The elimination of the biting pests was an added bonus after researchers unleashed a rat-eradication endeavor on the tiny islands.  
By Ruth Williams | February 28, 2018



Palmyra AtollKEVIN LAFFERTYOne thousand miles south of Hawaii, the Palmyra Atoll, a horseshoe-shaped chain of islets, is about as isolated as you can imagine, says Erin Mordecai, a biologist at Stanford University who has visited the islets to conduct ecology research. “It’s really, really remote and has never had a native human population,” she says. Year-round, the population varies between approximately five and 30 people—generally, scientific researchers and Nature Conservancy staff.
But the atoll is far from unspoiled, Mordecai continues. “The most human impact it’s had was during World War II when there were about 2,400 troops.” Considering the brevity of the soldiers’ inhabitation, the repercussions were immense. “They built airstrips on some of the islands. There’s still metal and debris that they left behind.” They also brought rats and mosquitoes, neither of which is native to the atoll. There are in fact no native mammals and only a few native insects.
With no predators and plenty of food, the rat population exploded. In 2011, it was estimated to have reached 40,000. “There’s not a lot of land . . . [so] they were everywhere,” says wildlife refuge manager Stefan Kropidlowski of the US Fish and Wildlife Service in Honolulu who oversees research visits to the atoll. Kropidlowski had not visited Palymra before the eradication, but “by all accounts,” he says, “if you walked though the jungle, they were in the trees, they were jumping up around you, they were crawling through the cabin screens at night, and it was a huge hassle to store food.”
From a conservation perspective, Kropidlowski says, “the rats were predating a lot of the seabirds and probably resulted in the extirpation of a number of ground-nesting [species].” So, when the atoll became a National Wildlife Refuge in the early 2000s, he says, “rat eradication was one of the major conservation priorities . . . to give the seabirds a chance to start coming back.”
Sea birds flying over Palmyra AtollKEVIN LAFFERTY
A 2011 atoll-wide rat-poisoning endeavor successfully eliminated the rodents, and, in the following years, conservation researchers documented the effects to the native wildlife. Among these scientists was Kevin Lafferty of the US Geological Survey and the University of California, Santa Barbara, who led the research. “We were looking at how the food web was changing after rat removal,” he explains.
But of course, “we were part of the food web,” says Lafferty. “Getting bitten by mosquitoes is the price you pay for working in paradise.” Therefore, after the rodent eradication, it became “just obvious that we weren’t being bitten [during the day] anymore.”
As Lafferty and his colleagues report in Biology Letters today (February 28), not a single Asian tiger mosquito (Aedes albopictus) has been found on Palmyra Atoll during a recent two-year survey. This unanticipated secondary extinction serves as a reminder of the interdependency and fragility of species within ecosystems.
“This is an interesting paper that opens up the fascinating possibility that eradicating one human-introduced pest, which would be the rats, could lead to the secondary elimination of another human-introduced pest, A. albopictus,” says entomologist Megan Fritz of the University of Maryland who was not involved with the study. “The findings have implications for conservation biology and habitat restoration and possibly even human health in sparsely populated tropical island communities.”
Indeed, “this study highlights an often under-sung impact of invasive species—disease vectoring,” Alex Wegmann, the Palmyra program director at the Nature Conservancy in Honolulu who was not involved with the study, writes in an email to The Scientist. “Rats do not carry yellow fever, but, in this case, they allowed the pathogen’s primary vector to persist at Palmyra for decades.”

