Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration

Rupestrian grasslands are vegetation complexes of the Cerrado biome (Brazilian savanna), exhibiting simultaneously great biodiversity and important open-pit mining areas. There is a strong demand for the conservation of remaining areas and restoration of degraded. This study evaluated, using next-generation sequencing, the diversity and ecological aspects of soil fungal communities in ferruginous rupestrian grassland areas preserved and degraded by bauxite mining in Brazil. In the preserved and degraded area, respectively, 565 and 478 amplicon sequence variants (ASVs) were detected. Basidiomycota and Ascomycota comprised nearly 72% of the DNA, but Ascomycota showed greater abundance than Basidiomycota in the degraded area (64% and 10%, respectively). In the preserved area, taxa of different hierarchical levels (Agaromycetes, Agaricales, Mortierelaceae, and Mortierella) associated with symbiosis and decomposition were predominant. However, taxa that colonize environments under extreme conditions and pathogens (Dothideomycetes, Pleoporales, Pleosporaceae, and Curvularia) prevailed in the degraded area. The degradation reduced the diversity, and modified the composition of taxa and predominant ecological functions in the community. The lack of fungi that facilitate plant establishment and development in the degraded area suggests the importance of seeking the restoration of this community to ensure the success of the ecological restoration of the environment. The topsoil of preserved area can be a source of inocula of several groups of fungi important for the restoration process but which occur in low abundance or are absent in the degraded area.

DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic

Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.

Cryptic fungal diversity revealed by DNA metabarcoding in historic wooden structures at Whalers Bay, Deception Island, maritime Antarctic

We provide the first assessment of fungal diversity associated with historic wooden structures at Whalers Bay (Heritage Monument 71), Deception Island, maritime Antarctic, using DNA metabarcoding. We detected a total of 177 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Monoblepharomycota, Rozellomycota, and Zoopagomycota. The assemblages were dominated by Helotiales sp. 1 and Herpotrichiellaceae sp. 1. Functional assignments indicated that the taxa detected were dominated by saprotrophic, plant and animal pathogenic, and symbiotic taxa. Metabarcoding revealed the presence of a rich and complex fungal community, which may be due to the wooden structures acting as baits attracting taxa to niches sheltered against extreme conditions, generating a hotspot for fungi in Antarctica. The sequences assigned included both cosmopolitan and endemic taxa, as well as potentially unreported diversity. The detection of DNA assigned to taxa of human and animal opportunistic pathogens raises a potential concern as Whalers Bay is one of the most popular visitor sites in Antarctica. The use of metabarcoding to detect DNA present in environmental samples does not confirm the presence of viable or metabolically active fungi and further studies using different culturing conditions and media, different growth temperatures and incubation periods, in combination with further molecular approaches such as shotgun sequencing are now required to clarify the functional ecology of these fungi.

Trichoderma: biological control efficiency and perspectives for the Brazilian Midwest states and Tocantins

Brazil is one of the world leaders in the agribusiness sector tending to directly influence a growing dependence on imported inputs, specifically synthetic agrochemicals. At the state level, in 2013, Tocantins stood out in first place in the ranking of agrochemical consumers, however, these products can cause several problems, such as poisoning to humans, environmental contamination, and increased resistance to phytopathogens. Biological control is an alternative to the use of agrochemicals towards eliminating pests naturally by using living organisms called Biological Control Agents (BCA). Currently, fungi of the Trichoderma genus are some of the most used organisms in biological pest control for their relevant characteristics that favor them in terms of survival in the environment, such as high capacity to adapt to ecological conditions, potential to colonize the rhizosphere of plants, mycoparasitism, production of volatile and non-volatile metabolites. In addition, it works on plant growth and productivity. In general, the use of Trichoderma favors the control of soil pathogens, such as Rhizoctonia, Pythium, Sclerotinia, and nematodes. Thus, this review aims to demonstrate the importance of using Trichoderma in biological control, as well as to present an overview and perspectives of research developed by respondents in the Brazilian Midwest region and Tocantins state.

Large-scale Degradation of the Tocantins-Araguaia River Basin

The Tocantins-Araguaia Basin is one of the largest river systems in South America, located entirely within Brazilian territory. In the last decades, capital-concentrating activities such as agribusiness, mining, and hydropower promoted extensive changes in land cover, hydrology, and environmental conditions. These changes are jeopardizing the basin's biodiversity and ecosystem services. Threats are escalating as poor environmental policies continue to be formulated, such as environmentally unsustainable hydropower plants, large-scale agriculture for commodity production, and aquaculture with non-native fish. If the current model persists, it will deepen the environmental crisis in the basin, compromising broad conservation goals and social development in the long term. Better policies will require thought and planning to minimize growing threats and ensure the basin's sustainability for future generations.

