Supplementary Materials

Supplementary Figure 1. Browsing intensity index by environmental treatment is shown.

5.5 5.0 4.5 Browsing intensity Browsing 4.0 3.5 3.0

AUT NET SED

Supplementary Figure 2. Clonal average size and clonal average browsing intensity are uncorrelated.

5.5

5.0

4.5

4.0 Browsing intensity Browsing

3.5

3.0

2.0 2.5 3.0 Body size (mm)

Supplementary Figure 3: Taxonomic trees of OTUs found in sequenced animals, highlighting presence/absence and relative abundance in AUT (A), NET (B) and SED (C) treatment groups. Node size represents the number of samples in the treatment group in which a given taxon is found, whereas node color represents the median relative abundance of the taxon among samples in the treatment group.

(A) Hymenobacter Pedobacter Prevotella Emticicia Adhaeribacter Porphyromonas [Prevotella] Paludibacter Leadbetterella Sediminibacterium Flavisolibacter Spirosoma Fluviicola Wautersiella Chryseobacterium Erysipelothrix Cloacibacterium Gemella Flavobacterium Enterococcus Capnocytophaga Granulicatella Leptotrichia Leuconostoc Lactobacillus Facklamia Sphingobacteriaceae Aerococcus Cytophagaceae [Paraprevotellaceae] Prevotellaceae Saprospiraceae Streptococcus Saccharopolyspora Cyclobacteriaceae Porphyromonadaceae Chlamydomonadaceae Chitinophagaceae Lactococcus Pilimelia Phormidiaceae Cryomorphaceae Aquificaceae [Weeksellaceae] Paenibacillus Erysipelotrichaceae Brevibacterium Gemellaceae Flavobacteriaceae Brevibacillus Enterococcaceae Actinomyces Carnobacteriaceae Leptotrichiaceae Salinicoccus Leuconostocaceae AK1AB1_02E N09 Lactobacillaceae Solirubrobacteraceae Staphylococcus Actinopolysporaceae Janibacter Aerococcaceae Sporichthyaceae Brachybacterium Pseudonocardiaceae Thermicanus Streptococcaceae Micromonosporaceae Yaniella RF39 Sphingobacteriales Exiguobacterium EW055 Bacteroidales Brevibacteriaceae Paenibacillaceae Streptophyta [Saprospirales] Rothia Rummeliibacillus Chlorophyta Actinomycetaceae Erysipelotrichales Flavobacteriales Oscillatoriales Stramenopiles Renibacterium Aquificales Sporosarcina Staphylococcaceae Gemellales Fusobacteriales Intrasporangiaceae Listeriaceae Gaiellales Sanguibacter Geobacillus Lactobacillales Solirubrobacterales Dermabacteraceae [Thermicanaceae] Yaniellaceae Cellulomonas Anoxybacillus [Exiguobacteraceae]

Curtobacterium Micrococcaceae Bacillus Planococcaceae Microbacterium Sanguibacteraceae Proteiniclasticum Cytophagia Bacteroidia TM7-3 Mollicutes Sphingobacteriia Cellulomonadaceae Salinibacterium [Saprospirae] Clostridium Bacillaceae Chloroplast Bacillales Aquificae Rhodococcus Erysipelotrichi Oscillatoriophycideae Fusobacteriia Caloramator Thermoleophilia Microbacteriaceae Bacilli Actinomycetales Gordonia Peptostreptococcus Clostridiaceae Mycobacterium Nocardiaceae Faecalibacterium Gordoniaceae Corynebacterium Peptostreptococcaceae WAL_1855D Mycobacteriaceae Ruminococcaceae Aeromicrobium Anaerococcus TM7 Tenericutes Corynebacteriaceae FBP Nocardioides Cyanobacteria Peptoniphilus Fusobacteria Lachnospiraceae Aquificae Propionicimonas GW-34 [Tissierellaceae] Nocardioidaceae Firmicutes Actinobacteria Actinobacteria Friedmanniella Finegoldia Clostridiales Propionibacterium G07 Propionibacteriaceae Bifidobacterium Bifidobacteriaceae Megasphaera Bifidobacteriales

Treponema Spirochaetaceae Spirochaetales Spirochaetes Dialister Clostridia Spirochaetes Rickettsiaceae Veillonellaceae Rickettsiales

