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 — https://doi.org/10.22541/au.160333930.03738003/v1 — This a preprint and has not been peer reviewed.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. tofu fungal-and-bacterial-community-composition-and-structure-in-fermented-hairy-tofu-mao- manuscript_Benucci_etal.pdf of evidence providing file Chromista, Hosted and Rhizaria soybean Platyhelminthes), microbiome. included tofu and sequencing the Nematoda amplicon in (e.g. LSU diversity bacterial and by (e.g. Diaporthe, as biocomplexity in Metazoa additional well Cercospora, detected as Protozoa, taxa (e.g. eukaryotic Clavispora), bacterial max), plants Non-target Candida, the (Glycine of Pyxidiophora, of detected. pathogens Entomomortierella, were and majority fungal pathogens, Metarhizium, The Sphingobacterium putative Legionella) Lactobacillus, mycelium. interest, (e.g. ‘hairy’ Acinetobacter, Of animal visible with and members. the Fusarium) Bacteroidota, abundant of and most consists Firmicutes, the which Flavobacterium Proteobacteria, (rind), LSU the most niche to in the outside abundant belonged were also the was OTUs and in (Mucormycota) detected, accurately Mucor in were especially to differences taxa Pichia. and able Significant and Trichosporon, were of data taxa. Torulaspora, over-abundance models by bacterial An followed forest 365 taxa, origin. random and fungal sample region learning fungal abundant of Yunnan Machine 170 niche the around and niches. market in of and both markets consists Mao markets classify region important the between this disentangle most found in to were four tofu Mao genes structure the hairy as marker community across that rDNA China diversity show 16S We in and and known China. composition LSU tofu of community ITS, ‘hairy’ bacterial the fermented and of fermented of fungal sequencing and communities tofu metagenomic communities of microbial high-throughput diversity in used interest We microbial resurgent concerning a tofu. Despite exists knowledge years. of little thousands foods, extends tofu fermenting of process The Abstract 2020 22, October 3 2 1 Niccol`o Benucci Maria Gian tofu) (Mao in tofu structure ‘hairy’ and fermented composition community bacterial and Fungal umn nttt fBtn hns cdm fSciences of Academy Chinese Botany of Institute Kunming University State Michigan university State Michigan 1 vial at available ixnWang Xinxin , https://authorea.com/users/369277/articles/488201- 2 iZhang Li , 1 3 rgr Bonito Gregory , 2 n uin Yu Fuqiang and , 3 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.

Shannon equitability index Shannon equitability index A Richness Richness A 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00

20 40 60 20 40 60 0 0

Inside

a b Ciba Inside a abab b Ciba

Outside Inside

Outside Inside

Ciba Longjin Ciba Longjin

Wanyao

Wanyao

Inside a b Inside

New District New

Outside New District New

Outside Longjin Longjin ITS ITS

Inside Inside Ciba

Ciba a b a a a abab b

Outside

Outside

Outside Outside

Wanyao Longjin Wanyao Longjin

Wanyao Wanyao

Inside Inside a b

New District New New District New Outside Outside New District New District B B 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00

20 40 60 80 20 40 60 80 0 0

Inside

a b Ciba ab a b ab Inside Ciba

Outside Inside

Outside Inside

Ciba Longjin Ciba Longjin

Wanyao

Wanyao

Inside a b

2 Inside

New District New

Outside New District New Outside LSU

Longjin LSU Longjin

Inside Inside Ciba

Ciba a b a b

Outside

Outside

Outside Outside

Wanyao Longjin Wanyao Longjin

Wanyao Wanyao

Inside Inside a b

New District New New District New Outside Outside New District New District C C

100 150 200 100 150 200 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00

50 50 0 0

Inside

a b Ciba

Inside a b ab b Ciba a b bc ac

Outside Inside

Outside Inside

Ciba Longjin Ciba Longjin

Wanyao

Wanyao

Inside Inside

New District New

Outside New District New

Outside Longjin 16S Longjin 16S

Inside Inside Ciba

Ciba a a a b

Outside

Outside

Outside Outside

Wanyao Longjin Wanyao Longjin

Wanyao Wanyao

Inside Inside a b a b

New District New New District New Outside Outside New District New District 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.

