Phenotypic and genotypic characterization of endophytic bacteria associated with transgenic and non-transgenic soybean plants

Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application

Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".

Screening Digitaria eriantha cv. Suvernola Endophytic Bacteria for Maize Growth Promotion

The search for sustainable agriculture has increased interest in using endophytic bacteria to reduce fertilizer use and increase stress resilience. Stress-adapted plants are a potential source of these bacteria. Some species of these plants have not yet been evaluated for this, such as pangolão grass, from which we considered endophytic bacteria as potential plant growth promoters. Bacteria from the root, colm, leaves, and rhizospheric soil were isolated, and 132 strains were evaluated for their in vitro biological nitrogen fixation, IAA and siderophores production, and phosphate solubilization. Each mechanism was also assessed under low N availability, water stress, and low-solubility Fe and P sources in maize greenhouse experiments. All strains synthesized IAA; 63 grew on N-free media, 114 synthesized siderophores, and 46 solubilized P, while 19 presented all four mechanisms. Overall, these strains had better performance than commercial inoculant in all experiments. Still, in vitro responses were not good predictors of in vivo effects, which indicates that the former should not be used for strain selection, since this could lead to not testing strains with good plant growth promotion potential. Their heterologous growth promotion in maize reinforces the potential of stress-adapted plant species as potential sources of strains for inoculants.

Screening of endophytic bacteria from potato tubers and their antagonistic activity against soil-borne potato pathogens

In order to appraise the bacterial endophyte communities that help resist disease in potato tuber, the separation, the population density, biodiversity and the antagonistic activity of endophytic bacteria, from the tuber peel of potato cultivars (Fontan90, Agria, Sante’a and Jeli89), were examined in the Fars province in Iran. In this study, the bacterial endophyte Colony Forming Units (CFU) were counted based on the most suitable dilution in petri dishes and expressed per g of wet weight of tuber tissue. The presence of bacteria was found mostly in the outer layer. A wide variety of endophyte species biodiversity was in Agria cultivar. To estimate the antagonistic effect of potato associated endophytic bacteria, 115 bacterial isolates were evaluated by dual culture method against main soil-borne potato pathogens Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, Streptomyces scabies and Ralstonia solanacearum. Endophyte strains were identified based on physiological, morphological and chemical characteristics and the 16S rRNA gene sequence analysis. The highest degree of the inhibitory activity in all layers of potato cultivars was related to Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola. Antagonistic activity of endophytic bacteria against the pathogens was significantly higher (p<0.01) in the examined strains from the outermost layer of tuber peel and decreased progressively toward the center of the tuber. In this research, Klebsiella variicola was reported as endophyte bacteria in the four commercial potatocultivars mentioned above, for the first time.

Transmission of tetracycline resistance genes and microbiomes from manure-borne black soldier fly larvae frass to rhizosphere soil and pakchoi endophytes

Manure treatment with black soldier fly larvae (BSFL) and BSFL frass application in crop land is a sustainable strategy; however, whether residual antibiotic resistance genes (ARGs) and their transmission risk are related to the manure BSFL treatment process is still unknown. In this paper, the effect of BSFL addition density on residual tetracycline resistance genes (TRGs) and transmission from frass to pakchoi was determined. The results showed that BSFL frass can provide sufficient nutrients for growth, improve the economic value of pakchoi, and reduce the risk of transmission of TRGs in chicken manure regardless of BSFL density. The potential hosts of the TRGs we detected were found in BSFL frass (Oblitimonas and Tissierella), rhizosphere soil (Mortierella and Fermentimonas), and pakchoi endophytes (Roseomonas). The present study concluded that BSFL frass produced by adding 100 BSFL per 100 g of chicken manure has the advantages of high value and low risk. These findings will provide important strategic guidance for animal manure disposal and theoretical support for preventing the transmission of TRGs in BSFL applications.

Probabilistically sampled and spectrally clustered plant species using phenotypic characteristics

Phenotypic characteristics of a plant species refers to its physical properties as cataloged by plant biologists at different research centers around the world. Clustering species based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of phenotypic data. This algorithm suffers from low accuracy and high computational complexity issues. To address the accuracy challenge, we propose the use of Spectral Clustering (SC) algorithm. To make the algorithm computationally cheap, we propose using sampling, specifically, Pivotal Sampling that is probability based. Since application of samplings to phenotypic data has not been explored much, for effective comparison, another sampling technique called Vector Quantization (VQ) is adapted for this data as well. VQ has recently generated promising results for genotypic data. The novelty of our SC with Pivotal Sampling algorithm is in constructing the crucial similarity matrix for the clustering algorithm and defining probabilities for the sampling technique. Although our algorithm can be applied to any plant species, we tested it on the phenotypic data obtained from about 2,400 Soybean species. SC with Pivotal Sampling achieves substantially more accuracy (in terms of Silhouette Values) than all the other proposed competitive clustering with sampling algorithms (i.e. SC with VQ, HC with Pivotal Sampling, and HC with VQ). The complexities of our SC with Pivotal Sampling algorithm and these three variants are almost the same because of the involved sampling. In addition to this, SC with Pivotal Sampling outperforms the standard HC algorithm in both accuracy and computational complexity. We experimentally show that we are up to 45% more accurate than HC in terms of clustering accuracy. The computational complexity of our algorithm is more than a magnitude less than that of HC.

