Genome of Rhizobium leucaenae strains CFN 299(T) and CPAO 29.8: searching for genes related to a successful symbiotic performance under stressful conditions.

BACKGROUND: Common bean (Phaseolus vulgaris L.) is the most important legume cropped worldwide for food production and its agronomic performance can be greatly improved if the benefits from symbiotic nitrogen fixation are maximized. The legume is known for its high promiscuity in nodulating with several Rhizobium species, but those belonging to the Rhizobium tropici "group" are the most successful and efficient in fixing nitrogen in tropical acid soils. Rhizobium leucaenae belongs to this group, which is abundant in the Brazilian "Cerrados" soils and frequently submitted to several environmental stresses. Here we present the first high-quality genome drafts of R. leucaenae, including the type strain CFN 299(T) and the very efficient strain CPAO 29.8. Our main objective was to identify features that explain the successful capacity of R. leucaenae in nodulating common bean under stressful environmental conditions. RESULTS: The genomes of R. leucaenae strains CFN 299(T) and CPAO 29.8 were estimated at 6.7-6.8 Mbp; 7015 and 6899 coding sequences (CDS) were predicted, respectively, 6264 of which are common to both strains. The genomes of both strains present a large number of CDS that may confer tolerance of high temperatures, acid soils, salinity and water deficiency. Types I, II, IV-pili, IV and V secretion systems were present in both strains and might help soil and host colonization as well as the symbiotic performance under stressful conditions. The symbiotic plasmid of CPAO 29.8 is highly similar to already described tropici pSyms, including five copies of nodD and three of nodA genes. R. leucaenae CFN 299(T) is capable of synthesizing Nod factors in the absence of flavonoids when submitted to osmotic stress, indicating that under abiotic stress the regulation of nod genes might be different. CONCLUSION: A detailed study of the genes putatively related to stress tolerance in R. leucaenae highlighted an intricate pattern comprising a variety of mechanisms that are probably orchestrated to tolerate the stressful conditions to which the strains are submitted on a daily basis. The capacity to synthesize Nod factors under abiotic stress might follow the same regulatory pathways as in CIAT 899(T) and may help both to improve bacterial survival and to expand host range to guarantee the perpetuation of the symbiosis.

The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes.

BACKGROUND: Burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of B. phenoliruptrix, BR3459a (=CLA1), which was originally isolated in Brazil from nodules of Mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species. RESULTS: Genomic comparisons with other pathogenic and non-pathogenic Burkholderia strains grouped B. phenoliruptrix BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the B. cepacia complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the bce genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of B. phymatum. Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic Burkholderia species strongly supports the definition of a new genus for the second branch, which would include BR3459a. CONCLUSIONS: The analyses of B. phenoliruptrix BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic Burkholderia raise concerns about large-scale applications in agriculture or for bioremediation.

Effect of leguminous lectins on the growth of Rhizobium tropici CIAT899.

Rhizobium tropici is a Gram-negative bacterium that induces nodules and fixed atmospheric nitrogen in symbiotic association with Phaseolus vulgaris (common bean) and some other leguminous species. Lectins are proteins that specifically bind to carbohydrates and, consequently, modulate different biological functions. In this study, the d-glucose/ d-mannose-binding lectins (from seeds of Dioclea megacarpa, D. rostrata and D. violacea) and D-galactose-binding lectins (from seeds of Bauhinia variegata, Erythina velutina and Vatairea macrocarpa) were purified using chromatographic techniques and evaluated for their effect on the growth of R. tropici CIAT899. All lectins were assayed with a satisfactory degree of purity according to SDS-PAGE analysis, and stimulated bacterial growth; in particular, the Dioclea rostrata lectin was the most active among all tested proteins. As confirmed in the present study, both d-galactose- and d-glucose/d-mannose-binding lectins purified from the seeds of leguminous plants may be powerful biotechnological tools to stimulate the growth of R. tropici CIAT99, thus improving symbiotic interaction between rhizobia and common bean and, hence, the production of this field crop.