Procrustes residual D Axis.2 A Distance to centroids D Axis.2 [9.3%] A

0.00 0.05 0.10 0.15 0.20 0.4 0.6 0.8

-0.10 -0.4 -0.2 0.0 0.2 0.4 0.00 0.10

Ciba a ab b b

Ciba a ab ab b

Market

Market

Longjin Longjin -0.10 0.00 0.10 p

-0.2 0.0 0.2 0.4 Procrustes Rotation p

=

= Wanyao Wanyao 0.0047

0.012

Axis.1 [10.7%] New District New New District New ITS -LSU Axis.1 ITS Niche Niche 0.00 0.05 0.10 0.15 0.20 0.5 0.6 0.7 0.8 m r

= 2 Inside a b Niche Inside Niche = Inside Outside Inside Outside 0.581 p 0.622 =

0.0074 Outside Outside E E

Procrustes residual Axis.2 B Distance to centroids Axis.2 [10.5%] B 0.00 0.05 0.10 0.15 0.20 0.5 0.6 0.7 0.8

-0.10 -0.4 -0.2 0.0 0.2 0.4 0.00 0.10

Ciba Ciba a a a b Market

Market

Market Market p Longjin Longjin -0.10 0.00 0.10

Procrustes Rotation =

-0.2 0.0 0.2 0.4

0.00019 Wanyao Wanyao

Axis.1 [11.4%] New District New New District New ITS -16S 3 LSU Axis.1 Ciba Longjin Wanyao NewDistrict Ciba Longjin Wanyao NewDistrict 0.00 0.05 0.10 0.15 0.20 0.6 0.7 0.8 m r = 2

= 0.396

0.843 Inside Niche Inside Niche a b p =

0.00034

Outside Outside F F Procrustes residual Axis.2 C Distance to centroids Axis.2 [7.6%] C

0.00 0.05 0.10 0.15 0.5 0.6 0.7 0.8

-0.10 -0.2 0.0 0.2 0.00 0.10

Ciba a b b b

Ciba -0.4 -0.2 0.0 0.2 a b b ab

Market Market

-0.10 -0.05 0.00 0.05 0.10 0.15 Longjin p Longjin p

Procrustes Rotation =

=

0.00016 Wanyao Wanyao 0.0001

Axis.1 [10.5%] New District New New District New LSU -16S Axis.1 16S 0.00 0.05 0.10 0.15 0.6 0.7 0.8 m r

= 2 Inside Niche Inside Niche = 0.508

0.742

Outside 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.

MDS2 - 17% MDS2 - 14.3% A -0.4 -0.2 -0.2 0.0 0.2 0.0 0.2 0.5 -0.5 -0.2 0.0 0.2 OOB =8.33% -0.2 0.0 0.2 0.4 MDS1 -30.8% MDS1 -21.5% ITS Market ITS Niche OOB =4.17% Market

MDS2 - 12% MDS2 - 13.7% B -0.2 -0.5 -0.2 0.0 0.2 0.4 0.0 0.2 Ciba Longjin Wanyao NewDistrict Niche OOB =12.5% OOB =12.5% -0.2 0.0 0.2 0.5 -0.2 0.0 0.2 0.5 MDS1 -38.4% MDS1 -20.6% Inside Outside LSU Market LSU Niche 4

