Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.

BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

An Actinobacterium Strain From Soil of Cerrado Promotes Phosphorus Solubilization and Plant Growth in Soybean Plants.

The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 µg ml-1 from phytate, 300 µg ml-1 from calcium phosphate, and 200 µg ml-1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha-1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future.

Phosphorus-solubilizing Trichoderma spp. from Amazon soils improve soybean plant growth.

Acidic soils rapidly retain applied phosphorus fertilizers and consequently present low availability of this nutrient to plants. The use of phosphate-solubilizing microorganisms to help plant phosphorus (P) absorption is a promising sustainable strategy for managing P deficiencies in agricultural soils. Trichoderma strains have been one of the most studied filamentous fungi for improving the production and development of several crop species mainly due to their capability for symbiotic associations and their ability to control soil-borne plant diseases. Thus, this work sought to bioprospect Trichoderma strains from the Amazon rainforest capable of solubilizing/mineralizing soil phosphate and promoting soybean growth. Soybean plants inoculated with selected Trichoderma strains were cultivated in soil under greenhouse conditions and under a gradient of rock phosphate and triple superphosphate. As a result, 19.5% of the isolated Trichoderma strains were able to solubilize phosphate. In addition, those strains produced different organic acids during the solubilization process. Trichoderma spp. strains showed positive responses in the promotion of soybean growth-from 2.1% to 41.1%-as well as in the efficiency of P uptake-up to 141%. These results reveal the potential of Trichoderma spp. from the Amazon biome as promising biofertilizer agents.

Large scale distribution of bacterial communities in the upper Paraná River floodplain

A bacterial community has a central role in nutrient cycle in aquatic habitats. Therefore, it is important to analyze how this community is distributed throughout different locations. Thirty-six different sites in the upper Paraná River floodplain were surveyed to determine the influence of environmental variable in bacterial community composition. The sites are classified as rivers, channels, and floodplain lakes connected or unconnected to the main river channel. The bacterial community structure was analyzed by fluorescent in situ hybridization (FISH) technique, based on frequency of the main domains Bacteria and Archaea, and subdivisions of the phylum Proteobacteria (Alpha-proteobacteria, Beta-proteobacteria, Gamma-proteobacteria) and the Cytophaga-Flavobacterium cluster. It has been demonstrated that the bacterial community differed in density and frequency of the studied groups. And these differences responded to distinct characteristics of the three main rivers of the floodplain as well as to the classification of the environments found in this floodplain. We conclude that dissimilarities in the bacterial community structure are related to environmental heterogeneity, and the limnological variables that most predicted bacterial communities in the upper Paraná River floodplain was total and ammoniacal nitrogen, orthophosphate and chlorophyll-a.

Large scale distribution of bacterial communities in the upper Paraná River floodplain.

A bacterial community has a central role in nutrient cycle in aquatic habitats. Therefore, it is important to analyze how this community is distributed throughout different locations. Thirty-six different sites in the upper Paraná River floodplain were surveyed to determine the influence of environmental variable in bacterial community composition. The sites are classified as rivers, channels, and floodplain lakes connected or unconnected to the main river channel. The bacterial community structure was analyzed by fluorescent in situ hybridization (FISH) technique, based on frequency of the main domains Bacteria and Archaea, and subdivisions of the phylum Proteobacteria (Alpha-proteobacteria, Beta-proteobacteria, Gamma-proteobacteria) and the Cytophaga-Flavobacterium cluster. It has been demonstrated that the bacterial community differed in density and frequency of the studied groups. And these differences responded to distinct characteristics of the three main rivers of the floodplain as well as to the classification of the environments found in this floodplain. We conclude that dissimilarities in the bacterial community structure are related to environmental heterogeneity, and the limnological variables that most predicted bacterial communities in the upper Paraná River floodplain was total and ammoniacal nitrogen, orthophosphate and chlorophyll-a.

Seasonal dynamics and community structure of bacterioplankton in upper Paraná River floodplain.

Knowing the bacterial community, as well as understanding how it changes during a hydrological pulse, is very important to understand nutrient cycles in floodplain systems. The bacterial community structure was analyzed in the 12 sites of upper Paraná River floodplain, and its changes during a flood pulse were described. In order to understand how high and low water phases change bacterial community by changing abiotical variables, the bacterial community distribution was determined in superficial water of 12 different sampling stations, every 3 months, from December 2010 to September 2011. The bacterial community structure and diversity was analyzed by fluorescent in situ hybridization, considering the main domains Bacteria and Archaea and the subdivisions of the phylum Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) and the Cytophaga-Flavobacterium cluster. Smaller densities were observed on ebb and low water periods and the highest density was observed in March 2011. The high water period caused a decrease in diversity because of the lost of equitability. The highest values of Shannon-Wiener index were found on December 2010 and September 2011. The nutrients runoff to the aquatic environments of the floodplain promoted an increase in the total bacterial density during the high water phase as well as changes in bacterial community composition. The bacterial community presented both spatial and temporal differences. Yet, temporal changes in limnological characteristics of the floodplain were the most important predictor of bacterial community and also influenced its diversity.

Spatial distribution of aquatic Oligochaeta in Ilha Grande National Park, Brazil / Distribuição espacial de Oligochaeta aquático no Parque Nacional de Ilha Grande, Brasil

Ilha Grande National Park is an important conservation unit localized in the Southern part of the upper Paraná river floodplain (Brazil) that includes diverse aquatic environments. Oligochaeta (Annelida) is a large group of invertebrates, with several small specimens inhabiting almost every possible niche at most freshwater ecosystem. The goal of the present study was to examine the spatial variation of Oligochaeta community in five floodplain lakes from the Ilha Grande National Park and relate the distribution with abiotic variables. Samples were taken at five sampling stations using a modified Petersen grab. Thirteen species of Oligochaeta belonging to two families Naididae and Tubificidae were recorded. Different patterns of richness and abiotic factors were identified among the lakes located in the island and at the margin of Paraná river. The different patterns of granulometric texture affected directly the distribution of the Oligochaeta assemblage of theses environments. The results of this study permit to infer that the Oligochaeta assemblage, in preserved areas, present a higher richness in relation to long term studies with more frequent samplings. We concluded that Ilha Grande National Park contributes for the preservation of benthic invertebrates.

O Parque Nacional de Ilha Grande é uma importante unidade de Conservação localizada ao Sul da Planície de Inundação do alto rio Paraná (Brasil) que abrange diversos ambientes aquáticos. Oligochaeta (Annelida) é um grupo de invertebrados, cujos pequenos espécimes habitam quase todos os nichos dos ecossistemas de água doce. O objetivo desse estudo foi o de analisar a variação espacial da comunidade de Oligochaeta em cinco lagoas de várzea do Parque Nacional de Ilha Grande e relacionar a sua distribuição às variáveis abióticas. As amostras foram coletadas em cinco locais usando pegador de Petersen modificado. Treze espécies de Oligochaeta pertencentes às famílias Naididae e Tubificidae foram encontradas. Foram identificados diferentes padrões de riqueza e de fatores abióticos entre as lagoas de várzea localizadas na ilha e na margem do rio Paraná. Os diferentes padrões de textura granulométrica afetaram diretamente a distribuição da assembleia de Oligochaeta entre esses ambientes. Os resultados deste estudo permitiram inferir que a assembléia de Oligochaeta, em áreas preservadas, apresenta maior riqueza em relação aos estudos de longo prazo com maior esforço amostral. Dessa forma, conclui-se que o Parque Nacional de Ilha Grande contribui para a preservação de invertebrados bentônicos.