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The genus Bradyrhizobium stands out among nitrogen-fixing legume-nodulating bacteria because it predominates among the efficient microsymbionts of forest, forage, and green manure legume species, as well as important species of grain legumes, such as soybean, cowpea, and peanut. Therefore, the diversity of Bradyrhizobium strains is a relevant resource from environmental and economic perspectives, and strains isolated from diverse legume species and land uses in Brazilian tropical ecosystems were assessed in this study. To accomplish this, sequences of four housekeeping genes ( atpD , dnaK , gyrB , and recA ) were individually analysed, with the first three also being considered using multilocus sequence analysis (MLSA). The sensitivity of the strains to different antibiotics, their tolerance to different levels of salinity, and their ability to nodulate soybean plants were also measured. The phylogenetic trees based on each individual gene, and on the concatenated housekeeping genes, revealed several strain clusters separated from any currently described species. The Bradyrhizobium strains studied were generally resistant to antibiotics. All strains were able to grow at salinity levels of up to 0.5% NaCl, whereas only strains UFLA03-142, UFLA03-143, UFLA03-145, and UFLA03-146 grew in the presence of 1% NaCl. Together, the results indicated that some of the strains studied were potential novel species, indicating that the various soils and ecosystems in Brazil may harbour an as yet unknown diversity of rhizobia. [ABSTRACT FROM AUTHOR]

Abstract: Forty-eight Burkholderia isolates from different land use systems in the Amazon region were compared to type strains of Burkholderia species for phenotypic and functional characteristics that can be used to promote plant growth. Most of these isolates (n =46) were obtained by using siratro (Macroptilium atropurpureum – 44) and common bean (Phaseolus vulgaris – 2) as the trap plant species; two isolates were obtained from nodules collected in the field from Indigofera suffruticosa and Pithecellobium sp. The evaluated characteristics were the following: colony characterisation on “79” medium, assimilation of different carbon sources, enzymatic activities, solubilisation of phosphates, nitrogenase activity and antifungal activity against Fusarium oxysporium f. sp. phaseoli. Whole cell protein profiles, 16S rRNA, gyrB, and recA gene sequencing and multilocus sequence typing were used to identify the isolates. The isolates showed different cultural and biochemical characteristics depending on the legume species from which they were obtained. Except for one isolate from I. suffruticosa, all isolates were able to solubilise calcium phosphate and present nitrogenase activity under free-living conditions. Only one isolate from common beans, showed antifungal activity. The forty four isolates from siratro nodules were identified as B. fungorum; isolates UFLA02-27 and UFLA02-28, obtained from common bean plants, were identified as B. contaminans; isolate INPA89A, isolated from Indigofera suffruticosa, was a close relative of B. caribensis but could not be assigned to an established species; isolate INPA42B, isolated from Pithecellobium sp., was identified as B. lata. This is the first report of nitrogenase activity in B. fungorum, B. lata and B. contaminans. [Copyright &y& Elsevier]

Abstract: The aim of the present study was to identify a collection of 35 Cupriavidus isolates at the species level and to examine their capacity to nodulate and fix N2. These isolates were previously obtained from the root nodules of two promiscuous trap species, Phaseolus vulgaris and Leucaena leucocephala, inoculated with soil samples collected near Sesbania virgata plants growing in Minas Gerais (Brazil) pastures. Phenotypic and genotypic methods applied for this study were SDS-PAGE of whole-cell proteins, and 16S rRNA and gyrB gene sequencing. To confirm the ability to nodulate and fix N2, the presence of the nodC and nifH genes was also determined, and an experiment was carried out with two representative isolates in order to authenticate them as legume nodule symbionts. All 35 isolates belonged to the betaproteobacterium Cupriavidus necator, they possessed the nodC and nifH genes, and two representative isolates were able to nodulate five different promiscuous legume species: Mimosa caesalpiniaefolia, L. leucocephala, Macroptilium atropurpureum, P. vulgaris and Vigna unguiculata. This is the first study to demonstrate that C. necator can nodulate legume species. [Copyright &y& Elsevier]