Veillonella BD7-3 mitochondria Verrucomicrobia Chloroflexi Acetobacteraceae Megamonas Rhodospirillales Roseomonas [Thermi] [Pedosphaerae] Planctomycetes Anaerolineae Selenomonas Thermoanaerobacterales Acidobacteria Telmatospirillum Peptococcaceae C0119 Gemmatimonadetes [Pedosphaerales] Thermomicrobia Rhodospirillaceae Peptococcus Caldicellulosiruptoraceae Chloroflexi Azospirillum SJA-15 Deinococci Ellin515 Caldicellulosiruptor Planctomycetia Alphaproteobacteria Skermanella JG30-KF-CM45 [Chloracidobacteria] Phyllobacteriaceae Solibacteres AKIW781 Proteobacteria Acidobacteria-6 Novispirillum Aurantimonadaceae Deinococcales Gemmatimonadetes Deltaproteobacteria Thermales Rhizobiales Rhizobiaceae Phyllobacterium Gemmatales RB41

Deinococcaceae Solibacterales Hyphomicrobiaceae Agrobacterium iii1-15 Thermaceae Myxococcales Betaproteobacteria Devosia Isosphaeraceae Bradyrhizobiaceae Nodes

Deinococcus Rhodoplanes Ellin6075 Bdellovibrionales Gammaproteobacteria Rhodobacterales Methylobacteriaceae Solibacteraceae Beijerinckiaceae Thermus Methylophilales Hyphomicrobium mb2424 Neisseriales Xanthobacteraceae Caulobacterales Bradyrhizobium 0.00000 Cystobacteraceae Methylocystaceae

Haliangiaceae Methylobacterium Bacteriovoracaceae Sphingomonadales Rhodobacteraceae Chelatococcus Bdellovibrionaceae Legionellales Xanthomonadales Xanthobacter Chromatiales 0.00483 Methylophilaceae Burkholderiales Oceanospirillales Neisseriaceae Alteromonadales Methylopila Aeromonadales Enterobacteriales Caulobacteraceae Rhodocyclales Paracoccus PseudomonadalesPasteurellales Rubellimicrobium 0.01930 Bdellovibrio Sphingomonadaceae Rhodobacter

Neisseria Amaricoccus Comamonadaceae Erythrobacteraceae Kingella Coxiellaceae Phenylobacterium Legionellaceae Sinobacteraceae Vitreoscilla Caulobacter Xanthomonadaceae 0.04340 Ectothiorhodospiraceae Aquitalea Alcaligenaceae Halomonadaceae Mycoplana Oxalobacteraceae [Chromatiaceae] Oceanospirillaceae Hydrogenophaga Rhodocyclaceae Shewanellaceae Sphingobium Pasteurellaceae Comamonas Pseudomonadaceae Aeromonadaceae Enterobacteriaceae Sphingopyxis Delftia Moraxellaceae Sphingomonas Variovorax Kaistobacter 0.07720 Limnohabitans Erythromicrobium Tepidimonas Rubrivivax Methylibium Nevskia Schlegelella Stenotrophomonas Achromobacter Pseudoxanthomonas Pigmentiphaga Halomonas Cupriavidus 0.12100 Alishewanella Marinomonas Collimonas Shewanella Ralstonia Hydrogenophilus Klebsiella Methyloversatilis Z-35 Haemophilus Psychrobacter Dechloromonas Acinetobacter proportion Median Gallibacterium Pseudomonas Enhydrobacter 0.17400

(B)

Hymenobacter Prevotella Pedobacter Porphyromonas Emticicia Adhaeribacter [Prevotella] Paludibacter Sediminibacterium Leadbetterella Flavisolibacter Spirosoma Fluviicola Wautersiella Chryseobacterium Erysipelothrix Cloacibacterium Gemella Flavobacterium

