Manoeli Lupatini

Network topology reveals high connectance levels and few key microbial genera within soils

Microbes have a central role in soil global biogeochemical process, yet specific microbe-microbe relationships are largely unknown. Analytical approaches as network analysis may shed new lights in understanding of microbial ecology and environmental microbiology. We investigated the soil bacterial community interactions through cultivation-independent methods in several land uses common in two Brazilian biomes. Using correlation network analysis we identified bacterial genera that presented important microbial associations within the soil community. The associations revealed nonrandomly structured microbial communities and clusters of operational taxonomic units (OTUs) that reflected relevant bacterial relationships. Possible keystone genera were found in each soil. Irrespective of the biome or land use studied only a small portion of OTUs showed positive or negative interaction with other members of the soil bacterial community. The more interactive genera were also more abundant however, within those genera, the abundance was not related to taxon importance as measured by the Betweenness Centrality. Most of the soil bacterial genera were important to the overall connectance of the network, whereas only few genera play a key role as connectors, mainly belonged to phyla Proteobacteria and Actinobacteria. Finally it was observed that each land use presented a different set of keystone genera and that no keystone genus presented a generalized distribution. Taking into account that species interactions could be more important to soil processes than species richness and abundance, especially in complex ecosystems, this approach might represent a step forward in microbial ecology beyond the conventional studies of microbial richness and abundance.

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome

The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.

Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.

Impactos da queima sobre atributos químicos, físicos e biológicos do solo

The objective of this study was to verify through literature review the possible impacts of the use of fire on the physical, chemical and biological attributes of soil. In relation to physical attributes, the fire may cause a decrease in the volume of macropores, the size of aggregates, the rate of infiltration of water into the soil and consequently its humidity, and an increase in the resistance to penetration of roots and soil density. Moreover, the soil becomes more susceptible to erosive process due to the removal of its vegetation cover. As for the chemical attributes, many studies focusing on chemical properties have reported an increase in levels of N, P, Ca, Mg, among others mineralized after the passage of fire because the ashes have high concentrations of these nutrients. Burning also reduces the input of organic matter and therefore alters the carbon cycle, contributing to the emission of greenhouse gases into the atmosphere. In relation to biological attributes, the action of flame reduces the availability of food (energy supply) for microorganisms, mainly reducing the population of mesofauna soil. In general, from the works reviewed, it appears that both the burning of pastures and natural fields as well as crop residues and forest areas, should be avoided as a routine practice, because in general, it directly or indirectly degrades the soil. However, depending on the situation and the production system, burning may be an indispensable alternative.

Mycorrhizal morphotyping and molecular characterization of Chondrogaster angustisporus Giachini, Castellano, Trappe & Oliveira, an ectomycorrhizal fungus from Eucalyptus

Chondrogaster angustisporus is a hypogeous ectomycorrhizal fungus described from fruiting bodies collected under Eucalyptus spp. in Brazil, Uruguay, and Australia. Due to its efficiency in promoting plant growth, we decided to characterize this fungus through mycorrhizal morphotyping and internal transcribed spacer (ITS) (rRNA) sequencing. DNA extracted from mycelium was amplified and sequenced using specific primers. Mycorrhizas were obtained aseptically and analyzed in terms of macroscopic and microscopic characteristics. When compared with other fungal DNA sequences available in the NBCI GenBank, the C. angustisporus sequence presented the highest similarity to an uncultured ectomycorrhizal fungus from the Seychelles. It also shows significant similarities to Gomphus, Ramaria, and Hysterangium species supporting the classification of Chondrogaster in the subclass Phallomycetidae in the gomphoid–phalloid group. The mycorrhizas were characterized by a narrow mantle with a single tissue layer densely arranged and organized as a net synenchyma with elongated hyphae. Interhyphal spaces were seen only in the external region where hyphae were more loosely organized. Bottle-shaped cystidia with bent necks were observed on the surface of the mantle. Emanating hyphae were larger than those in the mantle and presented a granular content. At regular intervals the hyphae were divided by septa with clamp connections. The Hartig net was of the common type, with typical palmetti and single hyphal rows and limited to the epidermal layer. The mycorrhizal description and the ITS sequence obtained are useful tools to identify this ectomycorrhizal fungus in culture and in association with Eucalyptus roots.

Copper resistance of different ectomycorrhizal fungi such as Pisolithus microcarpus, Pisolithus sp., Scleroderma sp. and Suillus sp.