Complete genome sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a heat-tolerant, nitrogen-fixing symbiont of Mimosa flocculosa.

The genus Burkholderia represents a challenge to the fields of taxonomy and phylogeny and, especially, to the understanding of the contrasting roles as either opportunistic pathogens or bacteria with biotechnological potential. Few genomes of nonpathogenic strains, especially of diazotrophic symbiotic bacteria, have been sequenced to improve understanding of the genus. Here, we contribute with the complete genome sequence of Burkholderia phenoliruptrix strain BR3459a (CLA1), an effective diazotrophic symbiont of the leguminous tree Mimosa flocculosa Burkart, which is endemic to South America.

Lectin from Canavalia brasiliensis seeds (ConBr) is a valuable biotechnological tool to stimulate the growth of Rhizobium tropici in vitro.

To study the interactions between a Rhizobium tropici strain and lectins isolated from the seeds of Canavalia ensiformis (ConA) and Canavalia brasiliensis (ConBr), a lectin fluorescence assay was performed. In addition, an experiment was designed to evaluate the effect of the two lectins on bacterial growth. Both lectins were found to bind to R. tropici cells, but the interactions were inhibited by D-mannose. Interestingly, only ConBr stimulated bacterial growth in proportion to the concentrations used (15.6-500 µg/mL), and the bacterial growth stimulation was inhibited by D-mannose as well. Structure/Function analyses by bioinformatics were carried out to evaluate the volume and carbohydrate recognition domain (CRD) configuration of ConA and ConBr. The difference of spatial arrangement and volume of CRD may indicate the variation between biological activities of both lectins. The results suggest that ConBr could be a promising tool for studies focusing on the interactions between rhizobia and host plants.

Persistência de inseticidas e parâmetros microbiológicos em solo sob sistemas de manejo / Persistence of insecticides and microbiological attributes in a soil under different management systems

O objetivo deste trabalho foi avaliar a degradação dos inseticidas bifentrina, permetrina e tiametoxam em um solo sob sistemas de integração lavoura-pecuária (SILP), plantio direto (SPD) e convencional (SC), e sua relação com atributos microbiológicos (carbono da biomassa microbiana, respiração basal e atividade das enzimas -glucosidase e fosfatase ácida). O experimento foi realizado utilizando solos incubados (0-10cm) com umidade a 75% da capacidade de campo e 28ºC por 51 dias. Além de aumentos de matéria orgânica, biomassa e atividade microbiana, o sistema SILP também favoreceu a degradação mais rápida dos três inseticidas no solo, em comparação aos outros sistemas avaliados. Dentre os inseticidas avaliados, o tiametoxam apresentou degradação lenta no solo, com valores de meia-vida (TD50) entre 46 e 89 dias. Os valores de TD50 para bifentrina ficaram entre 14 e 44 dias e para permetrina entre 9 e 47 dias, considerando todos os sistemas avaliados.

The aim of this research was to evaluate the degradation of bifenthrin, permethrin and thiamethoxam insecticides in a soil under crop-livestock integration (CLIS), no-tillage (NTS) and conventional (CS) systems and its relationship with microbiological attributes (microbial biomass C, basal soil respiration and activities of β-glucosidase and acid phosphatase). The experiment was carried out using incubated soil (0-10cm) with moisture content about 75% of field capacity at 28ºC for 51 days. Besides the increase in soil organic matter content, biomass and microbial activity, CLIS system also favored a faster degradation of the three insecticides in soil compared to the others. Among the evaluated insecticides, thiamethoxam showed the slowest degradation in soil with half-life (DT50) values between 46 and 89 days. Bifenthrin DT50 values were between 14 and 44 days and for permethrin between 9 and 47 days.

