DNA metabarcoding reveals compositional and functional differences in fungal communities among Amazonian canga formations

Alvares, 2013, Köppen’s climate classification map for Brazil, Meteorol. Z., 22, 711, 10.1127/0941-2948/2013/0507 Bengtsson-Palme, 2013, Improved software detection and extraction of ITS1 and ITS 2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data, Methods Ecol. Evol., 4, 914, 10.1111/2041-210X.12073 Berruti, 2017, ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards, Environ. Microbiol. Rep., 9, 658, 10.1111/1758-2229.12574 Botha, 2011, The importance and ecology of yeasts in soil, Soil Biol. Biochem., 43, 1, 10.1016/j.soilbio.2010.10.001 Carvalho, 2012, The mosaic of habitats in the high-altitude Brazilian rupestrian fields is a hotspot for arbuscular mycorrhizal fungi, Appl. Soil Ecol., 52, 9, 10.1016/j.apsoil.2011.10.001 Cerqueira, 2018, Amazon basin pasture soils reveal susceptibility to phytopathogens and lower fungal community dissimilarity than forest, Appl. Soil Ecol., 131, 1, 10.1016/j.apsoil.2018.07.004 Chávez, 2015, Filamentous fungi from extreme environments as a promising source of novel bioactive secondary metabolites, Front. Microbiol., 6, 903, 10.3389/fmicb.2015.00903 Chen, 2018, Beneficial services of arbuscular mycorrhizal fungi – from ecology to application, Front. Plant Sci., 9, 1270, 10.3389/fpls.2018.01270 Coleine, 2021, Black fungi inhabiting rock surfaces, 57 Comensoli, 2017, Iron and fungal physiology: a review of biotechnological opportunities, 31, 10.1016/bs.aambs.2016.11.001 Conway, 2017, UpSetR: an R package for the visualization of intersecting sets and their properties, Bioinformatics, 33, 2938, 10.1093/bioinformatics/btx364 Corrales, 2018, Ectomycorrhizal associations inthe tropics – biogeography, diversity patterns and ecosystem roles, New Phytol., 1076, 10.1111/nph.15151 Costa, 2021, Non-specific interactions of rhizospheric microbial communities support the establishment of Mimosa acutistipula var. ferrea in an Amazon rehabilitating mineland, Processes, 9, 2079, 10.3390/pr9112079 Culliney, 2013, Role of arthropods in maintaining soil fertility, Agriculture, 3, 629, 10.3390/agriculture3040629 Delgado, 2021, Soil fungal diversity of the aguarongo andean forest (Ecuador), Biology, 10, 1289, 10.3390/biology10121289 Deveau, 2018, Bacterial–fungal interactions: ecology, mechanisms and challenges, FEMS Microbiol. Rev., 42, 335, 10.1093/femsre/fuy008 Dong, 2021, Soil degradation influences soil bacterial and fungal community diversity in overgrazed alpine meadows of the Qinghai-Tibet Plateau, Sci. Rep., 11, 10.1038/s41598-021-91182-7 Francioli, 2021, DNA metabarcoding for the characterization of terrestrial microbiota—pitfalls and solutions, Microorganisms, 9, 361, 10.3390/microorganisms9020361 Gastauer, 2021, Landscape heterogeneity and habitat amount drive plant diversity in Amazonian canga ecosystems, Landsc. Ecol., 36, 393, 10.1007/s10980-020-01151-0 Geisen, 2021, Fungal root endophytes influence plants in a species-specific manner that depends on plant's growth stage, J. Ecol., 109, 1618 Geiser, 2006, Eurotiomycetes: eurotiomycetidae and chaetothyriomycetidae, Mycologia, 98, 1053, 10.1080/15572536.2006.11832633 Geml, 2014, Large-scale fungal diversity assessment in the Andean Yungas forests reveals Strong community turnover among forest types along an altitudinal