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The use of inoculants carrying diazotrophic and other plant growth–promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as “on farm” production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L. Merrill.) and Azospirillum brasilense for corn (Zea mays L.) or co-inoculation in soybean. The objective was to assess the microbiological quality of such inoculants concerning the target microorganisms and contaminants. In the laboratory, 18 samples taken in five states were serial diluted and spread on culture media for obtaining pure and morphologically distinct colonies of bacteria, totaling 85 isolates. Molecular analysis based on partial sequencing of the 16S rRNA gene revealed 25 genera of which 44% harbor species potentially pathogenic to humans; only one of the isolates was identified as Azospirillum brasilense, whereas no isolate was identified as Bradyrhizobium. Among 34 isolates belonging to genera harboring species potentially pathogenic to humans, 12 had no resistance to antibiotics, six presented intrinsic resistance, and 18 presented non-intrinsic resistance to at least one antibiotic. One of the samples analyzed with a shotgun-based metagenomics approach to check for the microbial diversity showed several genera of microorganisms, mainly Acetobacter (~ 32% of sequences) but not the target microorganism. The samples of inoculants produced on farm were highly contaminated with non-target microorganisms, some of them carrying multiple resistances to antibiotics.

The inoculation of seeds with nitrogen-fixing and plant-growth promoting bacteria is a well-established agricultural practice that has been increasingly adopted worldwide, decreasing costs and environmental impacts of food production. Most of the globally commercialized inoculants are for the soybean crop, and a method for recovery of Bradyrhizobium cells from inoculated soybean seeds for subsequent counting has been adopted by several laboratories of South America, especially to investigate the bacterial survival on seeds treated with pesticides. However, the use of inoculants containing Azospirillum brasilense in cereal crops has exponentially increased, requiring investigation about the recovery and counting of cells from inoculated seeds. We first verified that the method used for recovery and counting of viable cells of Bradyrhizobium from soybean seeds was not applicable for maize seeds inoculated with A. brasilense. We then modified several steps of the method, aiming at succeeding in recovering Azospirillum viable cells. The main limitation was identified in the nature of the seed tegument, dry and poor in nutrients, resulting in A. brasilense cell aggregation. Pre-hydration of seeds for 2 h in sterile distilled water, followed by shaking for 30 min in sterile distilled water with Tween 80 allowed proper counting of A. brasilense cells recovered from maize seeds. The method was successfully applied to count Azospirillum cells recovered from pre-inoculated maize seeds, and to estimate the impact of seed treatment with pesticides on cell survival.

Soybean [Glycine max (L.) Merr.] has great economic and nutritional importance mainly due to its high protein content. All plant's N needs can be met by the symbiosis with elite Bradyrhizobium strains applied as inoculants to the seeds at sowing time; however, the increasing use of pesticides in seed treatments can impair the contribution of the biological nitrogen fixation. In this study, we report decreases in cell survival of two strains, B. japonicum SEMIA 5079 and B. elkanii SEMIA 587 in seeds inoculated and treated with StandakTop™, composed of the fungicides pyraclostrobin and thiophanate-methyl and the insecticide fipronil, the pesticides most used in soybean seed treatment in several countries. Cell death was enhanced with the time of exposure to the pesticides, and B. elkanii was less tolerant, with almost no detectable viable cells after 15 days. Change in colony morphology with smaller colonies was observed in the presence of the pesticides, being more drastic with the time of exposure, and attributed to an adaptive response towards survival in the presence of the abiotic stress. However, morphological changes were reversible after elimination of the stressing agent and symbiotic performance under controlled greenhouse conditions was similar between strains that had been or not exposed to the pesticides. In addition, no changes in DNA profiles (BOX-PCR) of both strains were observed after the contact with the pesticides. In two field experiments, impacting effects of the pesticides were observed mainly on the total N accumulated in grains of plants relying on both N2-fixation and N-fertilizer. Our data indicate that StandakTop® affects parameters never reported before, including colony morphology of Bradyrhizobium spp. and N metabolism and/or N remobilization to soybean grains.