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

Functional and structural characterization of a novel GH3 β-glucosidase from the gut metagenome of the Brazilian Cerrado termite Syntermes wheeleri

In this study, a GH3 family β-glucosidase (Bgl7226) from metagenomic sequences of the Syntermes wheeleri gut, a Brazilian Cerrado termite, was expressed, purified and characterized. The enzyme showed two optimum pHs (pH 7 and pH 10), and a maximum optimum temperature of about 40 °C using 4-Nitrophenyl β-D-glucopyranoside (pNPG) as substrate. Bgl7226 showed higher enzymatic activity at basic pH, but higher affinity (K_m) at neutral pH. However, at neutral pH the Bgl7226 enzyme showed higher catalytic efficiency (k_cat/K_m) for pNPG substrate. Predictive analysis about the enzyme structure-function relationship by sequence alignment suggested the presence of multi-domains and conserved catalytic sites. Circular dichroism results showed that the secondary structure composition of the enzyme is pH-dependent. Small conformational changes occurred close to the optimum temperature of 40 ^o C, and seem important for the highest activity of Bgl7226 observed at pH 7 and 10. In addition, the small transition in the unfolding curves close to 40 ^o C is typical of intermediates associated with proteins structured in several domains. Bgl7226 has significant β-glucosidase activity which could be attractive for biotechnological applications, such as plant roots detoxification; specifically, our group is interested in cassava roots (Manihot esculenta) detoxification.

Latitude and chlorophyll a density drive the distribution of carbohydrate-active enzymes in the planktonic microbial fraction of the epipelagic zone

Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing the effects of environmental factors on driving the marine carbohydrate-active enzyme (CAZyme) distribution. We characterized the diversity of CAZyme genes and investigated the correlations between their distributions and biogeographic parameters (latitude, longitude, distance from the equator, site depth, water depth, chlorophyll density, salinity and temperature). Therefore, we accessed a subset of surface water samples (38 metagenomes) from the Global Ocean Sampling project. Only chlorophyll and latitude altered the distribution patterns of CAZymes, revealing the existence of two latitudinal gradients (positive and negative) of marine CAZyme abundance. Considering the importance of carbohydrates in microbial life, characterization of the spatial patterns of the genetic repertoire involved in carbohydrate metabolism represents an important step in improving our understanding of the metabolic strategies associated with the microbial marine carbon cycle and their effects on the productivity of marine ecosystems.

Morphological and molecular aspects of sclerotial development in the phytopathogenic fungus Sclerotinia sclerotiorum

Sclerotinia sclerotiorum (Lib.) de Bary produces a resistance structure called sclerotium, which guarantees its survival in soil for long periods. Morphological and melanization aspects during sclerotial development were evaluated by microscopy and qRT-PCR techniques. S. sclerotiorum produces sclerotia with different phases of maturation and melanization during growth in PDA medium. Using scanning electron microscopy we observed that there are no structural differences in the three stages of formation of melanized and non-melanized sclerotium. Through histochemical analysis we observed that the melanized sclerotium accumulates more glycogen and produces less protein than non-melanized sclerotia. Melanin was most commonly found in the rind of melanized sclerotia, and the highest concentration of lipofucsins was found in non-melanized sclerotia. These molecules are products of the lipid peroxidation pathway and are associated with oxidative stress during differentiation in fungi. The expression of histidine kinase (shk) and adenylate cyclase (sac) genes in melanized and non-melanized sclerotiawere also evaluated. The higher gene expression of shk and lesser expression of sac in non-melanized sclerotiais an indication of the participation of cell signaling in the development of these structures. The higher expression of polyketide synthase (pks), tyrosinase (tyr) and laccase (lac) in non-melanized sclerotia suggested that S. sclerotiorum can use the DHN and L-dopa pathways to produce melanin. Expression studies of the enzymes chitin synthase and glucan synthase suggest that this process occurs along with the formation of melanin. This is interesting since polysaccharides, such as chitin and β-1,3-glucan, serve as a scaffold to which the melanin granules are cross-linked.

Structural and functional characterization of a novel lipolytic enzyme from a Brazilian Cerrado soil metagenomic library

OBJECTIVE

To isolate putative lipase enzymes by screening a Cerrado soil metagenomic library with novel features.

RESULTS

Of 6720 clones evaluated, Clone W (10,000 bp) presented lipolytic activity and four predicted coding sequences, one of them LipW. Characterization of a predicted esterase/lipase, LipW, showed 28% sequence identity with an arylesterase from Pseudomonas fluorescens (pdb|3HEA) from protein database (PDB). Phylogenetic analysis showed LipW clustered with family V lipases; however, LipW was clustered in different subclade belonged to family V, suggesting a different subgroup of family V. In addition, LipW presented a difference in family V GH motif, a glycine replaced by a serine in GH motif. Estimated molecular weight and stokes radius values of LipW were 29,338.67-29,411.98 Da and 2.58-2.83 nm, respectively. Optimal enzyme activity was observed at pH 9.0-9.5 and at 40 °C. Circular dichroism analysis estimated secondary structures percentages as approximately 45% α-helix and 15% β-sheet, consistent with the 3D structure predicted by homology.

