LIFE SCIENCE

Fighting soil-borne diseases: a “cocktail” of bacteriophages


The “battlefield” of rhizosphere phages and soil-borne diseases. Photo courtesy of interviewee

Bacteriophages are a class of microorganisms that specifically “eat” a certain type of bacteria and are highly host-specific. Usually they do not infect non-host bacteria. Because of this specificity, scientists have been trying to use bacteriophages to control pathogenic bacteria in the soil that are harmful to crop growth.

On February 1, Microbiome published the latest research results of Academician Shen Qirong’s team from the College of Resources and Environmental Sciences of Nanjing Agricultural University online. The study found that soil-borne wilt caused by Fungi chinensis in soil was closely related to the community composition and host interaction characteristics of crop rhizosphere bacteriophages. This study demonstrates for the first time the potential influence of obligate phages of indigenous bacteria on the invasion of soil-borne pathogens, and provides a new theoretical basis for the use of bacteriophages to reduce soil biological barriers of P. wizen.

Microbiome official promotional video. Respondents provide

Self-developed root box to achieve in-situ tracking

“Soil biological barriers caused by soil-borne pathogens are an important cause of plant diseases and are a constant threat to food security and human health.” Wei Zhong, the corresponding author of the paper and a professor at Nanjing Agricultural University, told China Science News that the rhizosphere microbiome, as the first line of defense against the invasion of pathogenic bacteria, plays an important role in plant growth and health. For example, bacterial communities can reduce soil biological barriers, for example by competing for niches.

Bacteriophages are a class of microorganisms that obligately infect their host bacteria and are classified as viruses. It is widely found in marine and terrestrial natural ecosystems. For example, an obligate bacteriophage of Chlorella refers to a bacteriophage that can only infect pathogenic Bacterius, while an indigenous bacteriophage refers to a phage of other non-pathogenic bacteria (native to the soil) that live in the plant rhizosphere.

Indigenous bacterial obligate bacteriophages. Photo courtesy of interviewee

Wei Zhong introduced that bacteriophages can regulate the number of bacterial populations in the soil by infecting host bacteria, drive changes in the diversity and composition of bacterial communities, and then affect ecosystem functions.

“The abundance and diversity of bacteriophages in soil are high, but their relationship with the occurrence of soil-borne diseases has not been studied.” Wei Zhong explained that the abundance of bacteriophages can be understood as the number of bacteriophages in the rhizosphere soil, and diversity can be understood as the types of rhizosphere phages.

Wei Zhong told reporters that in order to understand the relationship between bacteriophages and the occurrence of soil biological barriers, it is necessary to understand what changes in the abundance and diversity of bacteriophages in the soil during the invasion of soil-borne pathogens, so as to find the mechanism and law of action.

“Continuous sampling and analysis of soils in the same area at different time nodes, that is, in situ tracking, can obtain more realistic and coherent data.” However, the traditional method is usually to remove plants and then collect the soil in the rhizosphere, which is destructive sampling and can prevent plants from growing.

Therefore, traditional methods can usually only sample different plants at different times, and cannot track the succession of rhizosphere microbial communities at different growth stages of individual plants.

Photo courtesy of interviewee

In order to solve this problem, the laboratory independently developed a non-destructive rhizosphere soil continuous in situ collection root box device. Wang Xiaofang, co-first author of the paper and associate professor of Nanjing Agricultural University, introduced that the root box is a three-layer cylindrical device, and the outer layer plays a supporting role. The inner layer, the root chamber, is the place where plant roots grow, and is a cylinder made of nylon mesh, which can limit the growth of plant roots. The middle layer is composed of 20 nylon mesh bags arranged in succession, and the soil in the nylon mesh bag can exchange biotic and abiotic substances with the surrounding soil and can be affected by plant roots.

Wang Xiaofang told China Science News that when the plant root system grows throughout the root chamber, the soil in the middle nylon mesh bag can be regarded as rhizosphere soil. Through the improved root box device, the rhizosphere soil of individual plants at different times during the whole growth period was continuously collected without destroying the plant root system, and the dynamic tracking of the rhizosphere microbial community composition of the same plant from transplanting to final disease was realized.

It is reported that the root box has been authorized for utility model patents.