gradient, Mol. Ecol., 23, 2452, 10.1111/mec.12765 Geml, 2022, Community dynamics of soil-borne fungal communities along elevation gradients in neotropical and palaeotropical forests, Mol. Ecol., 31, 2044, 10.1111/mec.16368 Giesemann, 2020, Dark septate endophytes and arbuscular mycorrhizal fungi (Paris-morphotype) affect the stable isotope composition of ‘classically’ non-mycorrhizal plants, Funct. Ecol., 34, 2453, 10.1111/1365-2435.13673 Giulietti, 2019, Edaphic endemism in the Amazon: vascular plants of the canga of Carajás, Brazil. Bot. Rev., 85, 357, 10.1007/s12229-019-09214-x Gordon Gostinčar, 2009, Extremotolerance in fungi- evolution on the edge, FEMS Microbiol. Ecol., 71, 2, 10.1111/j.1574-6941.2009.00794.x Gweon, 2015, PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform, Methods Ecol. Evol., 6, 973, 10.1111/2041-210X.12399 Halbwachs, 2013, Hyphae of waxcap fungi colonise plant roots, Fungal Ecol, 6, 487, 10.1016/j.funeco.2013.08.003 Ihrmark, 2012, New primers to amplify the fungal ITS2 region – evaluation by 454-sequencing of artificial and natural communities, FEMS Microbiol. Ecol., 82, 666, 10.1111/j.1574-6941.2012.01437.x Kües, 2015, How do Agaricomycetes shape their fruiting bodies? 1. Morphological aspects of development, Fungal Biol. Rev., 29, 63, 10.1016/j.fbr.2015.05.001 Lan, 2012, Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms, PLoS One, 7, 10.1371/journal.pone.0032491 Lekberg, 2018, More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?, New Phytol., 220, 971, 10.1111/nph.15035 Li, 2022, Soil fungal community and potential function in different forest ecosystems, Diversity, 14, 520, 10.3390/d14070520 Mahecha-Vásqueza, 2017, Diversity indices using arbuscular mycorrhizal fungi to evaluate the soil state in banana crops in Colombia, Appl. Soil Ecol., 109, 32, 10.1016/j.apsoil.2016.09.017 Martinez Arbizu, 2020 Maynard, 2019, Consistent trade-offs in fungal trait expression across broad spatial scales, Nat Microbiol, 4, 846, 10.1038/s41564-019-0361-5 McMurdie, 2013, Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, 10.1371/journal.pone.0061217 Meyer, 2022, 4 Mitre, 2018, Nutrient and water dynamics of Amazonian Canga Vegetation differ among physiognomies and from those of other Neotropical ecosystems, Plant Ecol., 219, 1341, 10.1007/s11258-018-0883-6 Moreira, 2020, Soil yeast communities in revegetated post-mining and adjacent native areas in Central Brazil, Microorganisms, 8, 1116, 10.3390/microorganisms8081116 Morin-Sardin, 2016, Effect of temperature, pH, and water activity on Mucor spp. growth on synthetic medium, cheese analog and cheese, Food Microbiol., 56, 69e79, 10.1016/j.fm.2015.11.019 Morin-Sardin, 2017, Mucor: a Janus-faced fungal genus with human health impact and industrial applications, Fungal Biol. Rev., 31, 12, 10.1016/j.fbr.2016.11.002 Mueller, 2016, Land use change in the Amazon rain forest favours generalist fungi, Funct. Ecol., 30, 1845, 10.1111/1365-2435.12651 Nguyen, 2016, FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild, Fungal Ecol, 20, 241, 10.1016/j.funeco.2015.06.006 Nilsson, 2019, The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications, Nucleic Acids Res., 47, D259, 10.1093/nar/gky1022 Nunes, 2015, Soil-vegetation relationships on a banded ironstone 'island', Carajás plateau, Brazilian eastern amazonia, An. Acad. Bras. Ciênc., 87, 2097, 10.1590/0001-376520152014-0106 