Starving mosquitoes to death

A. albopictus, one of the two mosquito species on the atoll, bites during the day and feeds preferentially on mammals, but can also bite birds. The other, Culex quinquefasciatus, bites at night and feeds preferentially on birds, but can also bite mammals. Without the rats, it was thought that A. albopictusmight bite birds and humans more often. “We hadn’t predicted that the mosquitoes would [die out],” Lafferty says.
After the rat eradication, researchers started noting how pleasant their trips had been, says Lafferty. Kropidlowski recalls his first visit to the atoll, a few years after the rodents were wiped out. “I had been told to expect lots of mosquitoes,” he says “but there were none.” He remembers noticing old bottles of insect repellent, gathering dust, unfinished.
The idea arose that perhaps the mosquitoes might have starved to death. “Normally, you come up with an idea like that and it just remains an idea,” Lafferty says. But, as luck would have it, Lafferty’s colleague at the University of California, Santa Barbara, and coauthor on the study, Hillary Young, had data on flying insects, including mosquitoes, that predated the rat eradication.
“It was very serendipitous and not planned or expected,” says Lafferty.
Because the researchers would still occasionally be bitten at night, the question was, had the daytime-biting, mammal-preferring A. albopictus really been wiped out? Lafferty’s team went to great lengths to try to capture members of the species—setting two different types of trap—before concluding that, yes, by the standards set by the World Health Organization (two years of sensitive surveillance without detection), A. albopictus was indeed gone.
It was clear the mosquitoes hadn’t switched to feeding more often on birds and humans, at least not in sufficient numbers to support the population. And there was another factor that the authors speculate may have contributed to the mosquitoes’ demise. Without the rats, there were far fewer freshwater receptacles in which mosquito larvae could hatch. The rodents would gnaw coconut shells in half, to eat the innards, and leave them littered about the islets, catching rainwater.
It would be nice to think that in areas with more people, such as cities, rat eradication might also eliminate mosquitoes, but this seems unlikely, says Fritz. “The modelling results from the paper suggest that larger human populations would likely be able to sustain A. albopictus populations.”
“I don’t think the main message of this paper is that we’ll be able to eradicate rats to get rid of mosquitoes,” agrees Lafferty. “The more important message is . . . the interdependence of species.”
If a species is driven to extinction, he says, “are we just going to lose that one species . . . or could we lose many? Even though we’re talking about two species we don’t like, here, it could just have easily been two species we did like. It could have been, for instance, an endangered flower and its pollinator.”
K.D. Lafferty et al., “Local extinction of the Asian tiger mosquito (Aedes albopictus) following rat eradication on Palmyra Atoll,” Biol Lett, doi:10.1098/rsbl.2017.0743, 2018.

Thursday, March 01, 2018

Warm Autumn ?- Could Still Plant Compadre Zoysia Seeded Lawn

The latest medium term climate notices issued on 28 February 2018 for March - May [ ie Australian autumn period] are predicting warmer days and nights for much of Australia in this Autumn period.

A more detailed map and analysis is available on the site http://www.bom.gov.au/climate/outlooks/#/temperature/maximum/median/seasonal/0 

Much of Australia is likely to be warmer over the next 3 months, both days and nights.

This presents an extended opportunity to get a new seeded zoysia turf area started and probably well matured in this period, rather than waiting for late next spring. However, it is prudent if considering this option, to get sowing under way in the next month or so to capitalise on the warmer weather.  Opportunities also are better if in north Australia, to start an area, mostly missing the very wet periods of the monsoon weather that can cause erosion and management issues for new areas.

Compadre zoysia seed still available - contact office@abovecapricorn.com.au for further information and pricing.  We also have a seres of information sheets available for establishing and maintaining zoysia turf in pdf electronic format - just ask!

Wednesday, February 28, 2018

How Viruses Attack Plants

How Viruses Attack Plants

Viruses are incapable of reproducing without the help of a host, whose cells copy their genetic material and fabricate the building blocks of new virus particles.
By Claire Asher | February 1, 2018


Most plant viruses are transmitted by insect vectors that cause damage to the plant and create an entry point for pathogens, or that tap into the phloem to feed. Once inside, viruses use the handful of genes in their tiny genomes to orchestrate the plant cells’ machinery, while evading the plant’s defenses. Below is a generalized depiction of this infection process for RNA viruses, the most common type of plant virus.
© PENS AND BEETLES STUDIOS
  1. Some viruses can infect plants when aphids and other insects tap into the phloem to feed. Such insect vectors can also pick up virus particles and carry them to new plant hosts.
  2. Other viruses infect plant cells through a wound site created by a leaf-munching insect such as a beetle.
© PENS AND BEETLES STUDIOS
  1. Viral capsid shell opens to release the viral genome, which is translated into proteins that direct the formation of a viral factory from membranes of the endoplasmic reticulum and other organelles.
  2. Antiviral proteins, such as those in the Argonaute family, patrol cells for invading pathogens, but they cannot break into the viral factories.
  3. Viral RNA is replicated and exported to the cytoplasm.
  4. Viral RNA and newly assembled viral particles move to other cells through plasmodesmata, which can be widened by virus-encoded movement proteins.
  5. Some virus particles enter the plant’s transport streams.
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This article infographic on virus attack on plants is also relevant to turf grasses.  There are quite a few virus diseases of relevance to turf, and this article offers some information on what happens with a generic infection, although some other pathways are also possible.

