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Taxonomic and functional resolution of the omics
In order to explore the RNA/protein dynamics in a microbiome setting, we first needed to characterize our test community over time at the molecular level. We previously genomically reconstructed and resolved the SEM1b community, retrieving 11 metagenome-assembled genomes (MAGs) as well as two isolate genomes (see “Methods” section)10, covering the taxonomic and functional niches that are required to convert cellulosic material to methane/CO2 in an anaerobic biogas reactor15. Taxonomic analysis of both 16S rRNA genes and the MAGs of SEM1b inferred population-level affiliations to Rumini(Clostridium) thermocellum (RCLO1), Clostridium sp. (CLOS1), Coprothermobacter proteolyticus (COPR1, BWF2A, SW3C), Tepidanaerobacter (TEPI1-2), Synergistales (SYNG1-2), Tissierellales (TISS1), and the methanogen Methanothermobacter (METH1)10, as depicted in Fig. 1a. Herein we estimated that the total genomic potential of SEM1b includes 39,144 open reading frames (ORFs) (Supplementary Data 1). Since ORFs with very high sequence similarity may produce RNAs and proteins that are indistinguishable in MT and MP data, all the ORFs were gathered into ORF-groups (ORFGs) during the MT and MP data processing (see “Methods” section), where a singleton ORFG is defined as a group with a single ORF, and thus a single gene. Using this approach, our MT and MP data identified 12552 (96% singleton) and 3235 (78% singletons) highly transcribed and translated ORFGs, respectively. The discrepancy between the singleton percentages was as expected, due to the fact that variations in DNA/RNA sequences are greater than in proteins since different codons can code for the same amino acid (codon degeneracy). Degeneracy also implies that the chance to distinguish between homologous genes using MT is greater than using MP. Previous MG analyses using assembly algorithms have shown that genomic regions difficult to assemble in a given environmental contig can harbor variants from multiple, closely related strains, which can be further linked to normal strain-level variability within a population and species divergence16,17,18. Within SEM1b, the ORFGs that contained multiple homologous ORFs predominantly originated from several strains of a single species. For example, in the MT, 444 non-singleton ORFGs (88% of the total) contained ORFs from different strains of the same species, whilst this was the case for 294 ORFGs (32%) in the MP.
Fig. 1: Life cycle of the SEM1b consortium and sampling scheme.

a In the SEM1b consortium, seven major microbial populations perform the metabolic processes that lead from saccharification to methanogenesis. In the first phase, RCLO1 and CLOS1 degrade the spruce substrate (predominantly cellulose and hemicellulose), thanks to a sophisticated and flexible enzymatic array, which releases simple oligosaccharides and sugars. Subsequently, the consortium grows (the protein concentration in the samples increases) up to t4 (23 h post inoculum), alongside the degradation (and fermentation) of mono- and disaccharides by RCLO1, CLOS1, TEPI1, TISS1, and COPR1+ strains. One of the sugars released from the degradation of xylan, xylose, is briefly accumulated (Fig. 4a). In addition, SCFAs are accumulated as a byproduct of microbial fermentation. In the last step, the synergetic partnership between TEP1 and METH1 (syntrophic acetate oxidizer and methanogen, respectively) converts the SCFAs and H2 to methane. The bars in the protein profile represent the maxima and minima of the measurements. b To characterize SEM1b, 24 flasks containing spruce media were inoculated with a SEM1b culture at t0. Starting from t1 (8 h), three flasks were opened every 5 h and their content processed. From the eight time points (plus t0) different omic- and meta-data were collected (depicted in the table). Every dot represents a replicate sample, and most measurements are taken in triplicate (except for cellulose degradation).

