Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut.

Supplementation with micronutrients, including vitamins, iron and zinc, is a key strategy to alleviate child malnutrition. However, association of gastrointestinal disorders with iron has led to ongoing debate over their administration. To better understand their impact on gut microbiota, we analyse the bacterial, protozoal, fungal and helminth communities of stool samples collected from a subset of 80 children at 12 and 24 months of age, previously enrolled into a large cluster randomized controlled trial of micronutrient supplementation in Pakistan (ClinicalTrials.gov identifier NCT00705445). We show that while bacterial diversity is reduced in supplemented children, vitamins and iron (as well as residence in a rural setting) may promote colonization with distinct protozoa and mucormycetes, whereas the addition of zinc appears to ameliorate this effect. We suggest that the risks and benefits of micronutrient interventions may depend on eukaryotic communities, potentially exacerbated by exposure to a rural setting. Larger studies are needed to evaluate the clinical significance of these findings and their impact on health outcomes.

Use of chitosan and tannins as alternatives to antibiotics to control mold growth on PDO Pecorino Toscano cheese rind.

The fungal microbiota usually growing on the cheese surface during ripening processes promote rind formation and the development of organoleptic characteristics, imparting positive sensory attributes to cheeses. As cheese contamination may also occur by undesirable molds, specific actions for preventing their growth are usually realized in dairy industries by using the antibiotic natamycin, which may represent a risk factor for human health and environmental sustainability. Here, agroindustrial by-products with natural antimicrobial properties, i.e. tannins and chitosan, were tested in a cheese-making trial producing PDO Tuscan pecorino cheese. Morphological and molecular methods revealed that the main components of rind fungal communities of PDO Tuscan pecorino cheese were represented by P. solitum, P. discolour and P. verrucosum. The use of chitosan on cheese rinds did not significantly affect the composition of rind fungal communities developing during the whole ripening process compared with controls treated with natamycin, whose numbers ranged from 3.4 ± 1.3 × 103 to 3.2 ± 1.8 × 104 and from 6.3 ± 3.5 × 102 to 4.0 ± 1.5 × 104, respectively. Overall, grape marc tannins and chitosan did not significantly affect the number and composition of fungal communities developing during PDO Pecorino Toscano cheese ripening, as well as its physical, chemical and nutritional profiles, showing that they may represent effective alternatives to the antibiotic natamycin.

Control of Fusarium wilt by wheat straw is associated with microbial network changes in watermelon rhizosphere.

Straw return is an effective strategy to alleviate soil-borne diseases. Though watermelon Fusarium wilt is a severe soil-borne disease, the effect of wheat straw on the disease remains unclear. Thus, we investigated the effects of wheat straw on soil bacterial and fungal communities by adding wheat straw to consecutive watermelon soil in the greenhouse condition. The microbiome changes were further investigated using network analysis based on 16S rDNA and internal transcribed spacer deep sequencing. Wheat straw addition increased the fungal community diversity, whereas the bacterial diversity was not affected. Compared to the control group, the relative abundance of some bacteria, including Actinobacteria, Chloroflexi, and Saccharibacteria, was increased with wheat straw addition. For fungi, the relative abundance of Fusarium was decreased with wheat straw addition. Microbial network analysis demonstrated that the fungal community has a more complex connection than the bacterial community. In addition, redundancy analysis indicated that the Fusarium genera were significantly related to the disease index. Taken together, the addition of wheat straw might affect the microbial community through increasing the relative abundance of phylum Actinobacteria, decreasing the relative abundance of Fusarium, and increasing the fungal network complexity to enhance the defense of watermelon against Fusarium wilt disease.

Effect of depleted uranium on a soil microcosm fungal community and influence of a plant-ectomycorrhizal association.

Fungi are one of the most biogeochemically active components of the soil microbiome, becoming particularly important in metal polluted terrestrial environments. There is scant information on the mycobiota of uranium (U) polluted sites and the effect of metallic depleted uranium (DU) stress on fungal communities in soil has not been reported. The present study aimed to establish the effect of DU contamination on a fungal community in soil using a culture-independent approach, fungal ribosomal intergenic spacer analysis (F-RISA). Experimental soil microcosms also included variants with plants (Pinus silvestris) and P. silvestris/Rhizopogon rubescens ectomycorrhizal associations. Soil contamination with DU resulted in the appearance of RISA bands of the ITS fragments of fungal metagenomic DNA that were characteristic of the genus Mortierella (Mortierellomycotina: Mucoromycota) in pine-free microcosms and for ectomycorrhizal fungi of the genus Scleroderma (Basidiomycota) in microcosms with mycorrhizal pines. The precise taxonomic affinity of the ITS fragments from the band appearing for non-mycorrhizal pines combined with DU remained uncertain, the most likely being related to the subphylum Zoopagomycotina. Thus, soil contamination by thermodynamically unstable metallic depleted uranium can cause a significant change in a soil fungal community under experimental conditions. These changes were also strongly affected by the presence of pine seedlings and their mycorrhizal status which impacted on DU biocorrosion and the release of bioavailable uranium species.

Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana.

Plants respond to phosphorus (P) limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi) starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomic marker ITS2, we examined the changes in root-associated fungal communities in the AM nonhost species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison with their P-deprived counterparts, while bulk soil communities remained unaltered. Moreover, plants carrying mutations in the phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM nonhost plant as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil.

Glyphosate application increased catabolic activity of gram-negative bacteria but impaired soil fungal community.

Glyphosate is a non-selective organophosphate herbicide that is widely used in agriculture, but its effects on soil microbial communities are highly variable and often contradictory, especially for high dose applications. We applied glyphosate at two rates: the recommended rate of 50 mg active ingredient kg-1 soil and 10-fold this rate to simulate multiple glyphosate applications during a growing season. After 6 months, we investigated the effects on the composition of soil microbial community, the catabolic activity and the genetic diversity of the bacterial community using phospholipid fatty acids (PLFAs), community level catabolic profiles (CLCPs), and 16S rRNA denaturing gradient gel electrophoresis (DGGE). Microbial biomass carbon (Cmic) was reduced by 45%, and the numbers of the cultivable bacteria and fungi were decreased by 84 and 63%, respectively, under the higher glyphosate application rate. According to the PLFA analysis, the fungal biomass was reduced by 29% under both application rates. However, the CLCPs showed that the catabolic activity of the gram-negative (G-) bacterial community was significantly increased under the high glyphosate application rate. Furthermore, the DGGE analysis indicated that the bacterial community in the soil that had received the high glyphosate application rate was dominated by G- bacteria. Real-time PCR results suggested that copies of the glyphosate tolerance gene (EPSPS) increased significantly in the treatment with the high glyphosate application rate. Our results indicated that fungi were impaired through glyphosate while G- bacteria played an important role in the tolerance of microbiota to glyphosate applications.

Reversal of visceral hypersensitivity in rat by Menthacarin® , a proprietary combination of essential oils from peppermint and caraway, coincides with mycobiome modulation.

BACKGROUND: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder associated with altered gastrointestinal microflora and increased nociception to colonic distension. This visceral hypersensitivity can be reversed in our rat maternal separation model by fungicides. Menthacarin® is a proprietary combination of essential oils from Mentha x piperita L. and Carum carvi. Because these oils exhibit antifungal and antibacterial properties, we investigated whether Menthacarin® can reverse existing visceral hypersensitivity in maternally separated rats. METHODS: In non-handled and maternally separated rats, we used the visceromotor responses to colorectal distension as measure for visceral sensitivity. We evaluated this response before and 24 hours after water-avoidance stress and after 7 days treatment with Menthacarin® or control. The pre- and post-treatment mycobiome and microbiome were characterized by sequencing of fungal internal transcribed spacer 1 (ITS-1) and bacterial 16s rDNA regions. In vitro antifungal and antimicrobial properties of Menthacarin® were studied with radial diffusion assay. KEY RESULTS: Menthacarin® inhibited in vitro growth of yeast and bacteria. Water-avoidance caused visceral hypersensitivity in maternally separated rats, and this was reversed by treatment. Multivariate analyses of ITS-1 and 16S high throughput data showed that maternal separation, induced changes in the myco- and microbiome. Menthacarin® treatment of non-handled and maternally separated rats shifted the mycobiomes to more similar compositions. CONCLUSIONS & INFERENCES: The development of visceral hypersensitivity in maternally separated rats and the Menthacarin® -mediated reversal of hypersensitivity is associated with changes in the mycobiome. Therefore, Menthacarin® may be a safe and effective treatment option that should be tested for IBS.

Combined Effects of Dissolved Nutrients and Oxygen on Plant Litter Decomposition and Associated Fungal Communities.

Aquatic ecosystems worldwide have been substantially altered by human activities, which often induce changes in multiple factors that can interact to produce complex effects. Here, we evaluated the combined effects of dissolved nutrients (nitrogen [N] and phosphorus [P]; three levels: concentration found in oligotrophic streams in the Cerrado biome, 10× and 100× enriched) and oxygen (O2; three levels: hypoxic [4% O2], depleted [55% O2], and saturated [96% O2]) on plant litter decomposition and associated fungal decomposers in laboratory microcosms simulating stream conditions under distinct scenarios of water quality deterioration. Senescent leaves of Maprounea guianensis were incubated for 10 days in an oligotrophic Cerrado stream to allow microbial colonization and subsequently incubated in microcosms for 21 days. Leaves lost 1.1-3.0% of their initial mass after 21 days, and this was not affected either by nutrients or oxygen levels. When considering simultaneous changes in nutrients and oxygen concentrations, simulating increased human pressure, fungal biomass accumulation, and sporulation rates were generally inhibited. Aquatic hyphomycete community structure was also affected by changes in nutrients and oxygen availability, with stronger effects found in hypoxic treatments than in depleted or saturated oxygen treatments. This study showed that the effects of simultaneous changes in the availability of dissolved nutrients and oxygen in aquatic environments can influence the activity and composition of fungal communities, although these effects were not translated into changes in litter decomposition rates.