MDS2 - 11.4% MDS2 - 18.2% C -0.4 -0.2 -0.2 0.0 0.2 0.0 0.2 0.4 -0.5 -0.2 0.0 0.2 0.5 OOB =9.72% -0.2 0.0 0.2 0.4 MDS1 -33.5% MDS1 -23.9% 16S Market 16S Niche OOB =1.39% 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. Dinemasporium japonicum Trichoderma koningiopsis Trichoderma Trichoderma lixii Trichoderma B A C Metarhizium anisopliae Metarhizium A Aureobasidium pullulans Aureobasidium Dinemasporium Corynespora cassiicola Trichoderma OTU OTU OTU Plectosphaerella Chaetosphaeriaceae Exserohilum rostratum Exserohilum Apiotrichum domesticum Apiotrichum Erysiphe polygoni Microdochium Microdochiaceae FOTU_113-Cutaneotrichosporon curvatus FOTU_113-Cutaneotrichosporon Diaporthe caulivora Diaporthe Metarhizium Hypocreaceae Plectosphaerellaceae Sclerotinia sclerotiorum Sclerotinia Gibberella Trichosporon asahii Trichosporon Corynespora FOTU_39-Wickerhamomyces anomalus FOTU_39-Wickerhamomyces Exserohilum Nigrospora oryzae FOTU_20-Cutaneotrichosporon jirovecii FOTU_20-Cutaneotrichosporon Alternaria alternata Alternaria Apiotrichum laibachii Apiotrichum Clavicipitaceae Corynesporascaceae Fusarium Fusarium solani Epicoccum nigrum Trichosporonaceae Trichosporon ovoides Trichosporon Aureobasidiaceae Aureobasidium Diaporthe Erysiphe Cutaneotrichosporon cutaneum Cutaneotrichosporon Nectriaceae Glomerellales Sclerotinia FOTU_55-Meyerozyma guilliermondii FOTU_55-Meyerozyma Xylariales FOTU_56-Kluyveromyces marxianus FOTU_56-Kluyveromyces Epicoccum Trichosphaeriaceae Nigrospora Sclerotiniaceae Coniochaetaceae Hypocreales FOTU_31-Cystofilobasidium ferigula FOTU_31-Cystofilobasidium Alternaria Cutaneotrichosporon Chaetosphaeriales Coniochaeta Pleosporaceae Apiotrichum Apiotrichum brassicae Apiotrichum Coniochaetales Erysiphaceae Trichosporon heliocopridis Trichosporon Trichosporon Diaporthaceae Pleosporales Didymellaceae Cutaneotrichosporon jirovecii Cutaneotrichosporon Boeremia Dothideomycetes Didymosphaeriaceae Boeremia exigua Boeremia Sordariomycetes BOTU_33-Lactobacillus mucosae BOTU_33-Lactobacillus Dothideales Paraphaeosphaeria EOTU_183-Schwanniomyces sp. EOTU_183-Schwanniomyces Trichosphaeriales Helotiales Cladosporium anthropophilum BOTU_125-Corynebacterium sp. BOTU_125-Corynebacterium FOTU_3- geotrichum FOTU_3-Dipodascus candidum FOTU_95-Geotrichum Cystofilobasidium ferigula Cystofilobasidium EOTU_89-Cystofilobasidium sp. EOTU_89-Cystofilobasidium Saccharomyces cerevisiae Saccharomyces Erysiphales FOTU_25-Candida inconspicua FOTU_25-Candida Leotiomycetes FOTU_22-Clavispora lusitaniae FOTU_22-Clavispora lusitaniae FOTU_17-Clavispora lusitaniae FOTU_34-Clavispora