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Whip smut is one of the most serious and widely spread sugarcane diseases. Plant-associated microbes play various roles in conferring advantages to the host plant. Understanding the microbes associated with sugarcane roots will help develop strategies for the biocontrol of smut. Therefore, the present study explored microbe-mediated sugarcane response to smut invasion via 16S rRNA and ITS metabarcoding survey of the rhizosphere soils of resistant and susceptible sugarcane varieties. The bacterial and fungal diversity in the rhizosphere soils differed between the resistant and susceptible varieties. The bacterial genera Sphingomonas, Microcoleus_Es-Yyy1400, Marmoricola, Reyranella, Promicromonospora, Iamia, Phenylobacterium, Aridibacter, Actinophytocola, and Edaphobacter and one fungal genus Cyphellophora were found associated with smut resistance in sugarcane. Detailed analysis revealed that the majority of bacteria were beneficial, including the actinomycete Marmoricola and Iamia and Reyranella with denitrification activity. Analysis of bacterial network interaction showed that three major groups interacted during smut invasion. Meanwhile, seven of these genera appeared to interact and promote each other's growth. Finally, functional annotation based on the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database predicted that the abundant bacteria are dominated by oxygenic photoautotrophy, photoautotrophy, and phototrophy functions, which may be related to smut resistance in sugarcane. The present study thus provides new insights into the dynamics of the sugarcane rhizosphere microbial community during smut invasion.

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Competition with invasive grasses is one of the most important drivers of tree planting failures, especially in tropical forests. A widely disseminated weeding approach has been glyphosate spraying, the most used herbicide globally in forestry and ecosystem restoration. However, glyphosate use in restoration is highly controversial and requires further studies to elucidate its effects on restoration processes and the environment. We evaluated the use of glyphosate in riparian forest restoration and its impacts on tree planting costs, weed control efficiency, planted seedling performance, herbaceous and woody species regeneration, soil bacteria, and environmental contamination, using mowing treatments as a reference and based on a controlled experiment established in the Brazilian Atlantic Forest. Glyphosate spraying reduced by one-half and one-third the accumulated aboveground biomass of, respectively, weeds in general and of the invasive grass Urochloa decumbens compared to mowing treatments, and it reduced the cost by half. The performance of planted tree seedlings was markedly favored by glyphosate spraying compared to mowing treatments, as expressed by improved seedling height (~twice higher), crown area (~5× higher), and basal area (~5× higher); the regeneration of both native woody and ruderal herbaceous plants were also enhanced. Neither glyphosate nor its metabolite Aminomethylphosphonic acid (AMPA) residues were detected in either water runoff or soil samples, but they were found at relatively high concentrations in the runoff sediments (from 1.32 to 24.75 mg/kg for glyphosate and from 1.75 to 76.13 mg/kg for AMPA). Soil bacteria communities differed before and after glyphosate spraying in comparison to mowing plots (without glyphosate). Glyphosate spraying was far more cost effective than mowing for controlling U. decumbens and greatly improved the performance of planted tree seedlings and natural regeneration, while not leaving residues in soil and water. However, the changes in the structure of bacterial communities and high concentration of glyphosate and AMPA residues in runoff sediments highlight the need for caution when using this herbicide in riparian buffers. We present alternatives for reducing glyphosate use and minimizing its risks in tree planting initiatives.

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Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.