Enterococcus Capnocytophaga

Granulicatella Leptotrichia Leuconostoc Lactobacillus

Facklamia

Aerococcus Cytophagaceae Prevotellaceae Sphingobacteriaceae [Paraprevotellaceae] Porphyromonadaceae Streptococcus Cyclobacteriaceae Saccharopolyspora Saprospiraceae Chlamydomonadaceae Chitinophagaceae Lactococcus Phormidiaceae Cryomorphaceae Pilimelia Aquificaceae [Weeksellaceae] Paenibacillus Erysipelotrichaceae Brevibacterium Gemellaceae Flavobacteriaceae Brevibacillus Enterococcaceae Actinomyces Carnobacteriaceae Leptotrichiaceae Salinicoccus Leuconostocaceae AK1AB1_02E N09 Lactobacillaceae Solirubrobacteraceae Staphylococcus Actinopolysporaceae Janibacter Aerococcaceae Sporichthyaceae Brachybacterium Pseudonocardiaceae Thermicanus Streptococcaceae Cytophagales Micromonosporaceae Yaniella EW055 Exiguobacterium RF39 Sphingobacteriales Bacteroidales Brevibacteriaceae Paenibacillaceae Streptophyta [Saprospirales] Rothia

Rummeliibacillus Aquificales Chlorophyta Actinomycetaceae Oscillatoriales Stramenopiles Flavobacteriales Erysipelotrichales Renibacterium Sporosarcina Staphylococcaceae Gemellales Fusobacteriales Intrasporangiaceae Sanguibacter Listeriaceae Gaiellales Geobacillus Lactobacillales Solirubrobacterales Dermabacteraceae [Thermicanaceae] Yaniellaceae Cellulomonas Anoxybacillus [Exiguobacteraceae] Micrococcaceae Curtobacterium Bacillus Planococcaceae Microbacterium Sanguibacteraceae Proteiniclasticum Cytophagia Sphingobacteriia Bacteroidia Mollicutes Cellulomonadaceae Salinibacterium Clostridium Bacillaceae Chloroplast TM7-3 [Saprospirae] Oscillatoriophycideae Bacillales Aquificae Flavobacteriia Rhodococcus Erysipelotrichi Fusobacteriia Caloramator Thermoleophilia Microbacteriaceae Actinomycetales Gordonia Peptostreptococcus Bacilli Clostridiaceae Mycobacterium Nocardiaceae Faecalibacterium Gordoniaceae Corynebacterium Peptostreptococcaceae WAL_1855D Mycobacteriaceae Ruminococcaceae Aeromicrobium Anaerococcus TM7 Tenericutes Corynebacteriaceae Cyanobacteria FBP Bacteroidetes Nocardioides Peptoniphilus Aquificae Fusobacteria Lachnospiraceae Propionicimonas GW-34 [Tissierellaceae] Nocardioidaceae Firmicutes Actinobacteria Actinobacteria Friedmanniella Finegoldia Clostridiales Propionibacterium G07 Propionibacteriaceae

Bifidobacterium Bifidobacteriaceae Megasphaera Bifidobacteriales

Treponema Spirochaetaceae Spirochaetales Spirochaetes Spirochaetes Dialister Clostridia Bacteria Rickettsiaceae Veillonellaceae Rickettsiales

BD7-3 Veillonella mitochondria Verrucomicrobia Chloroflexi Acetobacteraceae Megamonas Rhodospirillales Roseomonas [Thermi] [Pedosphaerae] Planctomycetes Anaerolineae Selenomonas Thermoanaerobacterales Acidobacteria Telmatospirillum Peptococcaceae C0119 Gemmatimonadetes [Pedosphaerales] Thermomicrobia Rhodospirillaceae Peptococcus Caldicellulosiruptoraceae Chloroflexi Azospirillum SJA-15 Deinococci Ellin515 Caldicellulosiruptor Planctomycetia Alphaproteobacteria Skermanella JG30-KF-CM45 [Chloracidobacteria] Phyllobacteriaceae Solibacteres AKIW781 Proteobacteria Novispirillum Acidobacteria-6 Aurantimonadaceae Deinococcales Gemmatimonadetes

Thermales Deltaproteobacteria Phyllobacterium Rhizobiales Rhizobiaceae Gemmatales RB41 Deinococcaceae Solibacterales Hyphomicrobiaceae Agrobacterium iii1-15 Thermaceae Myxococcales Betaproteobacteria Devosia Isosphaeraceae Bradyrhizobiaceae Nodes Deinococcus Ellin6075 Bdellovibrionales Gammaproteobacteria Rhodobacterales Methylobacteriaceae Rhodoplanes Solibacteraceae Beijerinckiaceae Thermus Methylophilales Hyphomicrobium mb2424 Neisseriales Xanthobacteraceae Caulobacterales Bradyrhizobium 0.00000 Cystobacteraceae Methylocystaceae