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All ORFs were annotated using KEGG Ontology (KO), and at least one term was found for 19070 (49%) representatives from our complete data set (Supplementary Data 2). The predominant ORF annotations included Membrane transport, Carbohydrate metabolism, Translation, Amino acid metabolism, and Replication and repair (Supplementary Fig. 1). As expected, these functional categories were also among the top five most abundant for the MT, and top six in MP (plus Energy metabolism), although in a different order. The Membrane transport category is poorly represented in the MP (2% of the terms), which is likely explained by well-known technical issues with the gel-based sample preparation method that we used, which limits the extraction of transmembrane proteins19. The most abundant annotation categories mentioned above are all in line with the community function of cellulose degradation. The abundance ranking of the KO categories was assessed using the Kendall τ, which takes values from −1 (opposite direction of the ranking) to +1 (total agreement in ranking). Its score is interpreted as a correlation measure; however, it is more conservative. The ranking is largely preserved from MG to MT (Kendall τ: 0.77, p  More

Systematic palaeontology
Clade Bilateria, Clade Protostomia
Vermilituus gregarius gen. et sp. nov.
Etymology: Genus name from vermis (Latin) meaning worm and lituus (Latin) meaning a curved trumpet, alluding to the shape of the fossils. Species name from gregarius (Latin), meaning flock or herd.
Holotype: YKLP 13079a, b (counterparts), U-shaped tube (Fig. 1a, b), 6.5-mm long, and reaching a maximum width of 0.6 mm: the holotype is associated with Vetulicola rectangulata YKLP 13075a, b. Paratypes (with preserved shell annulation), YKLP 13084 and 13085 (Fig. 1c, f) associated with V. rectangulata YKLP 13074, and YKLP 13082 and 13083 (Fig. 1e) associated with V. rectangulata YKLP 13073.
Fig. 1: Different styles of preservation and morphology of Vermilituus gregarius.

a, b Holotype, YKLP 13079a, flattened specimen showing U-shape morphology, under cross-polarised light (a) and fluorescence light (b). c Paratype YKLP 13084, partial 3D with well-preserved annulation, J-shape morphology. d, h YKLP 13086 under direct light (d) and fluorescence light (h), white arrow shows possible soft tissues. e Paratypes YKLP 13082 and 13083, preserved in 3D with annulation visible proximally: sinusoidal shape and J-shape morphology, respectively (the latter is broken distally and shows sediment fill). f Paratype YKLP 13085, partial 3D with well-preserved annulation, sinusoidal morphology. g, i–k Scanning electron microscopy images. g YKLP 13087 with J-shape morphology. i, j YKLP 13088, boxed area in “i” shows possible paired soft tissues at the termination, magnified in “j”. k YKLP 13089, with possible paired soft tissues at the terminal end. Scale bars: a–d, g–i, k, 500 μm; e, f, 1 mm; j, 200 μm.

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Referred material: About 192 specimens from Ercaicun, 75 from Mafang and 10 from Jianshan associated with Vetulicola rectangulata, all in the collections of the Yunnan Key Laboratory for Palaeobiology (YKLP). In total, 17 specimens from Xiaolantian and 55 specimens from Heimadi associated with Vetulicola cuneata, all in the collections of the Chengjiang Fossil Museum (CJHMD, Supplementary data file).
Locality: Ercaicun (type locality), Mafang and Jianshan localities in the Haikou area of Kunming, and Xiaolantian and Heimadi in Chengjiang County, Yunnan Province, China (for localities see ref. 5).
Horizon: Yu’anshan Member, Chiungchussu Formation, Eoredlichia-Wutingaspis trilobite Biozone, Nangaoan Stage of Chinese regional usage, Cambrian Series 2, Stage 3. All specimens are from rapidly sedimented ‘event beds’5.
Diagnosis for genus (monotypic) and species. Small (0.8–7.2-mm long) elongated, conical tubes having three general forms, as a U-shape, J-shape or complex sinusoid, the latter being the dominant type: occasionally the tube also begins with a 360° planispiral coil before straightening. Coiling can be both dextral and sinistral and is in a single plane. The proximal end of the tube blunts (no bulb-like origin). Tubes increase in diameter very slowly, the proximal diameter being about 0.2 mm and the distal diameter reaching 1 mm. No longitudinal ornament. The transverse ornament of the tube consists of distinct annulation, there being about 12–16 annulae per mm. Most tubes are discrete, but in some cases two or more tubes cross. The tube wall appears to be very thin, and there is no evidence of internal septae, pseudopunctae or punctae. Paired crescentic structures are preserved at the open end of the tube in some specimens.
Host–symbiont association
All specimens of Vermilituus gregarius are associated with vetulicolians, a group of extinct animals of disputed phylogenetic affinity that possessed a convex anterior part with frontal and lateral openings, articulating with a tail-like posterior extension (Figs. 2–6; Supplementary Figs. 1 and 2; for a summary of vetulicolians see ref. 6). The soft anatomy of these animals is largely unknown, but the anterior part of Vetulicola has been hypothesised to comprise a pharynx with gill-like structures that flexed by means of horizontal and longitudinal muscle fibres attached to four flexible plates covered by a thin outer membrane (see below).
Fig. 2: Vetulicola cuneata infested by Vermilituus gregarius.

