Microbial Diversity of Brazilian Biomes

Streptomyces spp. Isolated from Marine and Caatinga Biomes in Brazil for the Biological Control of Duponchelia fovealis

Actinobacteria have been drawing attention due to their potential for the development of new pest control products. We hereby assess the effects of Streptomyces isolated from marine and caatinga biomes against Duponchelia fovealis Zeller (Lepidoptera: Crambidae), a pest associated with the strawberry culture at a global scale. To this end, eggs deposited by adults were immersed for 5 s in a bacterial suspension, and the larvae were fed on leaflets placed in glass tubes containing bacterial suspensions. In both treatments, the control was a saline solution. The bioassays demonstrated that the Streptomyces strains were able to cause the death of D. fovealis eggs (≈ 40%) and larvae (≈ 65%) compared to untreated eggs (1.4%) and larvae (2.0%). The crude extract of strain T49 and the chitinase extract of strain T26 affected larval growth when applied directly to the thorax of first-instar larvae (larval-adult lifespan of 65.3 ± 0.5 days and 67.5 ± 0.7 days, respectively; survival of 61.2 ± 1.2%) in relation to the control treatment (larval-adult lifespan of 41.75 ± 0.2 days and survival of 83.7 ± 2.6%). The Streptomyces spp. strains T41, T49, and T50 caused antifeeding activity. Apart from larval mortality, the adults that emerged from the larvae exposed to the extracts presented morphological abnormalities, and the moths' chitin spectra showed clear alterations to the pupa and wings. Our studies show, for the very first time, that Streptomyces isolated from the marine environment and the Caatinga biome are effective at provoking the mortality of D. fovealis and are promising agents for developing new products with biological control properties.

Thinning Partially Mitigates the Impact of Atlantic Forest Replacement by Pine Monocultures on the Soil Microbiome

Forest replacement by exotic plantations drive important changes at the level of the overstory, understory and forest floor. In the Atlantic Forest of northern Argentina, large areas have been replaced by loblolly pine (Pinus taeda L.) monocultures. Plant and litter transformation, together with harvesting operations, change microclimatic conditions and edaphic properties. Management practices such as thinning promote the development of native understory vegetation and could counterbalance negative effects of forest replacement on soil. Here, the effects of pine plantations and thinning on physical, chemical and microbiological soil properties were assessed. Bacterial, archaeal, and fungal community structure were analyzed using a metabarcoding approach targeting ribosomal markers. Forest replacement and, to a lesser extent, thinning practices in the pine plantations induced significant changes in soil physico-chemical properties and associated shifts in bacterial and fungal communities. Most measured physical and chemical properties were altered due to forest replacement, but a few of these properties reached values similar to natural forests under the thinning operation. Fungal alpha diversity decreased in pine plantations, whereas bacterial alpha diversity tended to increase but with little statistical support. Shifts in community composition were observed for both fungal and bacterial domains, and were mostly related to changes in plant understory composition, soil carbon, organic matter, water content, pH and bulk density. Among several other changes, highly abundant phyla such as Proteobacteria (driven by many genera) and Mortierellomycota (mainly driven by Mortierella) decreased in relative abundance in the plantations, whereas Acidobacteria (mainly driven by Acidothermus and Candidatus Koribacter) and Basidiomycota (mainly driven by the ectomycorrhiza Russula) showed the opposite response. Taken together, these results provide insights into the effects of forest replacement on belowground properties and elucidate the potentially beneficial effect of thinning practices in intensive plantation systems through promoting the understory development. Although thinning did not entirely counterbalance the effects of forest replacement on physical, chemical and biological soil properties, the strategy helped mitigating the effects and might promote resilience of these properties by the end of the rotation cycle, if subsequent management practices compatible with the development of a native understory vegetation are applied.

Exploring the Brazilian diversity of Aspergillus sp. strains for lovastatin and itaconic acid production

Filamentous fungi are well known for producing secondary metabolites applied in various industrial segments. Among these, lovastatin and itaconic acid, produced by Aspergillus terreus, have applications in the pharmaceutical and chemical industries. Lovastatin is primarily used for the control of hypercholesterolemia, while itaconic acid is a building block for the production of synthetic fibers, coating adhesives, among others. In this study, for the first time, 35 strains of Aspergillus sp. from four Brazilian culture collections were evaluated for lovastatin and itaconic acid production and compared to a reference strain, ATCC 20542. From an initial screening, the strains ATCC 20542, URM 224, URM1876, URM 5061, URM 5254, URM 5256, URM 5650, and URM 5961 were selected for genomic comparison. Among tested strains, the locus corresponding to the lovastatin genomic cluster was assembled, showing that all genes essential for lovastatin biosynthesis were present in producing URM 5961 and URM 5650 strains, with 100% and 98.5% similarity to ATCC 20542, respectively. However, in the no producing URM 1876, URM 224, URM 5254, URM 5061, and URM 5256 strains, this cluster was either fragmented or missing. Among the 35 strains evaluated for itaconic acid production in this study, only three strains had titers above 0.5 g/L, 16 strains had production below 0.5 g/L, and the remaining 18 strains had no production, with the highest production of itaconic acid observed in the URM 5254 strain with 2.2 g/L. The essential genes for itaconic acid production, mttA, cadA msfA were also mapped, where all three genes linked to itaconic acid production were found in a single contig in the assembly of each strain. In contrast to lovastatin loci, there is no correlation between the level of itaconic acid production and genetic polymorphisms in the genes associated with its biosynthesis.

Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater

Overcoming recalcitrance of lignin has motivated bioprospecting of high-yielding enzymes from environmental ligninolytic microorganisms associated with lignocellulose degrading-systems. Here, we performed isolation of 21 ligninolytic strains belonging to the genus Klebsiella spp., driven by the presence of lignin in the media. The fastest-growing strains (FP10-5.23, FP10-5.22 and P3TM1) reached the stationary phase in approximately 24 h, in the media containing lignin as the main carbon source. The strains showed biochemical evidence of ligninolytic potential in liquid- and solid media-converting dyes, which the molecular structures are similar to lignin fragments. In liquid medium, higher levels of dye decolorization was observed for P3TM.1 in the presence of methylene blue, reaching 98% decolorization in 48 h. The highest index values (1.25) were found for isolates P3TM.1 and FP10-5.23, in the presence of toluidine blue. The genomic analysis revealed the presence of more than 20 genes associated with known prokaryotic lignin-degrading systems. Identification of peroxidases (lignin peroxidase-LiP, dye-decolorizing peroxidase-DyP, manganese peroxidase-MnP) and auxiliary activities (AA2, AA3, AA6 and AA10 families) among the genetic repertoire suggest the ability to produce extracellular enzymes able to attack phenolic and non-phenolic lignin structures. Our results suggest that the Klebsiella spp. associated with fresh water and soil may play important role in the cycling of recalcitrant molecules in the Caatinga (desert-like Brazilian biome), and represent a potential source of lignin-degrading enzymes with biotechnological applications.

Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome

Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.

Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.