Haliangiaceae Methylobacterium

Bacteriovoracaceae Sphingomonadales Rhodobacteraceae Chelatococcus Bdellovibrionaceae Legionellales Xanthomonadales Xanthobacter 0.00469 Methylophilaceae Oceanospirillales Chromatiales Burkholderiales Alteromonadales Methylopila Neisseriaceae Enterobacteriales Rhodocyclales Caulobacteraceae Aeromonadales Pasteurellales Paracoccus Pseudomonadales Rubellimicrobium 0.01880 Bdellovibrio Sphingomonadaceae Rhodobacter

Neisseria Amaricoccus Comamonadaceae Erythrobacteraceae Kingella Coxiellaceae Phenylobacterium Legionellaceae Vitreoscilla Sinobacteraceae Caulobacter Xanthomonadaceae Aquitalea Alcaligenaceae 0.04220 Ectothiorhodospiraceae Mycoplana Halomonadaceae Oxalobacteraceae Oceanospirillaceae Hydrogenophaga [Chromatiaceae] Sphingobium Rhodocyclaceae EnterobacteriaceaeShewanellaceae Comamonas Pseudomonadaceae Aeromonadaceae Pasteurellaceae Sphingopyxis Delftia Moraxellaceae Sphingomonas Variovorax Kaistobacter 0.07510 Limnohabitans Erythromicrobium Tepidimonas Rubrivivax Methylibium Nevskia Schlegelella Stenotrophomonas Achromobacter Pseudoxanthomonas Pigmentiphaga 0.11700 Halomonas Cupriavidus Marinomonas Collimonas Hydrogenophilus Alishewanella Ralstonia Haemophilus Psychrobacter Enhydrobacter Shewanella Methyloversatilis Z-35 Gallibacterium

Dechloromonas Klebsiella proportion Median Pseudomonas Acinetobacter 0.16900

(C) Hymenobacter [Prevotella] Prevotella Emticicia Adhaeribacter Pedobacter Porphyromonas Leadbetterella Paludibacter Sediminibacterium Spirosoma Flavisolibacter Fluviicola Wautersiella Chryseobacterium Erysipelothrix Cloacibacterium Gemella Flavobacterium

Enterococcus Capnocytophaga

Granulicatella Leptotrichia Leuconostoc Lactobacillus Facklamia

Aerococcus Cytophagaceae Prevotellaceae Sphingobacteriaceae Porphyromonadaceae Cyclobacteriaceae [Paraprevotellaceae] Streptococcus Saprospiraceae Saccharopolyspora Chlamydomonadaceae Chitinophagaceae Lactococcus Phormidiaceae Cryomorphaceae Pilimelia Aquificaceae [Weeksellaceae] Paenibacillus Erysipelotrichaceae Brevibacterium Gemellaceae Flavobacteriaceae Enterococcaceae Brevibacillus Actinomyces Carnobacteriaceae Leptotrichiaceae Salinicoccus Leuconostocaceae AK1AB1_02E N09 Lactobacillaceae Solirubrobacteraceae Staphylococcus Actinopolysporaceae Janibacter Aerococcaceae Sporichthyaceae Brachybacterium Pseudonocardiaceae Thermicanus Streptococcaceae Cytophagales Micromonosporaceae Yaniella Exiguobacterium Bacteroidales RF39 Sphingobacteriales Streptophyta [Saprospirales] Brevibacteriaceae Paenibacillaceae Stramenopiles EW055 Rothia Rummeliibacillus Aquificales Chlorophyta Flavobacteriales Actinomycetaceae Gemellales Renibacterium Oscillatoriales Sporosarcina Staphylococcaceae Erysipelotrichales Fusobacteriales Intrasporangiaceae Listeriaceae Gaiellales Sanguibacter Geobacillus Lactobacillales Solirubrobacterales Dermabacteraceae [Thermicanaceae] Yaniellaceae Cellulomonas Anoxybacillus [Exiguobacteraceae] Micrococcaceae Curtobacterium Bacillus Planococcaceae Microbacterium Sanguibacteraceae Proteiniclasticum Cytophagia Sphingobacteriia Mollicutes Bacteroidia Cellulomonadaceae Salinibacterium Clostridium Bacillaceae Chloroplast TM7-3 [Saprospirae] Bacillales Erysipelotrichi Oscillatoriophycideae Rhodococcus Aquificae Flavobacteriia Fusobacteriia Caloramator Thermoleophilia Microbacteriaceae Actinomycetales Gordonia Peptostreptococcus Bacilli Clostridiaceae Mycobacterium Nocardiaceae Faecalibacterium Gordoniaceae Corynebacterium Peptostreptococcaceae WAL_1855D Mycobacteriaceae Ruminococcaceae Aeromicrobium Anaerococcus TM7Tenericutes Corynebacteriaceae FBP Cyanobacteria Bacteroidetes Nocardioides Peptoniphilus Fusobacteria Lachnospiraceae Aquificae Propionicimonas GW-34 [Tissierellaceae] Nocardioidaceae Firmicutes Actinobacteria Actinobacteria Friedmanniella Finegoldia Clostridiales Propionibacterium G07 Propionibacteriaceae Bifidobacterium Bifidobacteriaceae Megasphaera Bifidobacteriales