FOTU_2- FOTU_2-Geotrichum Diaporthales Market r.g. value Trichosporonales EOTU_103-Debaryomyces sp. EOTU_103-Debaryomyces EOTU_21-Magnusiomyces sp. EOTU_21-Magnusiomyces Torulaspora delbrueckii Torulaspora Mycosphaerellaceae BOTU_162-Streptococcus sp. BOTU_162-Streptococcus EOTU_31-Kluyveromyces sp. EOTU_31-Kluyveromyces sp. EOTU_19-Wickerhamiella sp. EOTU_178-Cephaloascus Cladosporium Cystofilobasidium infirmominiatum Cystofilobasidium Cutaneotrichosporon curvatus Cutaneotrichosporon Tremellomycetes BOTU_1-Alcaligenes faecalis BOTU_1-Alcaligenes Cladosporiaceae Cystofilobasidiales EOTU_13-Lodderomyces sp. EOTU_13-Lodderomyces EOTU_45-Asterotremella sp. EOTU_45-Asterotremella kudriavzevii FOTU_23-Pichia Capnodiales FOTU_14-Candida tropicalis FOTU_14-Candida Aspergillaceae Saccharomycopsis crataegensis Saccharomycopsis Cystofilobasidiaceae Penicillium Cystofilobasidium BOTU_16-Acinetobacter sp. BOTU_16-Acinetobacter Eurotiomycetes Saccharomyces Lachancea BOTU_12-Enterococcus sp. BOTU_12-Enterococcus Kazachstania barnettii Kazachstania Eurotiales Torulaspora BOTU_22-Lactobacillus sp. BOTU_22-Lactobacillus sp. BOTU_9-Pseudomonas BOTU_11-Lactobacillus sp. BOTU_11-Lactobacillus EOTU_18-Trichosporon sp. EOTU_18-Trichosporon catenulata FOTU_7-Diutina BOTU_92-Leuconostoc sp. BOTU_92-Leuconostoc sp. BOTU_10-Leuconostoc BOTU_24-Pediococcus sp. BOTU_24-Pediococcus Saccharomycetaceae BOTU_15-Acetobacter sp. BOTU_15-Acetobacter EOTU_4-Trichosporon sp. EOTU_4-Trichosporon Hannaella luteola EOTU_5-Saturnispora sp. EOTU_5-Saturnispora sp. FOTU_6-Trichosporon FOTU_88-Dipodascaceae BOTU_3-Lactococcus sp. BOTU_3-Lactococcus Guehomyces Guehomyces pullulans EOTU_3-Torulaspora sp. EOTU_3-Torulaspora sp. FOTU_12-Lachancea Kluyveromyces marxianus Kluyveromyces BOTU_2-Providencia sp. BOTU_2-Providencia EOTU_1-Geotrichum sp. EOTU_1-Geotrichum Meyerozyma guilliermondii Kazachstania Kluyveromyces Eukaryota Lodderomyces elongisporus BOTU_13-Weissella sp. BOTU_13-Weissella sp. BOTU_6-Citrobacter sp. BOTU_4-Chishuiella Vishniacozyma victoriae Vishniacozyma Basidiomycota Hannaella Saccharomycopsis Wallemiomycetes Fungi Bulleribasidiaceae Meyerozyma BOTU_31-Pantoea sp. BOTU_31-Pantoea BOTU_5-Weissella sp. BOTU_5-Weissella Wallemiales Filobasidiales Lodderomyces Filobasidiaceae EOTU_2-Candida sp. EOTU_2-Candida sp. EOTU_10-Diutina Chytridiomycetes Vishniacozyma Microbotryomycetes Debaryomyces hansenii Tremellales Rhodotorula mucilaginosa Rhodotorula Naganishia albida Naganishia Chytridiomycota Wallemiaceae Debaryomycetaceae Debaryomyces EOTU_30-Pichia sp. EOTU_30-Pichia