Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a “dilution-to-extinction” approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg⁻¹), in triplicate. Soils were incubated for 38 days, with CO₂ measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO₂ emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

Roots can recruit beneficial microorganisms to suppress plant pathogens. However, conventional and organic practices differently shape the soil microbiome and consequently the root protection. Here, we investigated the suppressive activity of soil microbiome against the root-knot nematode (RKN) Meloidogyne incognita in horticultural areas under organic or conventional practices and the microbiome profiles in non-inoculated (RKN-absent) and inoculated (RKN-present) rhizospheres. Soils were collected from neighboring areas under long-term conventional or organic practices, but physicochemically similar. After a set of bio-tests in autoclaved and non-autoclaved soils, we concluded that the soil suppressiveness was of biological origin. However, plant growth, RKN suppression and defense induction were higher in organic soils. Also, RKN was highly suppressed when the organic soil microbiome was transferred to infested substrates. We used Illumina MiSeq platform to determine bacterial and fungal profiles in organic and conventional tomato rhizospheres, inoculated or not with M. incognita. Our data suggest that despite the higher bacterial abundance in the conventional RKN-absent rhizosphere, the organic RKN-present rhizosphere recruited more efficiently antagonistic bacteria and fungi. Microbiome α-diversity increased in the organic RKN-present rhizosphere. Antagonistic bacterial genera Pseudomonas, Serratia, Bradyrhizobium, Burkholderia and Azospirillum and fungal genera Beauveria, Clonostachys, Metarhizium, Purpureocillium and Arthrobotrys were highly abundant only in the organic RKN-present rhizosphere. This work suggests the organic and conventional practices interfere in the rhizosphere microbiome composition and consequently in the suppression of RKN, where organic practices intensified the assembly of bacterial and fungal antagonists in the presence of M. incognita.

Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.

Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG’s reconstructed from the Amazon’s tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.

Ectomycorrhizal fungi are ubiquitous in forest ecosystems, benefitting plants principally by increasing the uptake of water and nutrients such as calcium from the soil. Previous work has demonstrated accumulation of crystallites in eucalypt ectomycorrhizas, but detailed morphological and chemical characterization of these crystals has not been performed. In this work, cross sections of acetic acid-treated and cleared ectomycorrhizal fragments were visualized by polarized light microscopy to evaluate the location of crystals within cortical root cells. Ectomycorrhizal sections were also observed by scanning electron microscopy (SEM) coupled with energy dispersive x-ray (EDS) microprobe analysis. The predominant forms of crystals were crystal sand (granules) and concretions. Calcium, carbon and oxygen were detected by EDS as constituent elements and similar elemental profiles were observed between both crystal morphologies. All analyzed crystalline structures were characterized as calcium oxalate crystals. This is the first report of the stoichiometry and morphology of crystals occurring in eucalypt ectomycorrhizas in tropical soils. The data corroborates the role of ectomycorrhizae in the uptake and accumulation of calcium in the form of calcium oxalate crystals in hybrid eucalypt plants.

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.

Roots can recruit beneficial microorganisms to suppress plant pathogens. However, conventional and organic practices differently shape the soil microbiome and consequently the root protection. Here, we investigated the suppressive activity of soil microbiome against the root-knot nematode (RKN) Meloidogyne incognita in horticultural areas under organic or conventional practices and the microbiome profiles in non-inoculated (RKN-absent) and inoculated (RKN-present) rhizospheres. Soils were collected from neighboring areas under long-term conventional or organic practices, but physicochemically similar. After a set of bio-tests in autoclaved and non-autoclaved soils, we concluded that the soil suppressiveness was of biological origin. However, plant growth, RKN suppression and defense induction were higher in organic soils. Also, RKN was highly suppressed when the organic soil microbiome was transferred to infested substrates. We used Illumina MiSeq platform to determine bacterial and fungal profiles in organic and conventional tomato rhizospheres, inoculated or not with M. incognita. Our data suggest that despite the higher bacterial abundance in the conventional RKN-absent rhizosphere, the organic RKN-present rhizosphere recruited more efficiently antagonistic bacteria and fungi. Microbiome α-diversity increased in the organic RKN-present rhizosphere. Antagonistic bacterial genera Pseudomonas, Serratia, Bradyrhizobium, Burkholderia and Azospirillum and fungal genera Beauveria, Clonostachys, Metarhizium, Purpureocillium and Arthrobotrys were highly abundant only in the organic RKN-present rhizosphere. This work suggests the organic and conventional practices interfere in the rhizosphere microbiome composition and consequently in the suppression of RKN, where organic practices intensified the assembly of bacterial and fungal antagonists in the presence of M. incognita.

Grapevine cultivars are distributed worldwide, nevertheless the fermentation of its grape berries renders distinct wine products that are highly associated to the local fungal community. Despite the symbiotic association between wine and the fungal metabolism, impacting both the terroir and mycotoxin production, few studies have explored the vineyard ecosystem fungal community using both molecular marker sequencing and mycotoxin production assessment. In this study, we investigated the fungal community of three grapevine cultivars (Vitis vinifera L.) in two tropical vineyards. Illumina MiSeq sequencing was performed on two biocompartments: grape berries (GB) and grapevine soil (GS); yielding a total of 578,495 fungal internal transcribed spacer 1 reads, which were used for taxonomic classification. GB and GS fungal communities were mainly constituted by Ascomycota phylum. GS harbors a significant richer and more diverse fungal community than GB. Among GB samples, Syrah grape berries exclusively shared fungal community included wine-associated yeasts (e.g. Saccharomycopsis vini) that may play key roles in wine terroir. Mycotoxin production assessment revealed the high potential of Aspergillus section Flavi and Penicillium section Citrina isolates to produce aflatoxin B1-B2 and citrinin, respectively. This is the first study to employ next-generation sequencing to investigate vineyard associated fungal community in Brazil. Our findings provide valuable insights on the available tools for fungal ecology assessment applied to food products emphasizing the coexistence between classical and molecular tools.

Temperature and water activity (a_w) are both responsible for the growth and production of ochratoxin A (OTA) by Aspergillus species in coffee. To prove this, we tested the effect of environmental factors combined with green coffee composition on the risk of OTA production as well as the efficiency of using Saccharomyces cerevisiae to control the growth of Aspergillus ochraceus, A. westerdijkiae, and A. carbonarius, OTA production and biosynthetic genes expression regulation levels. The results showed a higher growth rate and OTA risk index (ORI) for the three fungal isolates at 21 °C and 0.98 a_w. Temperature affected the growth of the isolates negatively. The ORI was influenced synergistically by a_w and antagonistically by temperature. The best condition for biological control by using S. cerevisiae CCMA 0159 was observed at 28 °C and 0.99 a_w. Temperature and a_w directly affected OTA production and biological control efficiency, but at different values. A. carbonarius CCDCA 10507 showed better growth and a greater risk of contamination in coffee. S. cerevisiae CCMA 0159 significantly reduced the risk of contamination by Aspergillus using substrate competition as strategies, acting on down regulation of OTA’s biosynthetic gene expression, including hal and p450.