Spirochaetaceae Treponema Spirochaetes Spirochaetales Dialister Clostridia Spirochaetes Rickettsiaceae Veillonellaceae Bacteria Rickettsiales

Veillonella BD7-3 mitochondria Verrucomicrobia Chloroflexi Acetobacteraceae Megamonas Rhodospirillales Roseomonas

[Pedosphaerae] [Thermi] Planctomycetes Anaerolineae Selenomonas Thermoanaerobacterales Acidobacteria Telmatospirillum C0119 Peptococcaceae Gemmatimonadetes [Pedosphaerales] Thermomicrobia Rhodospirillaceae Peptococcus Caldicellulosiruptoraceae Chloroflexi Azospirillum SJA-15 Deinococci Ellin515 Caldicellulosiruptor Planctomycetia Alphaproteobacteria Skermanella JG30-KF-CM45 [Chloracidobacteria] Phyllobacteriaceae Solibacteres AKIW781 Proteobacteria Novispirillum Acidobacteria-6 Aurantimonadaceae Deinococcales Gemmatimonadetes Deltaproteobacteria Thermales Rhizobiales Rhizobiaceae Phyllobacterium Gemmatales

RB41 Deinococcaceae Solibacterales Hyphomicrobiaceae Agrobacterium iii1-15 Thermaceae Myxococcales Betaproteobacteria Devosia Isosphaeraceae Bradyrhizobiaceae Nodes Deinococcus Ellin6075 Bdellovibrionales Gammaproteobacteria Rhodobacterales Methylobacteriaceae Rhodoplanes Solibacteraceae Beijerinckiaceae Thermus Methylophilales Hyphomicrobium mb2424 Neisseriales Xanthobacteraceae Caulobacterales Bradyrhizobium 0.0000 Cystobacteraceae Methylocystaceae

Haliangiaceae Methylobacterium Sphingomonadales Bacteriovoracaceae Chelatococcus Legionellales Rhodobacteraceae Bdellovibrionaceae Xanthomonadales Chromatiales Xanthobacter 0.0048 Methylophilaceae Alteromonadales Oceanospirillales Burkholderiales Methylopila Neisseriaceae Enterobacteriales Rhodocyclales Pasteurellales Caulobacteraceae Aeromonadales Paracoccus Pseudomonadales Rubellimicrobium 0.0192 Bdellovibrio Sphingomonadaceae Rhodobacter

Neisseria Amaricoccus Comamonadaceae Erythrobacteraceae Kingella Coxiellaceae Phenylobacterium Legionellaceae Sinobacteraceae Vitreoscilla Caulobacter Alcaligenaceae Xanthomonadaceae Aquitalea Ectothiorhodospiraceae 0.0432 Mycoplana Oxalobacteraceae [Chromatiaceae] Halomonadaceae Hydrogenophaga Rhodocyclaceae Shewanellaceae Oceanospirillaceae Sphingobium Comamonas Aeromonadaceae Enterobacteriaceae Sphingopyxis Pseudomonadaceae Pasteurellaceae Delftia Sphingomonas Variovorax Moraxellaceae Kaistobacter 0.0769 Limnohabitans Erythromicrobium Tepidimonas Rubrivivax Methylibium Nevskia Schlegelella Stenotrophomonas Pseudoxanthomonas Achromobacter Halomonas Pigmentiphaga Cupriavidus Marinomonas 0.1200 Shewanella Alishewanella Collimonas Hydrogenophilus Haemophilus Klebsiella Ralstonia Methyloversatilis Psychrobacter Z-35 Gallibacterium Enhydrobacter Dechloromonas Acinetobacter proportion Median Pseudomonas 0.1730

