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      The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley

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          Abstract

          Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra-annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.

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          Fitting Linear Mixed-Effects Models Usinglme4

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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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                Author and article information

                Journal
                9214478
                2614
                Mol Ecol
                Mol Ecol
                Molecular ecology
                0962-1083
                1365-294X
                21 October 2022
                October 2022
                25 August 2022
                01 November 2022
                : 31
                : 19
                : 4962-4978
                Affiliations
                [1 ]Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
                [2 ]Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
                [3 ]Division of Epidemiology, University of California Berkeley, Berkeley, California, USA
                [4 ]Division of Environmental Health Sciences, University of California Berkeley, Berkeley, California, USA
                Author notes

                AUTHOR CONTRIBUTIONS

                Robert Wagner and John W. Taylor designed the research approach while Justin Remais, Jennifer R. Head and John W. Taylor initially conceived of the project. Robert Wagner, John W. Taylor, Cheng Gao and Liliam Montoya collected and analyzed samples and Robert Wagner performed all statistical analyses, generated all visualizations and directed the structure of the text. All authors contributed to the writing and editing of the final manuscript.

                Correspondence Robert Wagner, Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, USA. robwagner@ 123456berkeley.edu
                Author information
                http://orcid.org/0000-0002-0809-7754
                http://orcid.org/0000-0002-5794-7700
                Article
                NIHMS1840026
                10.1111/mec.16640
                9624177
                35933707
                895d6d42-70e7-4f0a-a3b7-773cf5824a6c

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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                Categories
                Article

                Ecology
                air,coccidioides,dispersal,fungi,mycobiome,soil
                Ecology
                air, coccidioides, dispersal, fungi, mycobiome, soil

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