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This study aimed to evaluate the resilience of phytophysiognomies under influence of iron mining by assessing the occurrence, diversity, and symbiotic efficiency of native communities of nitrogen-fixing bacteria that nodulate leguminous plants (rhizobia) in soils of an area revegetated with grass after iron mining activities and in the phytophysiognomies in adjacent areas (Canga, Atlantic Forest, Cerrado, and Eucalyptus-planted forest). Experiments for capturing rhizobia through two species of promiscuous plants, siratro (Macroptilium atropurpureum) and cowpea (Vigna unguiculata), were conducted in a greenhouse. The rhizobial strains isolated were characterized phenotypically, genetically (16S rRNA sequencing and BOX-PCR fingerprinting), and regard symbiotic efficiency of biological nitrogen fixation (BNF) compared to mineral nitrogen and reference strains. Cowpea captured a higher density of rhizobia than siratro did. However, most of the strains captured by siratro had greater symbiotic efficiency. The revegetated area proved to be the community most efficient in N 2 fixation and was also the most diverse, whereas Canga was the least diverse. For the two trap species, the predominant genus captured in the revegetated area and in the phytophysiognomies was Bradyrhizobium. The greater symbiotic efficiency and the high genetic diversity of the rhizobial community in the revegetated area indicate the effectiveness of the soil rehabilitation process. The revegetated area and the phytophysiognomies proved to harbor strains with high biotechnological potential. Results indicate that the high functional redundancy of this group of bacteria contributes to the resilience of these phytophysiognomies and the revegetated area., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The nitrogen-fixing bacterial strain UFLA 01-1174 T was isolated from nodules of Campsiandra laurilifolia Benth. originating from the Amazon region, Brazil. Its taxonomic position was defined using a polyphasic approach. Analysis of the 16S rRNA gene placed the strain in the Bradyrhizobium genus, the closest species being B. guangdongense CCBAU 51649 T and B. guangzhouense CCBAU 51670 T , both with 99.8% similarity. Multilocus sequence analysis (MLSA) of recA, gyrB, glnII, rpoB, atpD, and dnaK indicated that UFLA 01-1174 T  is a new species, most closely related to B. stylosanthis BR 446 T (94.4%) and B. manausense BR 3351 T (93.7%). Average nucleotide identity (ANI) differentiated UFLA 01-1174 T from the closest species with values lower than 90%. The G + C content in the DNA of UFLA 01-1174 T  is 63.6 mol%. Based on this data, we conclude that the strain represents a new species. The name proposed is Bradyrhizobium campsiandrae, with UFLA 01-1174 T (= INPA 394B T  = LMG 10099 T ) as type strain.

Soybean (Glycine max L.) is an important legume that greatly benefits from inoculation with nitrogen-fixing bacteria. In a previous study, five efficient nitrogen-fixing bacterial strains, isolated from nodules of soybean inoculated with soil from semi-arid region, Northeast Brazil, were identified as a new group within the genus Bradyrhizobium. The taxonomic status of these strains was evaluated in this study. The phylogenetic analysis of the 16S rRNA gene showed the high similarity of the five strains to Bradyrhizobium brasilense UFLA03-321 T (100%), B. pachyrhizi PAC48 T (100%), B. ripae WR4 T (100%), B. elkanii USDA 76 T (99.91%), and B. macuxiense BR 10303 T (99.91%). However, multilocus sequence analysis of the housekeeping genes atpD, dnaK, gyrB, recA, and rpoB, average nucleotide identity, and digital DNA-DNA hybridization analyses supported the classification of the group as B. brasilense. Some phenotypic characteristics allowed differentiating the five strains and the type strain of B. brasilense from the two neighboring species (B. pachyrhizi PAC48 T and B. elkanii USDA 76 T ). The nodC and nifH genes' analyses showed that these strains belong to symbiovar sojae, together with B. elkanii (USDA 76 T ) and B. ferriligni (CCBAU 51502 T ). The present results support the classification of these five strains as Bradyrhizobium brasilense (symbiovar sojae).