The article was first published in the online edition of The Scientist, late February 2018.

Wednesday, February 21, 2018

The Plant Microbionome

Recently came across an article on this topic by Davide Bulgarelli and how manipulation of the composition of the organisms there might influence agricultural productivity.

A good read - but mostly ignored by mainstream agricultural scientists.

Appended below.
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How Manipulating the Plant Microbiome Could Improve Agriculture

It has become increasingly evident that, like animals, plants are not autonomous organisms but rather are populated by a cornucopia of diverse microorganisms.
By Davide Bulgarelli | February 1, 2018



MODELING THE MICROBIOME: Using synthetic communities of microbes to colonize Arabidopsis plants grown in a sterile substrate—the botanical equivalent of germ-free mice—researchers can begin to understand how the microbiome affects plant health.© SIMON FRASER/SCIENCE SOURCE
Afew years ago, as a postdoc in the lab of Paul Schulze-Lefert at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, I used next-generation sequencing to study the bacterial communities that populate roots of the model plant Arabidopsis thaliana. Although scientists had known for many years that roots interact with a variety of microorganisms, the composition of these communities was still poorly understood. As our sequencing data began rolling in, I was stunned by the staggering taxonomic diversity of bacteria that a single, tiny root can host. Yet there was an order in this apparent chaos. Almost invariably, members of the phyla Actinobacteria, Bacteroidetes, and Proteobacteria were enriched, differentiating the root specimens from the surrounding environment.
Subsequent studies by other labs supported our findings and posited Firmicutes as an additional dominant member of the plant microbiota. In addition to these bacterial groups, genomic surveys of plants have revealed certain fungal and eukaryotic microbes. And all of these groups of organisms are making themselves at home not just beneath the soil in and around plants’ roots, but in other tissues, such as leaves, as well.
This research immediately raised new questions: Why were certain microbes more abundant in roots and leaves? How did these microbial communities assemble? And most critically, how did they affect plant health?
Recently, in addition to genomic surveys of the microbes present in various plant tissues, researchers have begun to probe the functional consequences of these bacterial, fungal, and eukaryotic symbionts. A better understanding of the molecular dialog between plants and their microbiota could revolutionize agriculture. The world population is expected to reach 9.8 billion in 2050, more than 30 percent larger than at present. This will put enormous pressure on food production globally—pressure that won’t be relieved solely by the agrochemicals farmers currently use to increase yield and protect crops from pests and pathogens. To encourage a sustainable food source for humanity, radical changes in the crop production process are needed—changes that could come in the form of microbial manipulation.
The interface between plant roots and soil—a zone called the rhizosphere—and the root itself are sites of colonization for microbes capable of enhancing mineral uptake by the plant, of both actively synthesizing and modulating the plant’s synthesis of chemical compounds called phytohormones that modulate plant growth and development, and of protecting plants from soil-derived pests and pathogens. For these reasons, scientists are looking to manipulate the microbes populating this belowground habitat to sustainably increase crop production. And in my lab, we are looking at ancient varieties and wild relatives of crops as a source of insights into beneficial associations between plants and microbes that could be adapted for agricultural settings.