Common bean elite lines cultivated under nitrogen fertilization and inoculation with Rhizobium tropici / Linhagens elite de feijoeiro-comum cultivadas com fertilização nitrogenada e inoculação com Rhizhobium tropici

ABSTRACT:More efficient strains of Rhizobiumhave been selected for use in common bean. However, little effort was made with lines selection. The main goals of this research were to verify the presence of interaction involving common bean elite lines utilizing Nitrogen fertilization and Rhizobiuminoculation for grain yield and to identify lines with superior yields utilizing biological nitrogen fixation. Eight field trials were conducted at four location-years in Brazilian savanna, using randomized complete blocks design with three replications. Each trial was composed of 17 carioca elite lines. Every two tests in each location were planted side by side, one with mineral nitrogen fertilization (90kg) and the other one with inoculation with Rhizobium tropiciSEMIA 4080 strain. Elite lines interaction with nitrogen fertilization/inoculation was not important, so, it is possible to select lines for utilization in both growing systems. In some locations-years, interaction between lines and Rhizobiuminoculation was most affected by environment conditions, causing modification in lines classification according to the type of nitrogen supplying used. In general, the lines presented higher yields when fertilized with mineral nitrogen as compared with inoculation. The cultivar 'BRS Pontal' presented high and similar yields under both systems of nitrogen supply.

RESUMO:Estirpes de rizóbio mais eficientes têm sido selecionadas para uso em feijoeiro-comum. Entretanto, pouco tem sido feito na seleção de linhagens mais eficientes. Os objetivos desse trabalho foram verificar a presença de interação entre linhagens elite de feijoeiro-comum com uso de fertilização nitrogenada e inoculação com rizóbio, para produtividade de grãos e identificar linhagens com produção superior, quando inoculadas com rizóbio. Oito experimentos foram conduzidos em quatro locais/anos no cerrado brasileiro, compostos por 17 linhagens elite, em blocos ao acaso com três repetições. Em cada local/ano foram conduzidos dois experimentos, lado a lado: um com fertilização mineral de nitrogênio (90kg) e outro com inoculação com rizóbio. A interação entre as linhagens elite e o tipo de fornecimento de nitrogênio não foi importante, indicando que é possível selecionar linhagens para uso simultâneo nos dois sistemas de cultivo. Em alguns locais, a interação entre as linhagens e a inoculação com rizóbio foi mais afetada pelo ambiente, causando modificações na classificação das linhagens nos dois tipos de fornecimento de nitrogênio. De modo geral, a produtividade foi maior utilizando-se fertilização mineral, quando comparada com a inoculação. A cultivar 'BRS Pontal' apresentou produtividade alta e semelhante nos dois sistemas de fornecimento de nitrogênio.

Formigas como bioindicadores da qualidade do solo em sistema integrado lavoura-pecuária / Ants as bioindicators of soil quality in integrated crop-livestock system

O objetivo deste trabalho foi avaliar a comunidade de formigas em sistemas envolvendo a rotação entre lavoura e pecuária, sob plantio direto, comparado a outros sistemas de manejo e com sistemas naturais da região. O estudo foi conduzido no Município de Dourados, MS, sob Argissolo Vermelho distroférrico típico, num sistema integrado lavoura-pecuária, em plantio direto, rotacionado a cada dois anos. Outros sistemas de manejo avaliados, para comparação, incluíram o sistema convencional (aração e gradagem), sistema plantio direto e pastagem cultivada continuamente com Brachiaria decumbens, além de dois fragmentos de vegetação nativa, nos biomas Cerrado e Floresta Semidecídua. A coleta de solo foi realizada no período chuvoso (safra 2009/2010), sendo as amostragens de serapilheira realizadas com a utilização de extratores do tipo mini-Winkler, seguindo o protocolo ALL (Ants of the Leaf Litter). Os resultados indicaram morfoespécies de Strumygenys sp. e Hypoponera sp. como potencial bioindicadores de qualidade do solo. O estudo demonstrou que a importância da manutenção de fragmentos florestais (Cerrado e Floresta Semidecídua) e implementação de sistemas integrados, tais como lavoura-pecuária, são menos impactantes para a mesofauna de solo e contribuem para a conservação da diversidade de formigas e manutenção da qualidade do solo.