This study describes two Bradyrhizobium strains, UFLA03-164 T and UFLA03-153, which share more than 99% sequence similarity of the 16S rRNA with the type strains of 15 species in this genus. The concatenation of three housekeeping genes (recA, gyrB, and dnaK) indicated that both strains formed a single clade separate from known Bradyrhizobium species. B. viridifuturi, represented by SEMIA 690 T , is the closest neighboring species (96.2%). Low (< 92%) average nucleotide identity (ANI) was observed between strain UFLA03-164 T and any of the closest species on the phylogenetic trees based on concatenated housekeeping genes. The DNA G+C content of UFLA03-164 T is 63.25%. Phenotypic characteristics were determined for both UFLA strains. Based on the data, the two strains represent a new species for which the name Bradyrhizobium uaiense is proposed, with UFLA03-164 T (= LMG 31509 T ) as type strain.

Cowpea (Vigna unguiculata L.) is a legume species that considerably benefits from inoculation with nitrogen fixing bacteria of the genus Bradyrhizobium. One of the strains recommended for inoculation in cowpea in Brazil is UFLA03-84 (Bradyrhizobium sp.). The aim of our study was to define the taxonomic position of the UFLA03-84 strain and of two other strains of Bradyrhizobium (UFLA03-144 and INPA237B), all belonging to the same phylogenetic group and isolated from soils of the Brazilian Amazon. Multilocus sequence analysis (MLSA) of the housekeeping genes atpD, gyrB, recA, and rpoB grouped (with similarity higher than 99%) the three strains with Bradyrhizobium viridifuturi SEMIA 690 T . The analyses of average nucleotide identity and digital DNA-DNA hybridization supported classification of the group as Bradyrhizobium viridifuturi. The three strains exhibited similar behavior in relation to the most of the phenotypic characteristics evaluated. However, some characteristics exhibited variation, indicating phenotypic diversity within the species. Phylogenetic analysis of the nodC and nifH genes showed that the three strains are members of the same symbiovar (tropici) that contains type strains of Bradyrhizobium species coming from tropical soils (SEMIA 690 T B. viridifuturi, CNPSo 1112 T B. tropiciagri, CNPSo 2833 T B. embrapense, and B. brasilense UFLA03-321 T ).

Different fertilization and cropping systems may influence short- and long-term residues of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil. Soils from dryland (peanut) and paddy (rice) fields, which originated from the same nonagricultural land (forested), were treated with either chemical fertilizer, composted manure, or no fertilizer for 26 years before sampling, which occurred one year after the last applications. ARGs and MGEs were investigated using highly parallel qPCR and high-throughput sequencing. Six of the 11 antibiotics measured by LC-MS/MS were detected in the manure applied soil, but not in the nonmanured soils, indicating their source was from previous manure applications. Compared to the unfertilized control, manure application did not show a large accumulation of ARGs in either cropping system but there were some minor effects of soil management on indigenous ARGs. Paddy soil showed higher accumulation of these ARGs, which corresponded to higher microbial biomass than the dryland soil. Chemical fertilizer increased relative abundance of these ARGs in dryland soil but decreased their relative abundance in paddy soil. These results show how long-term common soil management practices affect the abundance and type of ARGs and MGEs in two very different soil environments, one aerobic and the other primarily anaerobic.

Three strains of nitrogen-fixing bacteria isolated from nodules of Inga sp. (INPA54B T ) and Swartzia sp. (INPA86A and INPA01-91A) in soils under native forest in the Brazilian Amazon were previously identified as belonging to the Bradyrhizobium genus. In this study, these strains were characterized using a polyphasic approach to establish their taxonomic position. The three strains shared more than 99.5% sequence similarity of the 16S rRNA gene with the type strains of five Bradyrhizobium species (B. japonicum USDA 6 T , B. liaoningense LMG 18230 T , B. ottawaense OO99 T , B. subterraneum 58 2-1 T and B. yuanmingense LMG 21827 T ). However, multilocus sequence analysis of two (recA and glnII) or three (atpD, gyrB, and recA) housekeeping genes indicated that these three strains represent a new Bradyrhizobium species, which is closely related to B. subterraneum 58 2-1 T and B. yuanmingense LMG 21827 T . DNA-DNA hybridization values between INPA54B T and B. subterraneum 58 2-1 T and B. yuanmingense LMG 21827 T were only 41.5 and 30.9%, respectively. Phenotypic characterization also allowed the differentiation of the novel species from B. subterraneum 58 2-1 T and B. yuanmingense LMG 21827 T . In the phylogenetic analysis of the nodC and nifH genes, the three strains showed similar sequences that were divergent from those of type strains of all Bradyrhizobium species. We concluded that these strains represent a novel species, for which the name Bradyrhizobium forestalis is proposed, with INPA54B T (= LMG 10044 T ) as type strain. The G+C content in the DNA of INPA54B T is 63.7 mol%.