Surveying the plant microbiome

The roots of land plants thrive in soil, one of the richest and most diverse microbial reservoirs on Earth. It has been estimated that a single gram of soil contains thousands of different bacterial species, not to mention other microorganisms such as archaea, fungi, and protists. Perhaps not surprisingly, the establishment of interactions with the soil biota represented a milestone for plants’ adaptation to the terrestrial environment. Fossil evidence suggests that the first such interactions with fungal members of the microbiome occurred as early as ~400 million years ago.1
PLANTS’ MICROBIAL COMMUNITIES: Like animals, plants host communities of microbes that influence a wide variety of their biological processes. Recent surveys of the plant microbiome have begun to document which species are present—including not just bacteria, but fungi and microscopic eukaryotes as well—and how they affect the plant’s health and functioning.
See full infographic: WEB | PDF
© MESA SCHUMACHER
Comparative studies indicate that soil characteristics such as nutrient and mineral availability are major determinants of the root microbiome. Just as digestive tract microbes interact with the food consumed by vertebrates, the root microbiome mediates the soil-based diet of plants. Also paralleling host/microbe interactions in the animal kingdom, individual members of the plant microbiome appear to be compartmentalized. I and other researchers working with Arabidopsis and with rice have identified at least three distinct microbiomes thriving at the root-soil interface: that in the rhizosphere; another one on the root surface, or rhizoplane; and a third one inside the root, an area known as the endosphere.2,3In all three compartments, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria dominate the bacterial communities in multiple plant species. The aboveground portions of plants such as leaves show similarly predictable microbial composition. (See illustration at left.)
While the categories of microbes that make up the plant microbiome are largely conserved, much variation exists in the species compositions of these communities across hosts. One key factor in determining how the microbiome is populated and maintained appears to be the plant’s release of organic compounds into the rhizosphere, a process known as rhizodeposition. The amount and composition of these organic deposits vary depending on plant species and developmental stage, but may account for up to 11 percent of net photosynthetically fixed carbon and 10 percent to 16 percent of total plant nitrogen.4 This process influences the chemical and physical composition of the rhizosphere and, in turn, provides signaling molecules and organic substrates for microbial growth.
ROOT BUGS: Plant roots and the interface between the roots and the soil—a zone called the rhizosphere—are home to diverse microbes that can affect mineral uptake by the plant.© BIOPHOTO ASSOCIATES/SCIENCE SOURCE
Another factor that likely shapes the composition of the plant microbiome is interaction between microbes. In 2016, Eric Kemen of the Max Planck Institute for Plant Breeding Research and colleagues surveyed the microbes thriving in and on wild Arabidopsis leaves at five natural sites in Germany sampled in different seasons. They then plotted correlations between the abundances of more than 90,000 pairs of microbial genera identified in their survey, revealing six “microbial hubs”—nodes with significantly more connections than other nodes within the network. These hubs were represented by the oomycete genus Albugo, the fungal genera Udeniomyces and Dioszegia, the bacterial genus Caulobacter, and two distinct members of the bacterial order Burkholderiales.5 Given the high degree of connectivity within the communities, it is likely that these microbial hubs play a disproportionate role in the microbiome, akin to that of keystone species in an ecosystem.
To validate this idea that certain species can drive the composition of the plant microbiome, Kemen’s team selected Albugo sp. and Dioszegia sp. as paradigmatic examples of microbial hubs. Albugooomycetes are eukaryotic pathogens of Arabidopsis with an obligate biotrophic lifestyle—meaning that they cannot be cultured outside their host. Consistent with the central role of Albugo in the plant’s microbial community, Arabidopsis that had been artificially infected with Albugo laibachii and maintained in potting soil under controlled conditions displayed a bacterial microbiome composition that was less variable across plants than that of uninfected individuals. Conversely, differences between the bacterial microbiomes of three distinct Arabidopsis strains were amplified in the presence of A. laibachii infection. The fungal microbiome, however, was not significantly affected by the presence of A. laibachii and another Albugo species.
I was stunned by the staggering taxonomic diversity of bacteria that a single, tiny root can host.
Kemen’s team conducted a parallel set of experiments with Dioszegia sp., which—unlike Albugo sp.—are culturable under laboratory conditions, and six bacterial isolates from Arabidopsis leaves. The results confirmed that the presence of the fungal species can strongly inhibit the growth of Caulobacter—plants whose leaves were inoculated with Dioszegia sp. showed a 100-fold reduction in the number of colony-forming units of Caulobacter sp.—mirroring the significant negative correlation observed between these two groups of microbes in the network analysis.5
In 2017, Harvard University’s Roberto Kolter and colleagues demonstrated that such microbial interactions are not limited to Arabidopsis. The researchers developed a simplified version of the maize root microbiome, consisting of seven bacterial strains previously identified in sequencing surveys. By using a leave-one-out approach to colonizing naive maize plants, they demonstrated that removal of Enterobacter cloacae disrupts the composition of the microbial community, which became dominated by Curtobacterium pusillum, while the other five species had nearly disappeared. Interestingly, this effect was limited to plant colonization: when the seven strains of bacteria were monitored in a substrate that did not contain maize seedlings, the community’s composition was significantly different from the one retrieved from roots, and the regulatory role exerted by E. cloacae was not detected.6
These studies suggest that individual members of the microbiome can have a disproportionate role in assembling and stabilizing the community. Deciphering the interactions within and between the various taxa populating leaves and roots will be required to understand the regulation of the plant microbiome.