Environments contaminated with heavy metals negatively impact the living organisms. Ectomycorrhizal fungi have shown important role in these impacted sites. Thus, this study aimed to evaluate the copper-resistance of ectomycorrhizal fungi isolates Pisolithus microcarpus - UFSC-Pt116; Pisolithus sp. - UFSC-PT24, Suillus sp. - UFSM RA 2.8 and Scleroderma sp. - UFSC-Sc124 to different copper doses in solid and liquid media. The copper doses tested were: 0.00, 0.25, 0.5, 0.75, 1.0 and 1.25 mmol L−1 in the solid medium and 0.00, 0.32, 0.64 and 0.96 mmol L−1 in the liquid medium. Copper was amended as copper sulphate in order to supplement the culture medium MNM at pH 4.8, with seven replicates to each fungus-dose combination. The fungal isolates were incubated for 30 days at 28 °C. UFSC-Pt116 showed high copper-resistance such as accessed by CL50 determinations (concentration to reduce 50% of the growth) as while as UFSC-PT24 displayed copper-resistance mechanism at 0.50 mmol L−1 in solid medium. The UFSC-PT24 and UFSC-Sc124 isolates have increased copper-resistance in liquid medium. The higher production of extracellular pigment was detected in UFSC-Pt116 cultures. The UFSC-Pt116 and UFSC-PT24 isolates showed higher resistance for copper and produced higher mycelium biomass than the other isolates. In this way, the isolates UFSG-Pt116 and UFSC-PT24 can be important candidates to survive in copper-contaminated areas, and can show important role in plants symbiosis in these contaminated sites.

Comportamento de Peltophorum dubium (Spreng.) Taub., Parapiptadenia rigida (Benth.) Brenan e Enterolobium contortisiliquum (Vell.) Morong cultivadas em solo contaminado com cobre

Soils contaminated by copper may interfere with the physiological development and establishment of plants. An alternative for the revegetation of these soils is the use of native species tolerant to copper. This study aimed to evaluate the tolerance of three native forest species to excess copper in the soil. The species used were: angico - Peltophorum dubium , canafistula - P. rigida and timbauva - Enterolobium contortisiliquum . The experiment was completely randomized in a 3 x 5 schedule, with three tree species and five doses of copper (0, 64, 128, 192 and 256 mg kg-1 soil) with six replicates. Plant height, shoot dry weight, length and specific root surface area and copper content in shoots and roots were determined. Canafistula and timbauva species showed storage of copper in roots and low translocation to the shoot. The shoot dry weight of timbauva and canafistula increased with small doses of copper while the shoot dry mass of angico was not affected by the doses tested. The timbauva and angico showed greater capacity for tolerance to copper contamination in the soil than did canafistula.

Symbiotic efficiency and genetic characteristics of Bradyrhizobium sp. strain UFSM LA 1.3 isolated from Lupinus albescens (H. et Arn)

Legume species belonging to the genus Lupinus are annual herb plants. The majority of them are indigenous to the Americas. They are known for nitrogen-fixing symbioses with soil bacteria collectively called rhizobia. The aim of this study was to characterize a rhizobium strain isolated from Lupinus albescens using phenotypic, symbiotic and molecular approaches. Strain UFSM LA 1.3 was tested in vitro according to several parameters: colony size, color and growing rate; acid or alkaline reaction in yeast mannitol media supplemented with bromothymol blue; gum production. Molecular characterization was evaluated by PCR technique using primers BOX A1-R and sequence analysis of the 16S-23S rDNA intergenic region (ITS). ITS sequencing fragments showed genetic similarity with Bradyrhizobium sp. The polymorphism observed by BOX-PCR have shown that strain differs from the reference strain SEMIA 928 and SEMIA 938. The symbiotic efficiency under axenic conditions of UFSM LA 1.3 was 94.6%, without statistical differences compared to the mineral nitrogen fertilized control, to which was applied solution of 400 mg of ammonium nitrate.

Variabilidade genética na região its do rDNA de isolados de trichoderma spp. (Biocontrolador) e Fusarium oxysporum f. sp. Chrysanthemi

A analise de caracteristicas morfologicas e culturais podem nao ser suficientes para uma caracterizacao precisa das especies de Trichoderma e Fusarium. Objetivou-se, neste trabalho, caracterizar a regiao do Espaco Interno Transcrito (ITS) do rDNA dos isolados UFSMT15.1, UFSMT16 e UFSMT17 de Trichoderma spp. utilizados no biocontrole de Fusarium oxysporum f. sp. chrysanthemi (isolado) UFSMF6. A extracao de DNA de cada isolado foi realizada a partir de micelio produzido em meio liquido Batata-Dextrose. As amostras de DNA genomico foram submetidas a Reacao em Cadeia da Polimerase (PCR) com os oligonucleotideos iniciadores universais ITS1 e ITS4 e o produto gerado foi sequenciado. Os fragmentos gerados pela amplificacao da PCR foram tratados com as enzimas de restricao HaeIII, HinfI e MboI. As regioes ITS1, ITS2 e 5.8S do rDNA desses isolados fungicos foram amplificadas com sucesso. A regiao ITS dos isolados UFSMT15.1, UFSMT16 e UFSMT17 de Trichoderma e o isolado UFSMF6 de Fusarium apresentaram uma banda simples com um fragmento de aproximadamente 600 pares de base (pb). As enzimas de restricao HaeIII, HinfI e MboI geraram polimorfismo de bandas entre os isolados. Com base nas analises da sequencia de DNA, os isolados UFSMT15.1, UFSMT16, UFSMT17 e UFSMF6 apresentaram maior similaridade com as especies Trichoderma koningiopsis, Hypocrea virens, Hypocrea lixii e Fusarium oxysporum, respectivamente.