sp. EOTU_27-Pichia Metschnikowiaceae Saccharomycopsidaceae Zoopagomycota EOTU_9-Mucor sp. EOTU_9-Mucor sp. EOTU_7-Pichia sp. FOTU_4-Pichia Clavispora lusitaniae Plantae Sporidiobolales Exobasidiomycetes Dacrymycetes Filobasidium Wallemia Geminibasidiomycetes Wickerhamomyces anomalus Wickerhamomyces Rozellomycota Leucosporidiaceae Incertae-sedis Clavispora reshetovae Zoopagomycetes Leucosporidiales Sporidiobolaceae Clavispora Rhodotorula Rhizophydiales Leucosporidium Candida tropicalis Mucoromycota Candida railenensis Geminibasidiales Candida metapsilosis Sporobolomyces ruberrimus Sporobolomyces Exobasidiales Dacrymycetales Sporobolomyces Geminibasidiaceae Wickerhamomyces Mortierellomycetes Rhodotorula kratochvilovae Rhodotorula Exobasidiaceae Dacrymycetaceae Exobasidium gracile Exobasidium Candida Diutina mesorugosa Diutina Phaffomycetaceae Dacryopinax spathularia Geminibasidium Zoopagales Mucoromycetes Dacryopinax Pichiaceae Exobasidium Candida sake Diutina catenulata Diutina Candida inconspicua Diutina Candida parapsilosis Dipodascaceae lipolytica Yarrowia Longjin Ciba Entomortierella lignicola Entomortierella Barnettozyma Mortierellales Geotrichum Entomortierella Mortierellaceae Entomortierella echinosphaera Entomortierella Benniella Yarrowia Geotrichum candidum Geotrichum Mucorales Pichia kluyveri Barnettozyma californica Barnettozyma Pichia norvegensis Lunasporangiospora Pichia Cyberlindnera Pichia fermentans Pichia kudriavzevii Magnusiomyces Cyberlindnera jadinii Dipodascus Cyberlindnera fabianii Magnusiomyces capitatus Linnemannia Necromycomortierella Necromycomortierella dichotoma Necromycomortierella Mucoraceae Dipodascus geotrichum Linnemannia elongata Dipodascus australiensis Mortierella polygonia Mortierella Mortierella Mucor saturninus Mucor nidicola Mucor Mucor circinelloides 0.00 0.02 0.04 0.06 0.00 0.02 0.04 0.06 Samples with counts 0.00 0.02 0.04 0.06 36 25 16 9 4 1 0 Nodes ITS Nodes 0.42 0.39 0.32 0.39 0.35 0.55 0.59 0.42 0.4 0.43 0.37 0.51 0.33 0.51 0.52 0.36 0.39 Top LSU OTUs to OTUs LSU Top 0.44 0.25 Top 16s OTUs to 16sOTUs Top 0.31 Schwanniomyces 0.35 Debaryomycetaceae classify markets classify to OTUs ITS Top classify markets classify classify markets classify 0.38 0.4 0.61 Hyphopichia 0.38 0.48 0.33 0.34 0.48 0.32 Cercospora sojina Mean Decrease Mean Decrease Mean Decrease 0.4 0.41 169.00 118.00 19.70 75.70 0.54 43.00 0.35 New District Wanyao 1.00 5.67 0.5 Wickerhamomycetaceae 0.65 Phaffomycetaceae 0.39 Meyerozyma Cyberlindnera in Accuracy in Accuracy in in Accuracy in Barnettozyma 0.37 0.65 0.34 Cercospora Wickerhamomyces 0.69

