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Fungal and Bacterial Community Composition and Structure In Fungal and bacterial community composition and structure in fermented `hairy' tofu (Mao tofu) Gian Maria Niccol`oBenucci1, Xinxin Wang2, Li Zhang3, Gregory Bonito2, and Fuqiang Yu3 1Michigan State university 2Michigan State University 3Kunming Institute of Botany Chinese Academy of Sciences October 22, 2020 Abstract The process of fermenting tofu extends thousands of years. Despite a resurgent interest in microbial communities and fermented foods, little knowledge exists concerning microbial diversity of communities of fermented `hairy' tofu known in China as Mao tofu. We used high-throughput metagenomic sequencing of the ITS, LSU and 16S rDNA marker genes to disentangle the Mao tofu fungal and bacterial community composition and diversity across the four most important markets in the Yunnan region of China. We show that hairy tofu in this region consists of around 170 fungal and 365 bacterial taxa. Significant differences in community structure were found between markets and niches. Machine learning random forest models were able to accurately classify both market and niche of sample origin. An over-abundance of yeast taxa were detected, and Geotrichum were the most abundant fungal taxa, followed by Torulaspora, Trichosporon, and Pichia. Mucor (Mucormycota) was also abundant in the LSU data and especially in the outside niche (rind), which consists of the visible `hairy' mycelium. The majority of the bacterial OTUs belonged to Proteobacteria, Firmicutes, and Bacteroidota, with Acinetobacter, Lactobacillus, Sphingobacterium and Flavobacterium the most abundant members. Of interest, putative fungal pathogens of plants (e.g. Cercospora, Diaporthe, Fusarium) and animal (e.g. Metarhizium, Entomomortierella, Pyxidiophora, Candida, Clavispora), as well as bacterial (e.g. Legionella) pathogens, were detected. Non-target eukaryotic taxa detected in by LSU amplicon sequencing included soybean (Glycine max), Protozoa, Metazoa (e.g. Nematoda and Platyhelminthes), Rhizaria and Chromista, providing evidence of additional biocomplexity and diversity in the tofu microbiome. Hosted file manuscript_Benucci_etal.pdf available at https://authorea.com/users/369277/articles/488201- fungal-and-bacterial-community-composition-and-structure-in-fermented-hairy-tofu-mao- tofu Posted on Authorea 22 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160333930.03738003/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 1 A ITS B LSU C 16S Inside Outside Inside Outside Inside Outside a abab b a b a a 80 a b a b 200 a b ab b a a a b 60 60 150 40 40 100 Richness 20 20 50 0 0 0 Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Ciba Ciba Longjin Longjin Longjin Wanyao Wanyao Wanyao New District New District New District a b a b a b 80 a b a b a b 200 a b a b 60 60 150 40 40 100 Richness 20 20 50 0 0 0 Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside A ITS B LSU C 16S Inside Outside Inside Outside Inside Outside a abab b ab a b ab a b bc ac 1.00 1.00 1.00 0.75 0.75 0.75 0.50 0.50 0.50 0.25 0.25 0.25 0.00 0.00 0.00 Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Ciba Longjin Wanyao New District Shannon equitability index equitability Shannon Ciba Ciba Ciba Longjin Longjin Longjin Wanyao Wanyao Wanyao New District New District New District a b 1.00 1.00 1.00 0.75 0.75 0.75 0.50 0.50 0.50 0.25 0.25 0.25 0.00 0.00 0.00 Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Inside Outside Shannon equitability index equitability Shannon Posted on Authorea 22 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160333930.03738003/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 2 A ITS B LSU C 16S 0.4 0.4 0.2 0.2 0.2 0.0 0.0 0.0 Axis.2 [9.3%] Axis.2 [7.6%] -0.2 Axis.2 [10.5%] -0.2 -0.2 -0.4 -0.4 -0.2 0.0 0.2 0.4 -0.2 0.0 0.2 0.4 -0.4 -0.2 0.0 0.2 Axis.1 [10.7%] Axis.1 [11.4%] Axis.1 [10.5%] Niche Inside Outside Market Ciba Longjin Wanyao New District D Market Niche E Market Niche F Market Niche a ab b b a b 0.8 a b b b 0.8 0.8 0.8 0.8 0.8 0.7 0.7 0.7 0.7 0.7 0.6 0.6 0.6 0.6 0.6 0.5 0.6 0.5 0.5 Distance to centroids 0.4 Distance to centroids Distance to centroids p = 0.0047 p = 0.0074 p = 0.0001 Ciba Longjin Wanyao New District Inside Outside Ciba Longjin Wanyao New District Inside Outside Ciba Longjin Wanyao New District Inside Outside A Procrustes Rotation B Procrustes Rotation C Procrustes Rotation ITS - LSU ITS - 16S LSU - 16S 0.10 0.10 0.10 0.00 0.00 0.00 Axis.2 Axis.2 Axis.2 -0.10 -0.10 -0.10 r = 0.581 r = 0.396 r = 0.508 2 2 2 m = 0.622 m = 0.843 m = 0.742 -0.10 0.00 0.10 -0.10 0.00 0.10 -0.10 -0.05 0.00 0.05 0.10 0.15 Axis.1 Axis.1 Axis.1 Niche Inside Outside Market Ciba Longjin Wanyao New District D Market Niche E Market Niche F Market Niche 0.20 a ab ab b 0.20 a a a b a b a b b ab 0.20 0.20 0.15 0.15 0.15 0.15 0.15 0.15 0.10 0.10 0.10 0.10 0.10 0.10 0.05 0.05 0.05 0.05 0.05 0.05 Procrustes residual Procrustes residual Procrustes residual 0.00 p = 0.012 0.00 0.00 p = 0.00019 0.00 p = 0.00034 0.00 p = 0.00016 0.00 Ciba Longjin Wanyao New District Inside Outside Ciba Longjin Wanyao New District Inside Outside Ciba Longjin Wanyao New District Inside Outside Posted on Authorea 22 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160333930.03738003/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 3 A ITS Market B LSU Market C 16S Market 0.5 0.2 0.4 0.2 0.2 0.0 0.0 0.0 MDS2 - 14.3% MDS2 - 13.7% -0.2 MDS2 - 18.2% -0.2 -0.2 OOB = 4.17% OOB = 12.5% OOB = 1.39% -0.5 -0.2 0.0 0.2 0.4 -0.2 0.0 0.2 0.5 -0.2 0.0 0.2 0.4 MDS1 - 21.5% MDS1 - 20.6% MDS1 - 23.9% Market Ciba Longjin Wanyao New District ITS Niche LSU Niche 16S Niche 0.2 0.4 0.2 0.0 0.2 0.0 -0.2 0.0 -0.2 MDS2 - 17% MDS2 - 12% MDS2 - 11.4% -0.4 -0.2 OOB = 8.33% OOB = 12.5% -0.4 OOB = 9.72% -0.5 -0.2 0.0 0.2 -0.2 0.0 0.2 0.5 -0.5 -0.2 0.0 0.2 0.5 MDS1 - 30.8% MDS1 - 38.4% MDS1 - 33.5% Niche Inside Outside Posted on Authorea 22 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160333930.03738003/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 4 Top ITS OTUs to Top ITS OTUs to A classify markets classify niches FOTU_95-Geotrichum candidum 0.42 FOTU_56-Kluyveromyces marxianus FOTU_3-Dipodascus geotrichum FOTU_15-Apiotrichum laibachii FOTU_56-Kluyveromyces marxianus FOTU_8-Pichia norvegensis FOTU_20-Cutaneotrichosporon jirovecii 0.51 FOTU_120-Saccharomycetales FOTU_31-Cystofilobasidium ferigula 0.36 FOTU_27-Magnusiomyces capitatus 0.19 FOTU_25-Candida inconspicua FOTU_14-Candida tropicalis FOTU_2-Geotrichum candidum FOTU_5-Pichia sp. 0.31 FOTU_88-Dipodascaceae FOTU_7-Diutina catenulata FOTU_113-Cutaneotrichosporon curvatus 0.31 FOTU_36-Pichia sp. 0.16 FOTU_39-Wickerhamomyces anomalus 0.35 FOTU_58-Diutina mesorugosa 0.28 FOTU_34-Clavispora lusitaniae 0.38 FOTU_33-Pichia fermentans OTU FOTU_55-Meyerozyma guilliermondii 0.38 FOTU_256-Saccharomycetales 0.41 FOTU_23-Pichia kudriavzevii 0.34 FOTU_112-Geotrichum sp. 0.3 FOTU_6-Trichosporon sp. 0.41 FOTU_147-Dipodascus geotrichum FOTU_17-Clavispora lusitaniae 0.35 FOTU_95-Geotrichum candidum 0.4 FOTU_22-Clavispora lusitaniae FOTU_9-Candida sp. 0.34 FOTU_4-Pichia sp. 0.65 FOTU_209-Trichosporon asahii 0.38 FOTU_14-Candida tropicalis 0.39 FOTU_124-Candida sp. 0.43 FOTU_7-Diutina catenulata FOTU_163-Geotrichum candidum 0.47 FOTU_12-Lachancea sp. 0.69 FOTU_43-Clavispora lusitaniae 0.00 0.02 0.04 0.06 0.00 0.02 0.04 0.06 Mean Decrease Mean Decrease in Accuracy in Accuracy Top LSU OTUs to Top LSU OTUs to B classify markets classify niches EOTU_89-Cystofilobasidium sp.
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