Enrichment of antibiotic resistance genes after sheep manure aerobic heap composting

In this study, physio-chemical properties, 45 antibiotics, 6 heavy metals, 42 antibiotic resistance genes (ARGs), 3 mobile genetic elements, and the bacterial community structure were investigated to analyze the fate of ARGs during sheep manure aerobic heap composting. Results showed that sheep manure heap composting could produce mature compost. The degradation processes reduced the total antibiotics content by 85%. The abundance of ARGs and mobile genetic elements (MGEs) were enriched 9-fold, with the major increases to sul and tet genes (sulI, sulII, tetQ, and tetX). Tetracycline and sulfonamide resistance genes were the most abundant ARGs after composting (more than 88% of all genes). The genes tetA, tetX and sulI were related to the most diverse bacteria that were most able to proliferate during heap composting. Therefore, sulI and tetX are the major ARGs to be controlled, and Actinobacteria and Bacteroidetes may be the major host bacteria.

Insights into factors driving the transmission of antibiotic resistance from sludge compost-amended soil to vegetables under cadmium stress

Sludge compost is often used as a fertilizer for crops, although it might be enriched with antibiotic resistance genes (ARGs) and heavy metals that cannot be removed through composting. A robust understanding of the factors affecting the transmission of ARGs to vegetables grown in soils treated with sludge products is lacking. In this study, target ARGs in the bulk and rhizosphere soils and endophytes of shallots under heavy metal stress (i.e., Cd) were assessed, and the factors driving the transmission of ARGs were identified. Cd stress resulted in an increase in the relative abundances of target ARGs in the bulk and rhizosphere soils and endophytes. The driving factors were different in soils and plants under different degrees of Cd stress. The fungal community composition was the main driving factor of ARG variation in both bulk and rhizosphere soils. Moreover, endophytic bacteria played a crucial role in transferring ARGs to plants. Higher Cd stress promoted the transfer of most target ARGs from the below-ground plant parts to the above-ground parts. These findings indicate that application of sludge contaminated with heavy metals, such as Cd, can facilitate the dissemination of ARGs into vegetables, which must be considered while assessing the risks to public health.

Deficit Alternate Drip Irrigation Increased Root-Soil-Plant Interaction, Tomato Yield, and Quality

To determine the soil mechanism in root-zone caused by water saving and the production response to alternate drip irrigation (ADI), the present study investigated the effects of deficit ADI on tomato growth using the conventional surface drip irrigation (CDI) as a control. The interactions among the experimental treatments on root index, photosynthetic efficiency, biomass accumulation, yield, fruit quality and irrigation water use efficiency (IWUE) were assessed and the inner mechanism of root-soil effecting on tomato growth, photosynthate distribution, yield and quality was discussed. ADI significantly enhanced root-soil interaction, promoted soil nitrogen and phosphorus absorption by tomato and tomato growth. However, different soil moisture deficits significantly affected tomato photosynthate accumulation and distribution, as well as fruit quality. With irrigation amount of 50% field capacity (F), ADI significantly increased soluble sugar, total soluble solid and lycopene by 38.08%, 19.48% and 30.05%, respectively, compared to those of CDI, but decreased irrigation amounts by 29.86% in comparison with the CDI one. ADI of 70% F could significantly distribute more photosynthate to fruits, thus enhanced tomato yields by 24.6% and improved IWUE by 17.05% compared to that of CDI. In addition, ADI of 70% F improved tomato fruits quality, and in particular organic acid was decreased by 43.75% and sugar-acid ratio was increased by 97% compared to CDI. However, ADI of 60% F distributed more photosynthate to plant, showing no significant difference of yields in comparison with CDI and ADI of 70% F, but a higher IWUE by 19.54% than that of CDI. ADI of 60% F significantly enhanced soluble sugar, total soluble solid, soluble protein, lycopene and sugar-acid ratio in tomato fruits by 2.06, 1.26, 1.61, 1.4 and 3.2 times respectively compared to CDI. Therefore, ADI of 60% or 70% F can be overall recommended for tomato production in a greenhouse, plant growth, fruit yield and quality, and IWUE.