OTU number Hanseniaspora Mycosphaerellaceae B Phaeodothis Saccharomycetales Wickerhamiella 0.53 Saccharomycodaceae Phaeosphaeriaceae Diutina Metschnikowiaceae Nigrospora 0.53 Trichosphaeriaceae incertae sedis Neoascochyta 0.42 Cephaloascaceae Pichia Clavispora Trichomonascaceae Pleosporales Didymellaceae Diaporthe Saturnispora Mycosphaerellales Saccharomycopsidaceae Pichiaceae Saccharomycetes Dipodascaceae incertae sedis Acremonium Diaporthaceae Dothideomycetes Hypocreales Cephaloascus Trichosphaeriales Geotrichum Yarrowia Capnodiales Diaporthales Magnusiomyces Sordariomycetes Cladosporium complex Nectriaceae Fusarium Microascales Microascaceae Saccharomycetaceae Davidiellaceae Kazachstania Microascus Williopsis Phyllachorales Kodamaea Ascomycota Phyllachora Coniochaetales Phyllachoraceae Debaryomyces Kluyveromyces Coniochaetaceae Lodderomyces Coniochaeta Torulaspora Laboulbeniomycetes Saccharomyces Herpotrichiellaceae Eurotiomycetes Aspergillaceae Chaetothyriales Kaseomyces Mortierellales Leotiomycetes Mortierellomycetes NA Capronia Mortierellaceae Aspergillus Lecanoromycetes Mucoromycota Candida Entomortierella Fungi Eukaryota Eurotiales Mucoromycetes Helotiales Trichocomaceae 5 Lecanorales Sclerotiniaceae Penicillium Kinetoplastea Protozoa Euglenozoa Pyxidiophorales Sclerotinia Pyxidiophoraceae FOTU_56-Kluyveromyces marxianus FOTU_56-Kluyveromyces Mucorales FOTU_27-Magnusiomyces capitatus FOTU_27-Magnusiomyces Plantae Basidiomycota Charophyta Pyxidiophora Trichosporonales Tremellomycetes Trichosporonaceae Metazoa FOTU_147-Dipodascus geotrichum FOTU_147-Dipodascus EOTU_23-Cutaneotrichosporon sp. EOTU_23-Cutaneotrichosporon Parabodonidae Apiotrichum Rhizaria Cutaneotrichosporon Bodonida Magnoliophyta FOTU_163-Geotrichum candidum FOTU_163-Geotrichum BOTU_115-Pseudoclavibacter sp. BOTU_115-Pseudoclavibacter Platyhelminthes Mucoraceae Tremellales Chromista FOTU_95-Geotrichum candidum FOTU_95-Geotrichum BOTU_125-Corynebacterium sp. BOTU_125-Corynebacterium Parabodo Tremellaceae Microbotryomycetes Exobasidiomycetes FOTU_209-Trichosporon asahii FOTU_209-Trichosporon FOTU_256-Saccharomycetales FOTU_120-Saccharomycetales Cystobasidiomycetes Nematoda Wallemiomycetes FOTU_43-Clavispora lusitaniae FOTU_43-Clavispora FOTU_15-Apiotrichum laibachii FOTU_15-Apiotrichum Mucor Magnoliopsida Trichosporon BOTU_90-Lactobacillus reuteri BOTU_90-Lactobacillus Myzozoa FOTU_58-Diutina mesorugosa FOTU_58-Diutina BOTU_104-Microbacteriaceae BOTU_17-Glutamicibacter sp. BOTU_17-Glutamicibacter EOTU_19-Wickerhamiella sp. EOTU_19-Wickerhamiella EOTU_145-Saccharomycetes BOTU_162-Streptococcus sp. BOTU_162-Streptococcus Cryptococcus Ciliophora Sporidiobolales EOTU_12-Debaryomyces sp. EOTU_12-Debaryomyces Cercozoa Cystofilobasidiales EOTU_93-Lodderomyces sp. EOTU_93-Lodderomyces sp. EOTU_86-Asterotremella FOTU_33-Pichia fermentans FOTU_33-Pichia tropicalis FOTU_14-Candida EOTU_132-Meyerozyma sp. EOTU_132-Meyerozyma BOTU_85-Streptococcus sp. BOTU_85-Streptococcus BOTU_41-Streptococcus sp. BOTU_41-Streptococcus Fabales Dinophyceae FOTU_8-Pichia norvegensis FOTU_8-Pichia EOTU_16-Barnettozyma sp. EOTU_16-Barnettozyma EOTU_135-Saturnispora sp. EOTU_135-Saturnispora BOTU_16-Acinetobacter sp. BOTU_16-Acinetobacter Chromadorea BOTU_12-Enterococcus sp. BOTU_12-Enterococcus sp. BOTU_51-Erysipelothrix Sporidiobolaceae Asterotremella Filobasidiaceae Wallemiales FOTU_7-Diutina catenulata FOTU_7-Diutina EOTU_219-Apiotrichum sp. EOTU_219-Apiotrichum sp. EOTU_111-Torulaspora Malasseziales Fabaceae Cystofilobasidiaceae FOTU_112-Geotrichum sp. FOTU_112-Geotrichum Wallemiaceae EOTU_22-Rhodotorula sp. EOTU_22-Rhodotorula BOTU_391-Morganella sp. BOTU_391-Morganella sp. BOTU_28-Lactococcus sp. BOTU_56-Leucobacter sp. BOTU_7-Acinetobacter Cystofilobasidium Filobasidiales EOTU_75-Apiotrichum sp. EOTU_75-Apiotrichum BOTU_15-Acetobacter sp. BOTU_15-Acetobacter BOTU_86-Aerococcaceae Leucosporidiales Sarcomonadea EOTU_5-Saturnispora sp. EOTU_5-Saturnispora Erythrobasidiales Glycine Glycine max EOTU_3-Torulaspora sp. EOTU_3-Torulaspora Rhabditida BOTU_2-Providencia sp. BOTU_2-Providencia Panagrolaimoidea Rhodotorula Naganishia Sporidiobolales BOTU_4-Chishuiella sp. BOTU_4-Chishuiella FOTU_124-Candida sp. FOTU_124-Candida Guehomyces Leucosporidiales Malasseziaceae Wallemia Panagrolaimidae Filobasidium Erythrobasidiaceae EOTU_159-Mucorales Rhodotorula Rhabditidae Cercomonadida Leucosporidium FOTU_9-Candida sp. FOTU_9-Candida EOTU_2-Candida sp. EOTU_2-Candida Malassezia Sporobolomyces FOTU_36-Pichia sp. FOTU_36-Pichia BOTU_131-Bacteria EOTU_11-Pichia sp. EOTU_11-Pichia sp. EOTU_39-Pichia Panagrolaimus Pelodera FOTU_5-Pichia sp. FOTU_5-Pichia EOTU_54-Fungi