Nickel (Ni)-a component of urease and hydrogenase-was the latest nutrient to be recognized as an essential element for plants. However, to date there are no records of Ni deficiency for annual species cultivated under field conditions, possibly because of the non-appearance of obvious and distinctive symptoms, i.e., a hidden (or latent) deficiency. Soybean, a crop cultivated on soils poor in extractable Ni, has a high dependence on biological nitrogen fixation (BNF), in which Ni plays a key role. Thus, we hypothesized that Ni fertilization in soybean genotypes results in a better nitrogen physiological function and in higher grain production due to the hidden deficiency of this micronutrient. To verify this hypothesis, two simultaneous experiments were carried out, under greenhouse and field conditions, with Ni supply of 0.0 or 0.5 mg of Ni kg -1 of soil. For this, we used 15 soybean genotypes and two soybean isogenic lines (urease positive, Eu3 ; urease activity-null, eu3-a , formerly eu3-e1 ). Plants were evaluated for yield, Ni and N concentration, photosynthesis, and N metabolism. Nickel fertilization resulted in greater grain yield in some genotypes, indicating the hidden deficiency of Ni in both conditions. Yield gains of up to 2.9 g per plant in greenhouse and up to 1,502 kg ha -1 in field conditions were associated with a promoted N metabolism, namely, leaf N concentration, ammonia, ureides, urea, and urease activity, which separated the genotypes into groups of Ni responsiveness. Nickel supply also positively affected photosynthesis in the genotypes, never causing detrimental effects, except for the eu3-a mutant, which due to the absence of ureolytic activity accumulated excess urea in leaves and had reduced yield. In summary, the effect of Ni on the plants was positive and the extent of this effect was controlled by genotype-environment interaction. The application of 0.5 mg kg -1 of Ni resulted in safe levels of this element in grains for human health consumption. Including Ni applications in fertilization programs may provide significant yield benefits in soybean production on low Ni soil. This might also be the case for other annual crops, especially legumes.

Sophora tomentosa is a pantropical legume species with potential for recovery of areas degraded by salinization, and for stabilization of sand dunes. However, few studies on this species have been carried out, and none regarding its symbiotic relationship with beneficial soil microorganisms. Therefore, this study aimed to evaluate the diversity of nitrogen-fixing bacteria isolated from nodules of Sophora tomentosa, and to analyze the occurrence of colonization of arbuscular mycorrhizal fungi on the roots of this legume in seafront soil. Thus, seeds, root nodules, and soil from the rhizosphere of Sophora tomentosa were collected. From the soil samples, trap cultures with this species were established to extract spores and to evaluate arbuscular mycorhizal fungi colonization in legume roots, as well as to capture rhizobia. Rhizobia strains were isolated from nodules collected in the field or from the trap cultures. Representative isolates of the groups obtained in the similarity dendrogram, based on phenotypic characteristics, had their 16S rRNA genes sequenced. The legume species showed nodules with indeterminate growth, and reddish color, distributed throughout the root. Fifty-one strains of these nodules were isolated, of which 21 were classified in the genus Bacillus, Brevibacillus, Paenibacillus, Rhizobium and especially Sinorhizobium. Strains closely related to Sinorhizobium adhaerens were the predominant bacteria in nodules. The other genera found, with the exception of Rhizobium, are probably endophytic bacteria in the nodules. Arbuscular mycorrhizal fungi was observed colonizing the roots, but arbuscular mycorhizal fungi spores were not found in the trap cultures. Therefore Sophora tomentosa is associated with both arbuscular mycorhizal fungi and nodulating nitrogen-fixing bacteria., (Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.)