a CJHMD 00031a, right view of the internal mould. Specimen infested with circa 20 V. gregarius. b CJHMD 00031b, left view of the internal mould. c Close-up of the area indicated in the box of image “a”, showing concentration of V. gregarius specimens in the anterior section. d, e CJHMD 00032b, interior surface of the right side (dorsal to top) of the anterior section, and close-up of a sinusoidal V. gregarius tube. f Enlargement of arrowed area in image “a”, showing concentration of three specimens along the central groove. An—anus, Ao—anterior opening, As—anterior section, Dp—posterodorsal projection, Lg—lateral groove, Lp—lateral pouch, Ls—lip-like structure, Ps—posterior section, S—segment, Vp—posteroventral projection (see ref. 2 for terminology). Scale bars: a, b, d 1 cm; c 5 mm; e, f 1 mm.

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Fig. 3: Vetulicola rectangulata infested by Vermilituus gregarius.

a, b YKLP 13073, left view of the internal mould of the anterior section (incomplete) and part of the posterior section. Specimen infested with circa 46 V. gregarius, with one aggregate toward the anterodorsal area (seen in “b”) comprising 29 specimens. c–f YKLP 13075, left view of the internal mould of the anterior section, and composite mould of the posterior section infested with 88 V. gregarius, including three aggregates of between 10 and 25 specimens (e.g., seen in “e”), and concentration of 24 specimens along the central groove (close-up in “f”): note that these are oriented with the narrow end associated with the groove. This specimen also shows four specimens in the tail (“d”). g, h YKLP 13074, right view of the internal mould of the anterior section infested with about 52 V. gregarius that form aggregates of between 5 and 14, including those that preserve annulation (“h”). Scale bars: a, c, g, 1 mm; b, d, e, f, h 2 mm.

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Fig. 4: Vetulicola cuneata, CJHMD 00033 showing taphonomic relationships with Vermilituus gregarius.

Stereo images have a tilt of 20°, to emphasise that both the worms and the Vetulicola are 3-dimensional. a, b Lateral view (stereo pair) of the whole specimen and c, d close-up of the anterior section (stereo pair), respectively. The specimen is a composite mould, with the external surface (ES) evident only in part of the posterior section, while most of the fossil shows an interior surface (see also Supplementary Fig. 3). Scale bars: a, b 1 cm; c, d 5 mm.

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Fig. 5: Host specificity of Vermilituus gregarius with Vetulicola cuneata.

a CJHMD 00033, Vetulicola cuneata preserved on rock slab with the fossil Eldonia. Vetulicola infested with circa 17 V. gregarius. Note that Eldonia was not infested. b CJHMD 00034, Vetulicola infested with circa 34 V. gregarius. c Close-up of the area indicated in the box of image “a”, showing one V. gregarius specimen near the anterior opening. d, e Close-up of the area indicated in the box of image “b”, showing concentration of three specimens along the central groove and one specimen at the position of the junction between the anterior and posterior section. Scale bars: a, b 1 cm; c–e 2 mm.