Samples with OTUs Niche r.g. value 36 25 16 9 4 1 0 Nodes LSU Nodes Rhodanobacteraceae Pseudoalteromonas Pseudoalteromonadaceae Rheinheimera Alteromonadaceae Ketogulonicigenium Methylobacillus 183.00 127.00 81.90 21.20 46.50 Rhodobacteraceae 1.00 6.06 Rhodobacter Shewanella Duganella Xanthomonadaceae Burkholderia complex Burkholderia Thioclava Oxalobacteraceae Polynucleobacter Tepidiphilus Shewanellaceae Stenotrophomonas Hydrogenophilaceae C Methylophilaceae Xanthomonadales Gluconobacter Comamonadaceae

OTU number Paracoccus Pseudochrobactrum Vibrio Janthinobacterium Ochrobactrum Vibrionaceae Lampropedia Rhodobacterales Acetobacteraceae Rhizobium complex Comamonas Ignatzschineria Alteromonadales Wohlfahrtiimonadaceae Paenochrobactrum Acetobacter Achromobacter Rhizobiaceae Burkholderiaceae Methylophaga Burkholderiales Vitreoscilla Nitrosococcales Acetobacterales Shinella Vibrionales Alcaligenes faecalis Alcaligenes Acidovorax Chromobacteriaceae Luteimonas Neisseria Neisseriaceae Methylophagaceae Devosia Methylobacterium-methylorubrum Pseudoxanthomonas Alcaligenes Alphaproteobacteria Parapusillimonas Orbales Alcaligenaceae Advenella Brevundimonas Cellvibrionales Devosiaceae Gammaproteobacteria Cardiobacteriales Rhizobiales Yersiniaceae Enterobacteriaceae Caulobacterales Erwiniaceae Micrococcaceae Koukoulia Caulobacteraceae Vogesella Orbaceae Beijerinckiaceae Legionella Cellvibrionaceae Pantoea Sphingomonadaceae Hafnia-obesumbacterium 0.00 0.02 0.04 0.06 0.00 0.02 0.04 0.06 0.00 0.02 0.04 0.06 Glutamicibacter Providencia Orbus Citrobacter Sphingomonadales Kocuria Sphingopyxis Pseudoclavibacter Hafniaceae Enterobacterales Legionellales Pseudomonadales Micrococcales Morganella Cellvibrio 0.39 0.23 0.31 0.31 0.19 0.23 Legionellaceae Rothia Proteobacteria 0.19 Dermabacteraceae 0.31 0.36 0.25 Pseudomonas 0.16 0.26 Microbacteriaceae 0.21 0.28 0.27 0.37 0.41 Acinetobacter 0.33 0.37 0.16 Proteus 0.25 0.3 Enhydrobacter Morganellaceae 0.35 0.15 0.28 0.36 Dietzia Sphingomonas 0.26 0.4 Azotobacter 0.33 Pseudomonadaceae 0.34 Brachybacterium Outside Inside 0.42 0.21 0.3 Moraxellaceae 0.16 Rhodococcus Corynebacteriales Rhodoluna Leucobacter Dietziaceae Actinobacteria Nocardiaceae 0.32 Dermacoccus 0.38 Prokaryota Butyricicoccaceae 0.23 Corynebacteriaceae 0.43 Corynebacterium Top LSU OTUs to OTUs LSU Top Oscillospirales Butyricicoccus Dermacoccaceae Veillonellales-selenomonadales Veillonella Top 16s OTUs to 16sOTUs Top Sanguibacter Rarobacteraceae Top ITS OTUs to OTUs ITS Top Brevibacteriaceae Bifidobacteriaceae Ruminococcaceae Selenomonas Psychrobacter 0.43 Sanguibacteraceae Actinobacteriota Demequinaceae 0.42 Arsenicicoccus Mean Decrease Mean Decrease Mean Decrease Intrasporangiaceae Veillonellaceae Bacteria classify niches classify niches