The use of mixed pastures of grasses with forage peanut (Arachis pintoi) is growing and offers promising results. This leguminous forage plant has a stoloniferous growth habit and tolerates more intense defoliation and shading. However, there are few studies on its symbiosis with nitrogen (N 2) fixing bacteria and no studies on genetic identification of its native microsymbionts. The aim of this study was to evaluate phenotypic and genetic diversity and the symbiotic efficiency of bacterial strains isolated from nodules of forage peanut intercropped with grasses in pasture areas. Root nodules were collected from the Belomonte cultivar in Itabela, Bahia, and BRS Mandobi cultivar in Lavras, Minas Gerais, Brazil. The areas of sample collection had contrasting physical and chemical characteristics. Samples of 10 plants per area and 5 nodules per plant were taken. The strains isolated from the nodules were analyzed for culture characteristics (growth period and change in pH of the culture medium), their 16S rRNA, gyrB and nifH genes were partially sequenced, and authentication and analysis of symbiotic efficiency in forage peanut plants were carried out. Both the authentication and symbiotic efficiency experiments were carried out in a greenhouse under axenic conditions, using A. pintoi cv. BRS Mandobi in a completely randomized design with four replications. Authentication was performed in long neck bottles (500 mL) filled with nutrient solution, and symbiotic efficiency was performed in polypropylene seedling plug pots containing a mixture of sand and vermiculite with a nutrient solution. A total of 74 bacterial strains were obtained from isolation of the forage peanut nodules, 40 from Itabela, and 34 from Lavras. Partial sequencing of the 16S rRNA gene was obtained for 48 strains, 30 from Itabela, and 18 from Lavras. The strains isolated from nodules of forage peanut in pasture areas of Itabela, were identified in the following genera: Bradyrhizobium (21), Rhizobium (5), Burkholderia (2), Kocuria (1), and Paenibacillus (1). The strains coming from soils of Lavras, were identified in the following genera: Bradyrhizobium (13), Rhizobium (2), Burkholderia (1), Mucilaginibacter (1), and Enterobacter (1). In the authentication experiment, 17 strains from Itabela, and 13 strains from Lavras, exhibited nodulation. From these authenticated strains, 18 were identified by 16S rRNA sequencing as belonging to the Bradyrhizobium genus. Of these strains, 11 from the two areas exhibited high symbiotic efficiency in A. pintoi , and their results were better than those of the strains currently approved as inoculants for this crop. The non-nodulating strains are probably nodule endophytes. Sequencing of the gyrB housekeeping gene, performed in 13 strains, confirms phylogenetic groups of potential new species among the strains isolated from A. pintoi , which include strains able to nodulate this species, belonging to a specific phylogenetic group of Bradyrhizobium. Sequences of nifH gene of efficient strains belonged to a group different from that formed by non-nodulating strains. Unlabelled Image • Rhizobia communities in forage peanut nodules are equal in different soils and climas. • Forage peanut nodules can harbour other genera as endophytes. • Forage peanut nodulates only with a specific group within Bradyrhizobium genus. • Most Bradyrhizobium strains nodulating forage peanut are efficient symbiotic N 2 -fixers. • Three 16SrRNA phylogenetic groups are probably new Bradyrhizobium species. [ABSTRACT FROM AUTHOR]

Mining activities modify the landscape and may have severe environmental impacts. The degree of recovery or disturbance of these environments must be determined, and microbiological indicators are most sensitive for this evaluation. The aim of this study was to evaluate the soil microbiological attributes of an area rehabilitated after iron mining activities and evaluate the adjacent phytophysiognomies. Soil samples were collected in a rehabilitated area revegetated with grass (RA) and in the phytophysiognomies of ironstone outcrops (IO), of neotropical savanna (NS), and of Atlantic Forest (AF) in two climate seasons (dry and rainy). Microbial biomass carbon, soil respiration, and enzyme activities (β-glucosidase, acid and alkaline phosphatase, arylsulfatase, urease, fluorescein diacetate hydrolysis) were determined, and the metabolic quotient ( q CO 2 ), the microbial quotient ( q Mic), and specific enzyme activities were calculated. Analyses of variance, means testing, and principal component analysis between the soil microbiological and physicochemical attributes were carried out. The microbiological indicators differed according to the type of phytophysiognomy and the season. Enzyme activities, microbial biomass, q CO 2 , soil respiration, and q Mic were sensitive in indicating differences among the phytophysiognomies, as well as organic carbon, total N, Fe, Cu, and Al 3+ contents, pH, potential acidity, cation exchange capacity, and clay and sand contents. The IO and NS phytophysiognomies exhibited the highest organic carbon and total N contents, whereas AF, NS, and IO exhibited the highest values of microbial biomass carbon. In both climate seasons, the AF exhibited higher values of soil respiration and enzyme activities. The Ironstone Outcrops exhibited high microbial biomass that was active in the processes of nutrient cycling, shown by its enzyme activities, whereas lower values of microbial biomass carbon and enzymes and higher values of q CO 2 were observed in RA. Nevertheless, RA exhibited higher specific enzyme activities and higher q Mic, indicating that the process of revegetation with grass favors activity of the microbial community, and promotes recovery of this area. [ABSTRACT FROM AUTHOR]