How exactly rhizosphere phages affect plant health

With the dynamic monitoring data obtained by in situ tracking of the root box, combined with the research methods of bacteriophage, metagenomic and culture groups, they discovered a new mechanism by which rhizosphere bacterial community changes affect plant health. 

Yang Keming, co-first author of the paper and a doctoral student at Nanjing Agricultural University, said that they found that there were significant differences in the composition and diversity of bacteriophage communities in the rhizosphere of healthy plants and phage communities in the rhizosphere of diseased plants. Higher abundance of cyclic bacteriophages of P. wizenis are present in the rhizosphere of healthy plants, which suppress the number of pathogenic bacteria through bottom-up density control.

Wei Zhong explained that bacteriophages and bacteria are a predatory parasitic relationship, similar to antibiotics, bacteriophages can directly destroy host bacteria through lytic infection. However, because phage replication also depends on the host bacteria, it will eventually control the number of pathogenic bacteria in a relatively low range, rather than completely eliminating the pathogenic bacteria. This is called density control.

Based on phage-bacterial co-occurrence analysis, the study identifies potential links between indigenous bacteria and their obligate bacteriophages. They hypothesized that the interaction of obligate bacteriophages of indigenous bacteria with indigenous bacteria would affect the occurrence of biological disorders of mycobacterium. This is because there are potential inhibitors or promoters of pathogenic bacteria in indigenous bacteria, which can directly inhibit or promote the occurrence of soil chlorina biological disorders. Therefore, not only the bacteriophage of the dead fungus can directly affect plant health, but also the obligate bacteriophage of indigenous bacteria can indirectly affect plant health.

To test this analysis, Yang said, they isolated indigenous bacteria and their obligate bacteriophages and validated them using indoor and potted experiments. It was found that obligate bacteriophages of indigenous bacteria could indirectly promote the occurrence of soil blancilla biological disorders by targeting beneficial indigenous bacteria.

Explore “Phage Cocktail Therapy”

“When establishing bacteriophage microecological therapy, in addition to paying attention to the role of obligate phages of pathogenic bacteria, the influence of obligate bacteriophages of indigenous bacteria rich in rhizosphere should also be comprehensively considered on the reduction of soil biological barriers.” Wei Zhong said that this is a recommendation for future strategies to reduce soil biological barriers.

Shen Qirong, academician of the Chinese Academy of Engineering and professor of Nanjing Agricultural University, told China Science News that the biological barriers of soil withered bacteria in China have caused serious losses in tomato, tobacco, ginger and other industries, and phage therapy has become a research hotspot as a green prevention and control method with wide application potential for efficient targeted reduction of soil-borne pathogens.

“This study reveals the microecological mechanism of soil Chlorella biodephytogenesis jointly mediated by obligate bacteriophages and indigenous bacterial bacteriophages in the rhizosphere of Chlorella. At the same time, bacteriophages that specifically attack the mycotic bacteria and indigenous bacteria were screened, and in the future, different bacteriophages could be combined to construct phage cocktails, and applied with bio-organic fertilizer to establish a technical strategy of ‘phage cocktail therapy’ and bio-organic fertilizer to regulate soil microflora, which provides a new solution strategy for preventing and controlling soil biological obstacles and solving production problems. Shen Qirong said.

“Soil bacteriophages play an important role in regulating the structure composition of microbial communities, material recycling, animal and plant and even human health, but due to the constraints of soil heterogeneity and research methods, the current recognition and attention to soil bacteriophages is far from enough.” Zhu Yongguan, academician of the Chinese Academy of Sciences and researcher of the Institute of Urban Environment of the Chinese Academy of Sciences, said that the study was based on metagenomics and culture omics and other methods, excavated the dark matter of the soil phage group from the perspective of obligate bacteriophages of pathogenic bacteria and obligate bacteriophages of indigenous bacteria, analyzed the dynamic succession law of soil phage community and bacterial community, and explained the importance of soil bacteriophage group in the field of agriculture and ecological environment, which is highly innovative.

“In the future, the research on soil bacteriophages can carry out in-depth and systematic phage work from the aspects of phage resource development and bacteriophage-bacterial group interaction, and solve agricultural and ecological environmental problems.” Zhu Yongguan said. (Source: Li Chen, China Science News)

Related paper information:https://doi.org/10.1186/s40168-023-01463-8



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