From composition to function

For years, researchers have observed that, despite the presence of pathogens and conditions favorable to infection, some regions produce plants that are less susceptible to disease than other areas. The soils in these areas, it turns out, support plant health via the microbiome.
Researchers are making strides in understanding the mechanisms underlying this support. In 2011, for example, a team led by Rodrigo Mendes, then at Wageningen University and Research Centre in the Netherlands, demonstrated that disease suppression was linked to the recruitment of a specific population of Pseudomonadaceae, a family of the phylum Proteobacteria. Using a PCR fingerprinting approach, the researchers discerned that this population could be grouped into ten haplotypes, which the team designated A to J. Of these, haplotypes A, B, and C represented some 90 percent of the isolated bacteria. When inoculated in soil, a representative strain of haplotype C suppressed the incidence of disease caused by the fungus Rhizoctonia solani on sugar beet roots, while, surprisingly, strains from haplotypes A or B did not.7
Similarly, in their study published last year, Kolter and colleagues found that maize plants inoculated with the seven selected bacterial strains showed significantly delayed development of Fusarium verticillioides, the causal agent of maize blight. This phenomenon was mediated by the specific strains chosen, and not by bacterial colonization per se, as seed treatment with a laboratory strain of Escherichia coli did not protect maize seedlings from pathogen development. Likewise, the seven strains together were required for the protective effect: inoculation with individual strains resulted in significantly less protection against F. verticilloides.
This method of combining sequencing data with microbial isolation is becoming a powerful tool to formulate testable hypotheses and gain novel insights into the function of the plant microbiome. Like Kolter, researchers are assembling microbial isolates into synthetic communities (SynComs) of known composition and testing their effects on host plants. This approach was once considered a daunting task, as only a very limited fraction—often less than 1 percent—of soil biota was considered culturable under laboratory conditions. But in 2015, Schulze-Lefert’s lab teamed up with Julia Vorholt’s group at ETH Zurich in Switzerland to investigate the proportion of Arabidopsis-associated bacteria that can be cultured, and found the 1 percent statistic to be a vast underestimate.
FUNGAL FINGERS: In addition to bacteria, the plant microbiome includes fungal species such as the Rhizoctonia solani shown here.© DENNIS KUNKEL MICROSCOPY/SCIENCE SOURCE
Comparing the taxonomic relationships among some 8,000 colony-forming microbes from leaves and roots of plants using cultivation-independent sequencing surveys of leaf and root microbiomes, the researchers demonstrated that more than 50 percent of the dominant members of the Arabidopsismicrobiome can be cultured in vitro.8 Taking advantage of this finding, the team assembled SynComs representative of the microbiota of the Arabidopsis roots and leaves and tested the communities’ capacities to colonize these tissues on plants grown in a sterile substrate—the botanical equivalent of germ-free mice. These experiments revealed that, upon plant inoculation, root and leaf isolates form microbial communities resembling the natural microbiomes of those tissues, demonstrating that the SynCom approach accurately recapitulates the effects of a complete microbiota.8
Since then, numerous researchers have begun to develop SynComs to further explore the function of the plant microbiome. Earlier this year, for example, Jeff Dangl of the University of North Carolina at Chapel Hill and colleagues used the SynCom approach to explore the role of the root microbiome in phosphate uptake. In nature, less than 5 percent of the phosphorus content of soils is available to plants. To circumvent this limitation, farmers rely on the application of chemical fertilizers, but this approach is not sustainable in the long term. Thus, understanding how plants and their associated microbes can thrive under sufficient and limiting phosphorus supplies is a priority. There is a huge body of literature documenting the contribution of arbuscular mycorrhizal fungi to phosphorus uptake in plants, but the role of the bacterial microbiota remains mysterious.
Scientists are looking to manipulate soil microbes to sustainably increase crop production—and novel insights into the plant microbiome are now facilitating the development of such agricultural tactics.
In experiments with Arabidopsis, which does not engage in symbiotic relationships with mycorrhizal fungi, Dangl and his colleagues compared the microbiomes of wild-type plants with those of mutant lines that had impaired phosphate starvation responses (PSRs)—a set of morphological, physiological, biochemical, and transcriptional activities evolved by plants to cope with phosphorus deficiency. Using a SynCom represented by 35 taxonomically diverse bacterial isolates from Arabidopsis and related plants, the researchers demonstrated that wild-type plants and mutants, grown on agar plates, assemble distinct root communities when exposed to both low and high phosphorus concentrations. Remarkably, SynCom inoculation reduced accumulation of phosphorus when plants were grown under limited conditions but not when plants were grown in the presence of abundant phosphate, suggesting that bacteria and plants compete for the element.
By monitoring a core set of 193 marker genes, the team observed that SynCom inoculation greatly enhanced PSR-related transcription in wild-type plants. When the researchers transferred inoculated wild-type plants grown with limited phosphorus to plates with sufficient supplies, they observed a striking result: 20- to 40-fold increases in phosphorus concentration in the plant stem, as compared with mock-inoculated controls. Such a dramatic increase in phosphorus uptake was not detected in inoculated plants initially grown with sufficient phosphorus. Therefore, initial plant-bacteria competition for phosphorus might be part of an adaptive mechanism to maximize PSR in plants.9
Further investigation into the binding sites of transcription factors on Arabidopsis DNA revealed that PHR1, a master regulator of PSR, and its paralog PHL1 contribute to transcriptional regulation of plant immunity. In particular, phr1;phl1 mutant plants display enhanced activation of plant immunity genes in response to phosphate starvation and to SynCom inoculation, compared with wild-type plants. Together, these data suggest that the nutritional status of the host is a driver of microbiome composition; through master regulators of mineral starvation, plants can modulate immune responses, which could, in turn, shape microbiome composition. (See “Holding Their Ground,” The Scientist, February 2016.)

