Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.

Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae, Bacillaceae, Gibberella, and Fusarium oxysporum, the healthy soil microbiome contained more Streptomyces Mirabilis, Bradyrhizobiaceae, Comamonadaceae, Mortierella, and nonpathogenic fungi of Fusarium. Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

Enhanced nitrogen and phosphorus removal from municipal wastewater in an anaerobic-aerobic-anoxic sequencing batch reactor with sludge fermentation products as carbon source.

Impacts of soil abiotic attributes on Fusarium wilt, focusing on bananas

Although the rhizomicrobiome has been extensively studied, little is known about the interactions between soil properties and the assemblage of plant growth-promoting microbes in the rhizosphere. Herein, we analysed the composition and structure of rhizomicrobiomes associated with soybean and alfalfa plants growing in different soil types using deep Illumina 16S rRNA sequencing. Soil pH, P and K significantly affected the composition of the soybean rhizomicrobiome, whereas soil pH and N had a significant effect on the alfalfa rhizomicrobiome. Plant biomass was influenced by plant species, the composition of the rhizomicrobiome, soil pH, N, P and plant growth stage. The beta diversity of the rhizomicrobiome was the second most influential factor on plant growth (biomass). Rhizomicrobes associated with plant biomass were identified and divided into four groups: (1) positively associated with soybean biomass; (2) negatively associated with soybean biomass; (3) positively associated with alfalfa biomass; and (4) negatively associated with alfalfa biomass. Genera assemblages among the four groups differentially responded to soil properties; Group 1 and Group 2 were significantly correlated with soil pH and P, whereas Group 3 and Group 4 were significantly correlated with soil N, K and C. The influence of soil properties on the relative abundance of plant biomass-associated rhizomicrobes differed between soybean and alfalfa. The results suggest the rhizomicrobiome has a pronounced influence on plant growth, and the rhizomicrobiome assemblage and plant growth-associated microbes are differentially structured by soil properties and leguminous plant species.

Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants.

Reductive soil disinfestation (RSD) has been proven to be an effective and environmentally friendly way to control many soilborne pathogens and diseases. In this study, the RSDs using ethanol (Et-RSD) and alfalfa (Al-RSD) as organic carbons were performed in a Rhizoctonia solani-infected soil, and the dissimilarities of microbial communities during the RSDs and after planting two seasons of cucumber seedlings in the RSDs-treated soil were respectively investigated by MiSeq pyrosequencing. The results showed that, as for bacteria, Coprococcus, Flavisolibacter, Rhodanobacter, Symbiobacterium, and UC-Ruminococcaceae became the dominant bacterial genera at the end of Al-RSD. In contrast, Et-RSD soil involved more bacteria belonging to Firmicutes, such as Sedimentibacter, UC-Gracilibacteraceae, and Desulfosporosinus. For fungi, Chaetomium significantly increased at the end of RSDs, while Rhizoctonia and Aspergillus significantly decreased. After planting two seasons of cucumber seedlings, those bacteria belonging to Firmicutes significantly decreased, but Lysobacter and Rhodanobacter belonging to the phylum Proteobacteria as well as UC-Sordariales and Humicola belonging to Ascomycota alternatively increased in Al- and Et-RSD-treated soils. Besides, some nitrification, denitrification, and nitrogen fixation genes were apparently increased in the RSD-treated soils, but the effect was more profound in Al-RSD than Et-RSD. Overall, Et-RSD could induced more antagonists belonging to Firmicutes under anaerobic condition, whereas Al-RSD could continuously stimulate some functional microorganisms (Lysobacter and Rhodanobacter) and further improve nitrogen transformation activities in the soil at the coming cropping season.

Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation

Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation

The invention provides a method for determining nitrogen or carbon isotope ratio of N2 or CO2 gas on the basis of an elemental analyzer-stable isotope mass spectrometer combined device. The method comprises the following steps of: continuously introducing inert gas from a gas inlet of an oxidation tube of an elemental analyzer; injecting the to-be-detected gas sample N2 or CO2 through a sampling port of a gas sampling device; causing the to-be-detected gas sample N2 or CO2 together with the inert gas enter into a stable isotope mass spectrometer through a reduction tube of the elemental analyzer; and determining the nitrogen or carbon isotope ratio by the stable isotope mass spectrometer. According to the method provided by the invention, working standard gas N2 and CO2 can be determined and meanwhile the pure natural abundant N2 and CO2 gas sample also can be determined; the required external device is saved when the stable isotope mass spectrometer is used for determining the gas sample; the method provided by the invention is simple, convenient and high in result accuracy.

Method for determining nitrogen or carbon isotope ratio of N2 or CO2 gas on basis of elemental analyzer-stable isotope mass spectrometer combined device

The invention discloses a continuous cultivation method of eustoma grandiflorum. The continuous cultivation method comprises the following steps: in the case of serious continuous cropping obstacle of the eustoma grandiflorum or higher wilt morbidity of the eustoma grandiflorum, controlling the soil to be higher than 25 degrees Celsius, carrying out strong reduction treatment on the land, and continuing to conventionally plant the eustoma grandiflorum after the strong reduction treatment; after continuous cropping of 1-2 years, carrying out the strong reduction treatment on the soil again, and continuing to conventionally plant the eustoma grandiflorum, and repeating the process to continuously plant the eustoma grandiflorum on the same land for a long time; and the specific process of the strong reduction treatment is as follows: adding bagasse or molasses to the soil, ploughing to uniformly mix the bagasse or molasses with the soil, then irrigating the soil to the maximum field capacity, and finally covering a plastic film on the land to isolate the gas exchange of the soil and the atmosphere. By adoption of the continuous cultivation method provided by the invention, effective guarantee can be provided for continuous production and soil resource protection; and moreover, the continuous cultivation method has the advantages of low cost, high benefit, simple operation and easy popularization in production.

Continuous cultivation method of eustoma grandiflorum

The invention discloses a method for measuring the nitrogen concentration based on a trace-gas preconcentration device-isotope ratio mass spectrometer (PreCon-IRMS). The method includes the steps that an isotope ratio mass spectrum serves as a nitrogen detector, the m/z 28 ion current intensity of a to-be-detected nitrogen sample is directly measured through the PreCon-IRMS, and then the concentration of the to-be-detected nitrogen sample is calculated according to the linear relationship between the m/z 28 ion current intensity of a standard nitrogen sample and the concentration. The method is easy to operate and short in measuring time.

Wang Fenghe

Papers

Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation

Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation

Method for determining nitrogen or carbon isotope ratio of N2 or CO2 gas on basis of elemental analyzer-stable isotope mass spectrometer combined device

Continuous cultivation method of eustoma grandiflorum

Method for measuring nitrogen concentration based on trace-gas preconcentration device-isotope ratio mass spectrometer