classify classify niches classify Bifidobacteriales Lachnospiraceae Nakamurellaceae Megasphaera Selenomonadaceae 0.47 Micromonosporaceae Actinomycetales Lachnospirales Brevibacterium Micromonosporales in Accuracy in Accuracy in in Accuracy in Lachnoclostridium Anaerocolumna Frankiales Bacteroidota Firmicutes Peptostreptococcales-tissierellales Actinomycetaceae Clostridia Anaerovoracaceae Verrucomicrobiota Bifidobacterium Rarobacter Amnipila Bdellovibrionota Negativicutes Actinomyces Nakamurella Flavobacteriales Verrucomicrobiae Gallicola Exiguobacteraceae Crocinitomicaceae Fusobacteriota Micromonospora Chryseobacterium Peptoniphilus Chishuiella Helcococcus Exiguobacterium Clostridiales Opitutales Paraclostridium Weeksellaceae Bacteroidia Dysgonomonadaceae Algoriella Peptoniphilaceae Opitutaceae Fluviicola Peptostreptococcaceae Cloacibacterium Peptoniphilus Alterococcus Planctomycetota Exiguobacterales Bdellovibrionales Empedobacter Acetoanaerobium Chloroflexi Deinococcota Gemmatimonadota Campilobacterota Staphylococcales Clostridiaceae Flavobacteriaceae Bacilli Peptostreptococcus Cytophagales Anaerolineae Staphylococcaceae Deinococcaceae Proteiniphilum Dyadobacter Bdellovibrionaceae Spirosomaceae Dysgonomonas Gemmatimonadetes Deinococci Paenibacillales Lactobacillales Deinococcales Clostridioides Bacillus Fusobacteriia Flavobacterium NA Clostridium sensu stricto Clostridium Sphingobacteriales Proteiniclasticum Clostridium perfringens Clostridium Fusobacteriales Macrococcus Staphylococcus Prevotellaceae Bdellovibrionia Bacillales Myroides Planococcaceae Weissella Leuconostocaceae Bacillaceae Erysipelotrichales Bdellovibrio Microscillaceae Jeotgalicoccus Thermales Bacteroidales Oceanobacillus Pedobacter Campylobacteria Chitinophagales Larkinella Lysinibacillus Leptotrichiaceae Deinococcus Gemmatimonadales Bacteriovoracales Paenibacillaceae Lactobacillaceae Thermaceae Prevotella Listeriaceae Paenibacillus Kurthia Enterococcaceae Gemmatimonadaceae Bacteroides Bacteroidaceae Sphingobacteriaceae Campylobacterales Bacteriovoracaceae Erysipelotrichaceae Chitinophagaceae Brochothrix Hypnocyclicus Saccharibacillus Vagococcaceae Sphingobacterium Fusobacteriaceae Brochothrix thermosphacta Brochothrix Erysipelothrix Breznakia Planctomycetes Sediminibacterium Streptococcaceae Arcticibacter Leuconostoc Arcobacteraceae Thermus Floricoccus Fusobacterium Pirellulales Vagococcus Pediococcus Peredibacter Aerococcaceae Arcobacter Enterococcus Samples with OTUs Pseudarcobacter Lactobacillus mucosae Lactobacillus Streptococcus Aerococcus Leuconostoc fallax Leuconostoc Lactococcus 36 25 16 Pseudoflavitalea Facklamia 9 4 1 Lactobacillus Pirellulaceae 0 Lactobacillus reuteri Lactobacillus Nodes 16S Nodes 365.0 254.0 163.0 92.0 41.4 11.1 1.0

OTU number