Supplementary Figure 4: Bacterial richness of autoclaved and untreated sediment. N=6 samples per treatment, 3 each collected at beginning and end of experiment.

Bacterial species richness species Bacterial 40 60 80 100 140

Autoclaved Natural

Sediment type

Supplementary Figure 5. Average microbiota diversity by clone and treatment using species richness after rarefying to an even sampling depth (A) or inverse Simpson index (B).

A 25

20

15

10 Richness +/- s.e.m. +/- Richness

5 treatment AUT NET 0 SED IXF1 F2-82 F2-918 NO-V-7 CZ-N2-6 CZ-N1-1 TR-EG-1 ES-DO1-1 DE-KA-F28 BE-WE-G59 BE-OHZ-T10 DE-K35-Mu10 clone B

7.5

5.0

Simpson Index +/- s.e.m. +/- Index Simpson 2.5

treatment AUT NET 0.0 SED IXF1 F2-82 F2-918 NO-V-7 CZ-N2-6 CZ-N1-1 TR-EG-1 ES-DO1-1 DE-KA-F28 BE-WE-G59 BE-OHZ-T10 DE-K35-Mu10 clone

Supplementary Figure 6. Shannon diversity index as a function of the browsing intensity calculated for each individual’s jar-mate. Lines represent linear regression; shaded area represents 95% confidence interval.

3

2 treatment AUT NET

Shannon SED 1

0 3.0 3.5 4.0 4.5 5.0 5.5 behavior

Supplementary Figure 7. Relationship between browsing intensity and proportion of sediment-derived bacteria in the microbiota using jar-mate’s browsing intensity as behavior proxy and different thresholds for defining sediment-derived bacteria. (A) Sediment-derived bacteria defined by log2-fold change of 5 or more between autoclaved and natural sediment samples (B) Sediment-derived bacteria defined by log2-fold change of 8 or more between autoclaved and natural sediment samples (C) Sediment-derived bacteria defined by log2-fold change of 10 or more between autoclaved and natural sediment samples.

(A)

Log2FC>5

treatment 0.6 AUT NET SED

0.4

0.2 Proportion sediment-derived bacteria sediment-derived Proportion 0.0

3.0 3.5 4.0 4.5 5.0 5.5 Jar-mate browsing intensity

(B)

Log2FC>8

treatment

0.6 AUT NET SED

0.4

0.2 Proportion sediment-derived bacteria sediment-derived Proportion 0.0

3.0 3.5 4.0 4.5 5.0 5.5 Jar-mate browsing intensity

(C)

Log2FC>10

treatment

0.6 AUT NET SED

0.4

0.2 Proportion sediment-derived bacteria sediment-derived Proportion 0.0

3.0 3.5 4.0 4.5 5.0 5.5 Jar-mate browsing intensity

Supplementary Table 1. Effect of treatment (NET or SED) and behavior on Shannon diversity index, using treatment-specific clonal average behavior (A) or jar-mate behavior (B) as behavior proxy.

A. Linear mixed-effects model with clone as random effect numDF denDF F-value p-value (Intercept) 1 124 262.61367 <.0001 treatment 1 124 11.76313 0.0008 trtbehavior 1 124 0.05191 0.8201 cloneavgsize 1 9 2.07427 0.1837 treatment:trtbeh 1 124 4.62296 0.0335 treatment:cloneavgsize 1 124 0.01471 0.9036

B. Analysis of variance Df Sum Sq Mean Sq F value Pr(>F) treatment 1 3.85 3.845 10.490 0.0015 ** jar-mate behavior 1 0.27 0.267 0.727 0.3953 treatment:behavior 1 0.72 0.722 1.969 0.1628 Residuals 138 50.58 0.367