The aim of this study was to evaluate the ant community in different systems involving the crop rotations between livestock, under no-tillage, compared to other management systems and natural systems of the Mid-Western region. The study was carried out in the Dourados, Mato Grosso do Sul State, Brazil, on a Typic Hapludox soil, in parcels including crop-livestock rotation production system under no-tillage, rotated every two years, no-tillage crop system, succession of crops under conventional tillage, continuous pasture and two fragments of native vegetation, Cerrado and Semideciduous Forest. The samples of soil were conducted during the rainy season (2009/2010), and litter sampling performed with the use of mini-Winkler extractors, following the protocol ALL (Ants of the Leaf Litter). The results indicated that the morphospecies of Strumygenys sp. and Hypoponera sp. as potential bioindicators of soil quality, depending on their frequency changes in response to different systems observed. The study have demonstrated the importance of maintaining forest fragments as stock of local biodiversity and showed that integrated systems, such as crop-livestock, are less impact ful to the meso-fauna and contribute to the conservation of ant and maintenance of soil quality.

Fixação biológica de nitrogênio e teores foliares de nutrientes na soja em função de doses de molibdênio e gesso agrícola / Biological nitrogen fixation and leaf nutrient concentration on soybean as a function of molybdenum and gypsum levels

A competitividade econômica da soja brasileira no mercado mundial se deve, em grande parte, aos benefícios da fixação biológica do nitrogênio na cultura. O trabalho foi conduzido a campo, sob sistema plantio direto, em condição de sequeiro, no Município de Maracaju-MS, com o objetivo de avaliar a nodulação, o crescimento, nutrição mineral e produtividade de grãos da soja submetida a diferentes doses de gesso agrícola e molibdênio. Foi utilizado o delineamento experimental de blocos ao acaso, com cinco repetições e esquema de parcelas subdivididas, sendo as parcelas representadas por quatro doses de gesso agrícola (0, 1.000, 2.000 e 3.000 kg ha-1) e as subparcelas, por quatro doses de molibdênio (0, 20, 40 e 60 g ha-1). Não houve efeito da interação gesso x Mo sobre a produtividade da soja. O gesso agrícola não influencia no teor foliar de N e na produtividade. O Mo proporciona incrementos na produtividade e no teor de proteínas dos grãos.

The economic competitiveness of Brazilian soybeans on the world market occurs, in large part, due to the benefits of biological nitrogen fixation in this crop. The field experiment was carried out in Maracaju, Mato Grosso do Sul State, Brazil, under no-tillage system, in rainfed condition. The aim was to evaluate nodulation, growth, mineral nutrition and grain yield of soybeans under different doses of gypsum and molybdenum. The experimental design used was a randomized block with five replicates and arranged in a split-plot squeme, with the plot represented by four doses of gypsum (0, 1.000, 2.000 and 3.000 kg ha-1) and the subplots by four doses of molybdenum (0, 20, 40 and 60 g ha-1). There were no interaction effects of Mo x gypsum for grain yield. Gypsum has no influence in the N leaf content and grain yield. Mo increases grain yield and protein levels in the grain.

Populações de oligoquetos (Annelida: Oligochaeta) em um Latossolo Vermelho submetido a sistemas de uso do solo / Population of earthworm (Annelida: Oligochaeta) in a Hapludox under soil used systems

O trabalho teve como objetivo avaliar a dinâmica da população de oligoquetos edáficos em sistemas de manejo agrícola e pecuário, tendo, como referência, uma área sob vegetação nativa. O trabalho foi conduzido no município de Dourados, MS, num solo classificado como Latossolo Vermelho distroférrico típico, sob sistema com preparo convencional (SC), plantio direto (SPD), integração lavoura/pecuária (SILP), pastagem contínua (PC) e sistema natural (SN). As amostragens foram realizadas nas safras de verão e inverno, no período de 2000 a 2003. Os sistemas SPD, SILP e PC favoreceram o desenvolvimento e estabelecimento da população dos oligoquetos edáficos. O sistema natural apresentou uma alta população de oligoquetos edáficos, sendo a grande maioria constituída pelos organismos da família Enchytraeidae. Dentre os sistemas produtivos, o SPD favoreceu a ocorrência dessa família.