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Reading Table

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NUR SHAMIMIE MAISARAH BINTI AZLI

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Soil health and microbiomes: Their vital role in modern agriculture

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Soil health is a crucial component of sustainable agriculture, influencing crop productivity, environmental quality, and overall ecosystem function. A key element of soil health is the soil microbiome, a diverse community of microorganisms, including bacteria, fungi, archaea, viruses, and protozoa. Understanding and managing the soil microbiome is essential for improving soil health and agricultural productivity.

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Nur Syahirah binti Yusri

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Soil microbes supercharge soybeans with less fertilizer.

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Harnessing the microorganisms found around plant roots could help crops flourish and improve the sustainability of agriculture and plant-based meat.

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If you are on a farm and scoop up a handful of soil,chances are what you hold in your palm isn't very healthy. The United Nations estimates that 40% of topsoil worldwide is moderately or severely degraded - a proportion they say could rise to 90% by 2050 if harmful agricultural practices, such as excessive fertilizer use, persist.

"Prosperity has been achieved by enhancing crop production through the extensive use of chemical fertilizers," says Haruko Takeyama, a microbiologist at Waseda University in Tokyo, Japan. But it has also had significant negative impacts on the environment and has degraded soil quality. And with the rise in global population, the need to use fertilizer is increasing - with 95% of human food derived from soil.

But Takeyama and her team think either boosting beneficial natural microorganisms or using soil microbes to help create more sustainable fertilizers, could be the secret to maintaining nutrient-rich, productive soils.
SOY AS A SPRINGBOARD
Some microorganisms help to promote plant growth and boost the availability of nutrients, says Takeyama. But relatively little is known about soil microbes, which is why her team at Waseda have spent more than three years gathering genomic and functional data on them.

The researchers' efforts are part of the Japanese government's Moonshot Research and Development Program - an initiative launched in 2020 to 'create disruptive innovation' to tackle some of the country's most pressing problems, including a rapidly aging population and climate change.

Takeyama's research falls under the fifth goal: creating a sustainable global food supply by tapping little-exploited biological resources by 2050. She heads a consortium of five research groups from universities, research institutes and companies, which are all seeking to understand and control soil microbes, plants, environment and their interactions - with a particular focus on soybeans.

"From a diet and market perspective, soybeans are probably one of the most important crops in Japan," says Satoru Shimokawa an agricultural economist at Waseda University. "However, our self-sufficiency is very low and the country relies on imports for 93% of its soybean needs".

Shimokawa leads a research group within the consortium that is attempting to bridge the gap between science and society.

Soy is the source of many traditional foods in Japan, from tofu to edamame beans. It's also one of few known edible crops that contain all the essential amino acids found in meat, and so offers an alternative source of protein.

As a result, soy is often used as the basis for a growing market in plant-based meats, foods that attempt to approximate the qualities of meats, such as mouthfeel, flavour and appearance. "Many venture companies have started to use soy as a new food material," says Takeyama.

From a microbiology standpoint, soybeans have a very interesting relationship with microbes, she adds. Legumes, including soybeans, form symbiotic relationships with bacteria, called rhizobia, that inhabit nodules on their roots. These rhizobia convert atmospheric nitrogen into ammonia that is useful for plant growth, through a process known as nitrogen fixing.

Rhizobia are part of a group of growth-promoting microbes that are being examined by Takeyama's team. For example, by seeding soybeans with rhizobia, the team has seen signs that the bacteria may be able to promote soybean growth. Takeyama's ultimate aim is to make some of these useful microbes stronger, she says. "But for that, we need more data."

Others, such as Tsuyoshi Tanaka and Naoko Ohkama- Ohtsu from the Tokyo University of Agriculture and Technology, try to use microbes in conjunction with recycled minerals from sewage to help crops grow.

As part of the Moonshot project, and in collaboration with a number of commercial companies, Tanaka and Ohkama-Ohtsu's team are developing the means to extract phosphorus from sewage to use as fertilizer. They hope to incorporate microbes - such as phosphorus-solubilizing bacteria and nitrogen-fixing bacteria - to help plants extract the maximum benefits from this product.
SOIL ATLAS
Back at Waseda, Takeyama's team uses a number of gene-sequencing techniques, including one she pioneered more than a decade ago, which allows microbes to be studied at a single-cell level. Doing this helps to identify which microbes are present and pinpoints their functions, she explains.

This information is keyed into a database called the Agricultural Soil Microbiome Atlas, which is housed and run by the Moonshot project team through Waseda. The atlas is a repository of soil physical and chemical properties, as well as genomic and functional data on its microbes.

More than 400,000 microbes have been categorized so far. Included is genomic data from soybeans, with a focus on the effects of microbe-plant interactions. This data has been put together by Minami Matsui at Yokohama City University and Toyoaki Anai at Kyushu University in Fukuoka, Japan.

Using this data, it has become possible to identify a good mix of microbes that support strong soybean growth. In the future, Takeyama hopes that the atlas will guide farmers toward microbial supplements and soil improvements that enhance communities of microbes beneficial to plant growth.

"And soybeans are just the beginning, we are also interested in expanding our work to other kinds of high-value crops," she adds.
CARBON DIOXIDE SINK
Another challenge is to develop an accurate method of measuring carbon dioxide in soils. Many scientists expect soils to act as carbon sinks, and as a result, finding a precise way to measure carbon in soils is a high priority.

A group, led by Satoshi Wada at Japan's national research institute, RIKEN, has created an optical system to monitor carbon dioxide, nitrous oxide and methane in soil and is developing a standard methodology to use it to assess agricultural carbon credits.

This technology could be incorporated into a crop monitoring and analysis technology known as an 'agricultural digital twin', which is being developed by another Moonshot researcher based at RIKEN, Yasunori Ichihashi. This system digitally simulates agricultural ecosystems to aid real-time management and analysis.

Meanwhile, Shimokawa is investigating consumer response, and trying to glean whether they will pay more for environmentally friendly food products. So far, his research shows that consumers respond best to messages highlighting personal benefits, such as better taste or nutrition.

Shimokawa sees his job as helping to create economically sound businesses based around sustainable agriculture. This work is crucial, says Takeyama, as the success of the project lies in promoting soil health monitoring globally and collaborations with food companies to develop more sustainable food products.

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Soil microbes supercharge soybeans with less fertilizer

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Harnessing the microorganisms found around plant roots could help crops flourish and improve the sustainability of agriculture and plant-based meat.

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How CRISPR/Cas Revolutionizes Plant Breeding: Accelerating Genetic Diversity and Trait Development

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Plant breeding at the speed of light- the power of CRISPR-Cas to generate directed genetic diversity at multiple sites | BMC Plant Biology | Full Text

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How Biophysics can be applied to enhance the agricultural industry

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