Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms

Progress in Microbial Fertilizer Regulation of Crop Growth and Soil Remediation Research

More food is needed to meet the demand of the global population, which is growing continuously. Chemical fertilizers have been used for a long time to increase crop yields, and may have negative effect on human health and the agricultural environment. In order to make ongoing agricultural development more sustainable, the use of chemical fertilizers will likely have to be reduced. Microbial fertilizer is a kind of nutrient-rich and environmentally friendly biological fertilizer made from plant growth-promoting bacteria (PGPR). Microbial fertilizers can regulate soil nutrient dynamics and promote soil nutrient cycling by improving soil microbial community changes. This process helps restore the soil ecosystem, which in turn promotes nutrient uptake, regulates crop growth, and enhances crop resistance to biotic and abiotic stresses. This paper reviews the classification of microbial fertilizers and their function in regulating crop growth, nitrogen fixation, phosphorus, potassium solubilization, and the production of phytohormones. We also summarize the role of PGPR in helping crops against biotic and abiotic stresses. Finally, we discuss the function and the mechanism of applying microbial fertilizers in soil remediation. This review helps us understand the research progress of microbial fertilizer and provides new perspectives regarding the future development of microbial agent in sustainable agriculture.

Microbial interactions within beneficial consortia promote soil health

By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.

Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus

Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.

Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers

Fungi offer a deep source of natural products but remain underutilized. Most biosynthetic gene clusters (BGCs) that can be detected are silent or "cryptic" in standard lab cultures and their products are thus not interrogated in routine screens. As genetic alterations are difficult and some strains can only be grown on agar, we have herein applied an agar-based high-throughput chemical genetic screen to identify inducers of fungal BGCs. Using R. solani and S. sclerotiorum as test cases, we report 13 cryptic metabolites in four compound groups, including sclerocyclane, a natural product with a novel scaffold. Steroids were the best elicitors and follow-up studies showed that plant-steroids trigger sclerocyclane synthesis, which shows antibiotic activity against B. plantarii, an ecological competitor of S. sclerotiorum. Our results open new paths to exploring the chemical ecology of fungal-plant interactions and provide a genetics-free approach for uncovering cryptic fungal metabolites.

Synergistic effects of crop residue and microbial inoculant on soil properties and soil disease resistance in a Chinese Mollisol

The soil-borne disease caused by Fusarium graminearum seriously affects the corn quality. Straw can greatly improve soil quality, but the effect is limited by its nature and environmental factors. This study explored the impact of straw-JF-1(biocontrol bacteria) combination on soil environment and soil disease resistance. The results showed that the combined treatment increased the proportion of soil large and small macro-aggregates by 22.50 and 3.84%, with soil organic carbon (SOC) content by 16.18 and 16.95%, respectively. Compared to treatment with returning straw to the field alone, the straw-JF-1 combination increased the soil content of humic acid, fulvic acid, and humin by 14.06, 5.50, and 4.37%, respectively. Moreover, A metagenomics showed that returning straw to the field alone increased the abundance of disease-causing fungi (Fusarium and Plectosphaerella), however, the straw-JF-1 combination significantly suppressed this phenomenon as well as improved the abundance of probiotic microorganisms such as Sphingomonas, Mortierella, Bacillus, and Pseudomonas. Functional analysis indicated that the combination of straw and JF-1 improved some bacterial functions, including inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperones and function unknown, fungal functions associated with plant and animal pathogens were effectively inhibited. Pot experiments showed that the straw-JF-1 combination effectively inhibited the Fusarium graminearum induced damage to maize seedlings. Therefore, the combination of straw and JF-1 could be a practical method for soil management.

Description of desferrioxamine-producing bacterium Chitinophaga agrisoli sp. nov., isolated from soil

A Gram-stain-negative, non-motile, yellow-pigmented and non-spore forming rod-shaped bacterium, designated strain BN140078^T, was isolated from farmland soil, Chungbuk, Republic of Korea. It was able to grow aerobically at 10-40 °C (optimum 28 °C), pH 5.5-7.5 (optimum pH 7.0) and with 0-2.0% (w/v) NaCl concentration (optimum 1.0%) on Reasoner's 2A (R2A) agar medium. Comparative 16S rRNA gene sequence analysis showed that the strain BN140078^T had 96.9%, 96.5% and 96.1% 16S rRNA gene similarities with Chitinophaga ginsengihumi KACC 17604^T, Chitinophaga rupis KACC 14521^T and Chitinophaga japonensis KACC 12057^T, respectively. The predominant respiratory quinone was menaquinone MK-7 and the major fatty acids (≥ 5%) were C_16:1 ω5c, iso-C_15:0, iso-C_17:0 3-OH and Summed Feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The polar lipids were composed of phosphatidylethanolamine, four unidentified amino lipids and six unidentified lipids. The genomic DNA G+C content was 49.5 mol%. The genome of strain BN140078^T comprises a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide products. The polyphasic taxonomic study clearly distinguished this strain from its closest phylogenetic neighbors. Thus, we propose that the BN140078^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agrisoli sp. nov. was proposed. The type strain is BN140078^T (=KCTC 62555^T = CCTCC AB 2018162^T).

Editorial: New Research on Soil Degradation and Restoration

The Virtual Special Issue (VSI) "New Research on Soil Degradation and Restoration" was proposed by the Guest-Editors (the authors of this editorial piece) to Journal of Environmental Management taking into account the following aspects: (a) Firstly, soil degradation is a main issue all over the world; (b) Secondly, physical, chemical and biological degradation of soil environments need detailed research, also going deeper in some new aspects poorly covered up to now; and (c) Similarly, new quality research on restoration of degraded soils, dumping sites, different areas affected by mining activities, and so on, would be clearly useful in order to prevent and/or solve critical environmental hazards. As a result, 110 manuscripts were submitted to the VSI by authors from around the world, and near 50 high quality works were finally published. The Guest-Editors of the VSI consider that the papers published will be of great interest for researchers working in this field, as well as for the overall community, as they include aspects clearly relevant at a global level.

Biocontrol potential of chitinases produced by newly isolated Chitinophaga sp. S167

A chitinolytic bacterium Chitinophaga sp. S167 producing extracellular chitinases was isolated from a soil sample in India. The extracellular chitinases produced by S167 were concentrated by ammonium sulphate precipitation (AS70) and seven bands corresponding to chitinases were observed by zymography. Optimum temperature and pH of AS70 were between 40 and 45 °C and pH 6.0 respectively with high stability at 20-40 °C and pH 5-7. AS70 inhibited the growth of Fusarium oxysporum, Alternaria alternata and Cladosporium sp. in vitro. The culture conditions for the high level production of extracellular chitinases were optimized resulting in 48-folds higher chitinase production. As the combination of chitinases could be more potent in biocontrol of plant diseases, it was checked if AS70 could control postharvest fungal infection caused by Fusarium oxysporum on tomatoes. AS70 treated tomatoes showed significant lower incidence of infection (11%) by F. oxysporum as compared with 100% in the control at 5 days post inoculation. Further, AS70 caused significant mortality in second stage juveniles of root knot nematode, Meloidogyne incognita, a major agriculture pest responsible for economic losses in agriculture. This study highlights the antifungal and nematicidal activity of chitinases produced by Chitinophaga sp. S167. To the best of our knowledge, this is the first report of the biocontrol potential of the chitinases produced by Chitinophaga sp.