What’s next?

Characterizing the plant microbiome and its function could be applied in an agricultural setting, better equipping our crops to grow in resource-poor environments and to fight off dangerous pathogens. Indeed, the private sector has begun to invest in this approach. One strategy many companies are pursuing is a form of plant probiotic, which consists of preparations of beneficial microbes to be mixed with seeds at sowing and again once the seedlings germinate. Another approach is to use plant breeding to select for varieties that have enhanced symbiosis with the microbiota.
Many questions remain about the plant microbiome, however—not least of which is how thousands of years of cultivation have changed crops’ relationships with the soil biota. Using a cultivation-independent approach, my colleagues and I recently demonstrated that wild ancestors and modern varieties of barley (Hordeum vulgare) host distinct microbiotas.10 Likewise, Jos Raaijmakers of the Netherlands Institute of Ecology and colleagues last year identified a shift in the structure of the microbiome of modern and ancestral varieties of common bean (Phaseolus vulgaris); Bacteroidetes were more abundant in wild relatives, and their contribution to the community was progressively replaced by Actinobacteria and Alphaproteobacteria in the more domesticated plants.11
How do these differences translate to altered functionality of the microbiome? Thanks to the experience gained by Arabidopsis scientists, we are now in a position to address this question, and developing SynComs from crops will be an important step in the process.
Luckily, the field is motivated to do just that, as well as to define a road map to achieve the translational potential of the plant microbiome. In a few years, the plant microbiome manipulations may have moved from the lab to the field.

Davide Bulgarelli is a principal investigator at the University of Dundee in the U.K. His research aims at understanding the structure, function, and host control of the microbiome thriving at the root-soil interface.

References

  1. P. Bonfante, A. Genre, “Plants and arbuscular mycorrhizal fungi: an evolutionary-developmental perspective,” Trends Plant Sci, 13:492-98, 2008.
  2. D. Bulgarelli et al., “Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota,” Nature, 488:91-95, 2012.
  3. J. Edwards et al., “Structure, variation, and assembly of the root-associated microbiomes of rice,” PNAS, 112:E911-E920, 2015.
  4. D.L. Jones et al., “Carbon flow in the rhizosphere: carbon trading at the soil-root interface,” Plant Soil, 321:5-33, 2009.
  5. M.T. Agler et al., “Microbial hub taxa link host and abiotic factors to plant microbiome variation,” PLOS Biol, 14:e1002352, 2016.
  6. B. Niu et al., “Simplified and representative bacterial community of maize roots,” PNAS,114:E2450-E2459, 2017.
  7. R. Mendes et al., “Deciphering the rhizosphere microbiome for disease-suppressive bacteria,” Science, 332:1097-100, 2011.
  8. Y. Bai et al., “Functional overlap of the Arabidopsis leaf and root microbiota,” Nature, 528:364-69, 2015.
  9. G. Castrillo et al., “Root microbiota drive direct integration of phosphate stress and immunity,” Nature, 543:513-18, 2017.
  10. D. Bulgarelli et al., “Structure and function of the bacterial root microbiota in wild and domesticated barley,” Cell Host Microbe, 17:392-403, 2015.
  11. J.E. PĂ©rez-Jaramillo et al., “Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits,” ISME J, 11:2244-57, 2017.