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BACKGROUND: The ecological phenomenon of fungal fairy rings is usually found in grasslands and caused by the growth of specific fairy ring fungi in soil. The fairy rings are classified into three zones (DARK, DEAD, and OUT), and they have the potential to increase crop yield. Among these fairy rings, distinct characteristics of type I fairy rings can be seen in the rings formed by Leucocalocybe mongolica (LM). Our studies addressed changes in the soil microbial structure due to LM fairy rings to enhance understand of this ecological phenomenon. METHODS: In the present study, we report the soil microbial analysis results (fungi and bacteria), including those of metabarcoding (16s rRNA, ITS), microbial quantity, and metagenomics surveys of soils collected from various fairy ring zones, of 6 LM fairy rings. All sampling sites cover the grasslands of Mongolian Plateau in China. RESULTS: First, we found through metabarcoding surveys that the difference in microbial diversity is relatively less in bacteria and that the abundance of fairy ring fungi (LM) is relatively high in DEAD zones. We also identified eight bacterial and fungal families, including Sphingobacteriaceae and Sphingomonadaceae that were enriched within the soils of fairy ring zones. Second, we found that the abundance of soil bacteria in the DEAD zones is sharply increased along with the growth of fairy ring fungi (LM). Third, we found through shotgun sequencing that fairy ring-infected zones, DARK and DEAD, exhibit greater genetic diversity than OUT zones. Finally, we showed that the fairy ring ecosystem is the center for a rich grassland microbial community. CONCLUSIONS: The reported data can improve our understanding of type I fairy rings and will be further insightful to the research on crop production.

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The effect of management (ecological and conventional) on functional groups of microorganisms of soil in agroecosystems with different resilience scores reported to climate variability in Anolaima, Colombia was evaluated. Were found clustering associated with management and cellulolytic bacteria and fungi abundances. No differences found in diversity of phosphate solubilizing or nitrogen-fixing microorganisms, related to management. The diversity of microbial functional groups was affected by the climatic condition of sampling season. Management was relevant in relationships between resilience scores to climate variability and cellulolytic microorganisms; in ecological agroecosystems, biodiversity knowledge, agroecological main structure, and the participation of farmers in organizations were important.(AU)

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The effect of management (ecological and conventional) on functional groups of microorganisms of soil in agroecosystems with different resilience scores reported to climate variability in Anolaima, Colombia was evaluated. Were found clustering associated with management and cellulolytic bacteria and fungi abundances. No differences found in diversity of phosphate solubilizing or nitrogen-fixing microorganisms, related to management. The diversity of microbial functional groups was affected by the climatic condition of sampling season. Management was relevant in relationships between resilience scores to climate variability and cellulolytic microorganisms; in ecological agroecosystems, biodiversity knowledge, agroecological main structure, and the participation of farmers in organizations were important.

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The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.

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Background Accompanying its rapid economic development and population growth, China is the world's third largest acid rain region, following Europe and North America. The effects of acid rain on forest ecosystem were widely researched, including the growth, the nutrient of the leaf and soil, and so on. However, there are few reports about the effects of acid rain on the soil microbial diversity. This study investigated the effects of acid rain on soil microbial community function under potted Masson pine seedlings (Pinus massoniana Lamb). Results After 7 months of treatment with simulated acid rain, the low acid load treatment (pH 5.5) stimulated soil microbial activity, and increased soil microbial diversity and richness, while the higher levels of acid application (pH 4.5, pH 3.5) resulted in lower soil microbial activity and had no significant effects on soil microbial diversity and richness. Principal component analysis showed that there was clear discrimination in the metabolic capability of the soil microbial community among the simulated acid rain and control treatments. Conclusion The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.

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Ecological succession is one of the most important concepts in ecology. However for microbial community succession, there is a lack of a solid theoretical framework regarding succession in microorganisms. This is in part due to microbial community complexity and plasticity but also because little is known about temporal patterns of microbial community shifts in different kinds of ecosystems, including arid soils. The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, is an arid zone with high diversity and endemisms that has recently been threatened by aquifer overexploitation. The gypsum-based soil system of the CCB is one of the most oligotrophic places in the world. We undertook a comparative 16S rRNA 454 pyrosequencing study to evaluate microbial community succession and recovery over a year after disturbance at two sites. Results were related to concurrent measurements of humidity, organic matter and total C and N content. While each site differed in both biogeochemistry and biodiversity, both present similar pattern of change at the beginning of the succession that diverged in later stages. After one year, experimentally disturbed soil was not similar to established and undisturbed adjacent soil communities indicating recovery and succession in disturbed soils is a long process.