The symbiotic N 2 -fixing genus Bradyrhizobium includes 29 species distributed throughout different geographic regions. Only five species have recently been described based on isolates from tropical soils, three species from Brazil ( B. manausense , B. ingae , B. neotropicale ) and two species from Peru ( B. paxllaere e B. icense ), although tropical region is considered to be the origin of legume rhizobia symbiosis. Besides, some authors suggested that Bradyrhizobium was introduced in Brazil with first soybeans inoculants from USA. In this work, 46 Bradyrhizobium strains were isolated from soils collected in different regions of Brazil (Midwest, Northeast, Southeast, and South), using soybean as a trap plant. These strains were characterized genetically by analyzing the 16S rRNA gene and five housekeeping genes ( atpD, gyrB, dnaK, recA , and rpoB ). They were also characterized in terms of their symbiotic efficiency with soybean plants grown under axenic conditions in Leonard jars. The phylogenetic analysis of housekeeping genes revealed the possible presence of novel species in the Northeast and Southeast soils, some of which exhibited high symbiotic efficiency with soybean plants. These results emphasize the great diversity among native strains belonging to Bradyrhizobium genus in Brazilian soils as well as potential ones to be used as inoculants. They also indicate that symbiotically efficient native bradyrhizobia occur in Brazilian soils and are independent of strains introduced as soybean inoculant. [ABSTRACT FROM AUTHOR]

• Soil fertility properties were more important for predicting β-glucosidase. • PXRF variables were more important to predict acid phosphatase and urease. • Spatial analysis allows better distinction of soil enzymes activity between seasons. Soil enzymes act in biogeochemical cycles of elements and are indicators of soil quality since they rapidly reflect changes of the environmental conditions. Moreover, enzymes are related to soil physicochemical properties, but their spatial distribution has been rarely evaluated. The hypothesis of this work is that soil properties related to fertility and texture (F), total contents of chemical elements obtained by portable X-ray fluorescence (pX) spectrometry and terrain attributes (T) can be used as predictor variables to soil enzyme activity, along with phytophysiognomy and season information. The objective of this work was to predict soil enzymes activity and assess its spatial variability in the most common phytophysiognomies of the Quadrilátero Ferrífero mineral province, in Brazil. Soil samples were collected in four phytophysiognomies during both dry and humid seasons. Activity of β-glucosidase, acid phosphatase, alkaline phosphatase, urease, and hydrolysis of fluorescein diacetate (FDA) was determined. Phytophysiognomy, season, F, T, and pX, were used together or separately to predict the enzymes activity through conditional random forest algorithm and the accuracy was assessed via leave-one-out cross validation. The generated models were accurate, with coefficient of determination (R2) varying from 0.63 (FDA by pX) to 0.82 (β-glucosidase by F). F variables were more important for the predictions, while pX variables were more important for predicting acid phosphatase and urease. The accurate models using T variables allowed the generation of maps showing the enzymes variability along the phytophysiognomies. This approach can accelerate the determination of soil enzymes activity across the landscape. [ABSTRACT FROM AUTHOR]

• Microbial attributes are the best discriminants of coffee fields with higher yields. • Microbial biomass, β-glucosidase and urease were higher in coffee fields with higher yields. • Cation exchange capacity, base saturation and Ca were more related to higher coffee yields. • Climatic conditions strongly affected most soil quality attributes. One of the main challenges faced by the rapidly growing human population is to increase agricultural sustainability. Soil quality is an essential aspect of agricultural sustainability, but farmers have generally assessed this based on conventional chemical and physical indicators, with little application of indicators of soil functions, such as soil microbiological attributes. These indicators may respond faster to changes in soil conditions and thus they could correlate better with the growth/yield of crops such as coffee. The aim of this study was to investigate the potential of soil microbiological indicators in assessment of soil quality for sustained coffee production, compared to or combined with conventional soil physical and chemical indicators. To accomplish that, two observational studies were performed by measuring soil microbiological, physical, and chemical attributes in coffee field areas with contrasting records of coffee yield but under similar edaphic and climatic conditions in the Cerrado (Brazilian tropical savanna) region of Minas Gerais, Brazil. In the first study, two neighboring field areas with contrasting yield were selected for each of the following three cultivars: Catuaí Vermelho IAC 99, Catuaí Vermelho IAC 144, and Rubi MG 1192. Samples were taken in two seasons (dry and rainy) of the year. In the second study, four neighboring field areas cropped with the cultivar Catuaí Vermelho IAC 144 were chosen based on their contrasting yield records. In both studies, the experimental procedure consisted of collecting four composite soil samples (each composed of four subsamples) taken at a depth of 0–10 cm from each field area within the area of canopy projection of the coffee plant. The microbiological attributes evaluated were microbial biomass carbon; microbial basal respiration; metabolic quotient; urease, β-glucosidase, and arylsulfatase enzyme activities; and fluorescein diacetate hydrolysis. The physical and chemical attributes evaluated were texture, pH, organic matter content, and fertility. Climatic conditions affected the responses and must be considered in evaluation and elaboration of soil quality indexes. The physical and chemical attributes that were most closely related to higher coffee yields were Ca contents, organic matter content, effective cation exchange capacity, and base saturation in both studies in the rainy season. Microbial biomass carbon, metabolic quotient, and β-glucosidase and urease activities were positively related to higher coffee yields, and these attributes exhibited greater ability to discriminate the production potential of the soil than chemical and physical attributes did, in both seasons and studies. [ABSTRACT FROM AUTHOR]