Oksanen Panaro, 2000, Evaluation of DNA fragment sizing and quantification by the Agilent 2100 Bioanalyzer, Clin. Chem., 46, 1851, 10.1093/clinchem/46.11.1851 Piercey-Normore, 2017, Interface between fungi and green algae in lichen associations, Botany, 95, 1005, 10.1139/cjb-2017-0037 Pinto-Figueroa, 2019, Archaeorhizomycetes spatial distribution in soils along wide elevational and environmental gradients reveal co-abundance patterns with other fungal saprobes and potential weathering capacities, Front. Microbiol., 10, 656, 10.3389/fmicb.2019.00656 Quan, 2020, A re-evaluation of the Chaetothyriales using criteria of comparative biology, Fungal Divers., 103, 47, 10.1007/s13225-020-00452-8 2020 Ritter, 2019, Locality or habitat? Exploring predictors of biodiversity in Amazonia, Ecography, 42, 321, 10.1111/ecog.03833 Ritter, 2020, Advancing biodiversity assessments with environmental DNA: long-read technologies help reveal the drivers of Amazonian fungal diversity, Ecol. Evol., 10, 7509, 10.1002/ece3.6477 Rodríguez-Rodríguez, 2021, Native arbuscular mycorrhizal fungi respond to rehabilitation in iron ore mining areas from the Eastern Brazilian Amazon, Pedobiologia, 89, 10.1016/j.pedobi.2021.150768 Rognes, 2016, VSEARCH: a versatile open source tool for metagenomics, PeerJ, 4, 10.7717/peerj.2584 Schaefer, 2016, Geoambientes, solos e estoques de carbono na Serra Sul de Carajás, Pará, Brasil, Bol. Mus. Para. Emílio Goeldi. Cienc. Nat., 11, 85, 10.46357/bcnaturais.v11i1.462 Selbmann, 2020, Shed light in the DaRk lineagEs of the fungal tree of life-STRES, Life, 10, 362, 10.3390/life10120362 Skirycz, 2014, Canga biodiversity, a matter of mining, Front. Plant Sci., 5, 10.3389/fpls.2014.00653 Taylor, 2016, Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for Illumina amplicon sequencing, Appl. Environ. Microbiol., 82, 7217, 10.1128/AEM.02576-16 Tedersoo, 2014, Global diversity and geography of soil fungi, Science, 346, 10.1126/science.1256688 Tedersoo, 2020, Regional-Scale in-depth analysis of soil fungal diversity reveals strong pH and plant species effects in Northern Europe, Front. Microbiol., 11, 1953, 10.3389/fmicb.2020.01953 Tedersoo, 2021, The Global Soil Mycobiome consortium dataset for boosting fungal diversity research, Fungal Divers., 111, 573, 10.1007/s13225-021-00493-7 Vasco-Palacios, 2020, Carbon content and pH as important drivers of fungal community structure in three Amazon forests, Plant Soil, 450, 111, 10.1007/s11104-019-04218-3 Větrovský, 2020, GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies, Sci. Data, 7, 228, 10.1038/s41597-020-0567-7 Vincent, 2020, The multiple facets of plant–fungal interactions revealed through plant and fungal secretomics, Front. Plant Sci., 10, 1626, 10.3389/fpls.2019.01626 Wang, 2020, Grand challenges in the research of fungal interactions with animals, Front. Fungal Biol., 1, 10.3389/ffunb.2020.602032 Wearn, 2012, Species and organ specificity of fungal endophytes in herbaceous grassland plants, J. Ecol., 100, 1085 White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, 315 Wickham, 2016 Yahr, 2016, Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches, Philos. Trans. R. Soc. B Biol. Sci., 371, 10.1098/rstb.2015.0336 Yang, 2017, Links between soil fungal diversity and plant and soil properties on the Loess Plateau, Front. Microbiol., 8, 2198, 10.3389/fmicb.2017.02198