Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations

Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.

Rahnella aquatilis JZ-GX1 alleviates iron deficiency chlorosis in Cinnamomum camphora by secreting desferrioxamine and reshaping the soil fungal community

Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. Rahnella aquatilis JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in Cinnamomum camphora, and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe²⁺ and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography-mass spectrometry (LC-MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of C. camphora, which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient C. camphora caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in C. camphora rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe²⁺ contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the C. camphora rhizosphere soil and increased the abundances of specific taxa, such as Glomus, Mortierella, Trichoderma, and Penicillium. Therefore, R. aquatilis JZ-GX1 application promoted iron absorption in C. camphora trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris)

The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon’s diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.

Functional characterization of culturable fungi from microbiomes of the "conical cobs" Mexican maize (Zea mays L.) landrace

Mexican maize landraces, produced for local consumption, are adapted to different environmental conditions, and their yield is affected by abiotic and biotic factors, including the use of agrochemicals. The search for sustainable alternatives to agrochemicals includes the study of the culturable microbial communities. In this study, the fungal communities associated with 2 Mexican maize landraces reddish and bluish "conical cobs" were found to be comprised of Ascomycota fungi, represented by 89 strains within 6 orders (Pleosporales, Hypocreales, Onygenales, Capnodiales, Helotiales, and Eurotiales) and 16 genera. Cellulases and metallophores production were the primary enzymatic products and plant growth-promoting activities were detected among the isolates. Penicillium, Didymella, and Fusarium strains had the most active enzymatic and plant growth promoting activities, however, Aspergillus sp. HES2-2.2, Talaromyces sp. RS1-7, and Penicillium sp. HFS3-3 showed antagonistic activity against the four phytopathogenic Fusarium strains Fusarium oxysporum, Fusarium sambucinum, Fusarium fujikuroi and Fusarium incarnatum-equiseti and also a high and diverse production of enzymatic and plant growth promoting activities; here we identified fungal strains as candidates to promote maize growth.

Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field

A Gram-negative, rod-shaped bacterium, strain Duganella callida DN04^T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar Duganella species are D. sacchari Sac-22^T, D. ginsengisoli DCY83^T, and D. radicis Sac-41^T with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04^T to D. sacchari Sac-22^T and D. zoogloeoides 115^T and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04^T is most similar to D. sacchari Sac-22^T and other Duganella and Massilia strains, there are also distinct differences. DN04^T can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C_15 : 0 iso (24.6 %), C_15 : 1 isoG (19.4 %), C_17 : 0 iso3-OH (16.8 %), and summed feature 3 (C_16:1 ⍵7c and/or C_16:1 ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04^T is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % (Massilia plicata NZ CP038026^T), and the most similar ANI (average nucleotide identity) score was 84.8 % (D. radicis KCTC 22382^T), which indicates that DN04^T is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to D. radicis KCTC 22382^T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose Duganella callida sp. nov. as a novel species within the Duganella genus (type strain DN04^T=NRRL B-65552^T=LMG 31736^T).

High-Throughput Customization of Plant Microbiomes for Sustainable Agriculture

Soil microorganisms can form a stable dynamic system with plant root systems. The composition of the soil microorganism community is related to the growth and stress resistance of plants; in turn, soil microorganisms are also regulated by plant genotypes and root exudates. Therefore, research on how to identify microorganisms that are beneficial or harmful to plants, study the interaction between microorganisms and plants, and form stable microbial communities for better plant growth plays an important role in sustainable agriculture. It is of great significance to identify and analyze rhizosphere microorganisms and plant endophytes through high-throughput methods, especially to analyze which microorganisms are beneficial to plants, which are harmful to plants, and which are opportunistic pathogens. This review provides a theoretical basis and outlook for the utilization of beneficial microbes in sustainable agriculture.