CONCLUSION

Our results demonstrate the isolation of novel family V lipolytic enzyme with biotechnological applications from a metagenomic library.

Diversity and Pathogenicity of Rhizoctonia Species from the Brazilian Cerrado

Eighty-one Rhizoctonia-like isolates were identified based on morphology and nuclei-staining methods from natural and agricultural soils of the Cerrado (Brazilian savanna). The nucleotide similarity analysis of ITS1-5.8S-ITS2 regions identified 14 different taxa, with 39.5% of isolates assigned to Waitea circinata (zeae, oryzae, and circinata varieties), while 37.0% belonged to Thanatephorus cucumeris anastomosis groups (AGs) AG1-IB, AG1-ID, AG1-IE, AG4-HGI, and AG4-HGIII. Ceratobasidium spp. AG-A, AG-F, AG-Fa, AG-P, and AG-R comprised 23.5%. Rhizoctonia zeae (19.8%), R. solani AG1-IE (18.6%), and binucleate Rhizoctonia AG-A (8.6%) were the most frequent anamorphic states found. Root rot severity caused by the different taxa varied from low to high on common beans, and tended to be low to average in maize. Twenty-two isolates were pathogenic to both hosts, suggesting difficulties in managing Rhizoctonia root rots with crop rotation. These results suggest that cropping history affects the geographical arrangement of AGs, with a prevalence of AG1 in the tropical zone from central to north Brazil while the AG4 group was most prevalent from central to subtropical south. W. circinata var. zeae was predominant in soils under maize production. To our knowledge, this is the first report on the occurrence of W. circinata var. circinata in Brazil.

The Gut Microbiota of Workers of the Litter-Feeding Termite Syntermes wheeleri (Termitidae: Syntermitinae): Archaeal, Bacterial, and Fungal Communities

The gut microbiota of termites allows them to thrive on a variety of different materials such as wood, litter, and soil. For that reason, they play important roles in the decomposition of biomass in diverse biomes. This function is essential in the savanna, where litter-feeding termites are one of the few invertebrates active during the dry season. In this study, we describe the gut microbiota of workers (third and fourth instars) of the species Syntermes wheeleri, a litter-feeding termite from the Brazilian savanna. Results of 16S and 18S ribosomal RNA (rRNA) gene-targeted pyrosequencing using primers sets specific to each domain have revealed its bacterial, archaeal, and fungal diversities. Firmicutes accounted for more than half of the operational taxonomic units of the Bacteria domain. The most abundant fungal species were from the class Dothideomycetes of the phylum Ascomycota. The methanogenic orders Methanobacteriales, Methanosarcinales, and Methanomicrobiales of the phylum Euryarchaeota accounted for the greatest part of the Archaea detected in this termite. A comparison of the gut microbiota of the two instars revealed a difference in operational taxonomic unit (OTU) abundance but not in species richness. This description of the whole gut microbiota represents the first study to evaluate relationships among bacteria, archaea, fungi, and host in S. wheeleri.

Biochemical and metabolic profiles of Trichoderma strains isolated from common bean crops in the Brazilian Cerrado, and potential antagonism against Sclerotinia sclerotiorum

Some species of Trichoderma have successfully been used in the commercial biological control of fungal pathogens, e.g., Sclerotinia sclerotiorum, an economically important pathogen of common beans (Phaseolus vulgaris L.). The objectives of the present study were (1) to provide molecular characterization of Trichoderma strains isolated from the Brazilian Cerrado; (2) to assess the metabolic profile of each strain by means of Biolog FF Microplates; and (3) to evaluate the ability of each strain to antagonize S. sclerotiorum via the production of cell wall-degrading enzymes (CWDEs), volatile antibiotics, and dual-culture tests. Among 21 isolates, we identified 42.86% as Trichoderma asperellum, 33.33% as Trichoderma harzianum, 14.29% as Trichoderma tomentosum, 4.76% as Trichoderma koningiopsis, and 4.76% as Trichoderma erinaceum. Trichoderma asperellum showed the highest CWDE activity. However, no species secreted a specific group of CWDEs. Trichoderma asperellum 364/01, T. asperellum 483/02, and T. asperellum 356/02 exhibited high and medium specific activities for key enzymes in the mycoparasitic process, but a low capacity for antagonism. We observed no significant correlation between CWDE and antagonism, or between metabolic profile and antagonism. The diversity of Trichoderma species, and in particular of T. harzianum, was clearly reflected in their metabolic profiles. Our findings indicate that the selection of Trichoderma candidates for biological control should be based primarily on the environmental fitness of competitive isolates and the target pathogen.