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Fig. 6: Reconstruction of Vetulicola cuneata (left) and V. rectangulata (right) in life.

Infestation by Vermilituus gregarius is below the surface of the anterior section, that is, within the exoskeleton. Reconstructions are based on specimens about 6-cm long.

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Vermilituus gregarius occurs in four specimens of Vetulicola cuneata from the Chengjiang region (Figs. 2, 4, and 5), plus six specimens of Vetulicola rectangulata from the Haikou region (Fig. 3; Supplementary Figs. 1 and 2; Supplementary data file). Overall, at least 400 specimens of V. rectangulata and 80 specimens of V. cuneata have been collected from the Chengjiang biota (YKLP and CJHMD collections), meaning that Vermilituus gregarius is a rare associate of vetulicolians. Vetulicolian fossils occur as composite moulds where the rock splits through the specimen, each part containing components of both the external and internal surfaces (Supplementary Fig. 3). For the anterior part of Vetulicola, we interpret Vermilituus gregarius as occupying the space between the interior of the exoskeleton, and the convex surface that appears to demarcate the position of the internal anatomy (Figs. 2a–c, 3a, b, g, 4a, b; Supplementary Figs. 1b–e, 2a, b).
The number of Vermilituus gregarius per associated vetulicolian is variable, ranging from a single tube to 88 individuals (Supplementary data file), and in some cases, V. gregarius occurs in local aggregates of up to 25 individuals, for example in YKLP 13075 (Fig. 3c, e, f). In most cases where V. gregarius aggregates, the individuals are discrete, but occasionally some overlap. The overall size of V. gregarius is from 0.8 to 7.2 mm in length, with maximum diameter ranging from 0.4 to 1 mm (proximal width is circa 0.2 mm). Average tube length varies within individual Vetulicola specimens (Supplementary data file), by a minimum of 1.6 mm (specimens associated with CJHMD 00031) to a maximum of 6.4 mm (specimens associated with YKLP 13073).
Rather than representing post-mortem assemblages, or the result of Vermilituus scavenging or colonising vetulicolian carcasses, all evidence suggests that Vermilituus attached to the body surfaces of living vetulicolians. All infested vetulicolians are preserved within ‘event beds’5. This means that they were rapidly buried by sediment, and therefore post-mortem colonisation at the seabed is highly unlikely. Tubes of Vermilituus gregarius occur almost exclusively inside the vetulicolians, rather than the external body surface, and preferentially within the anterior part (Figs. 2–5; Supplementary Figs. 1 and 2). They are absent from other fossils preserved adjacent on the same slabs (Fig. 5a), and indeed have never been observed in other Chengjiang fossils in our investigations over the last three decades. Most specimens of V. gregarius occur in the anterior section of the vetulicolian body (n  > 345) (Figs. 2–5, Supplementary Figs. 1 and 2), with just 4 specimens associated with the posterior section of the most-infested specimen in our collection (YKLP 13075, Fig. 3d). In this rare case, V. gregarius may have over-spilled onto the external surface of the animal or has been displaced post-mortem. Among those in the anterior part, most are located in the convex area between the central groove and the fin-like margins, with some concentrations often in the anterodorsal region (Fig. 3a, b). Only a few tubes of V. gregarius occur along the margins of Vetulicola. In one case, at least 10 U-shaped tubes grow with a posterior orientation in Vetulicola YKLP 10906 (Supplementary Fig. 1e). In Vetulicola YKLP 13075, there is a clear association of 24 V. gregarius with the central groove (Fig. 3f), each having a distinctive orientation with the narrow end of the tube pointing towards the groove.
The consistent occurrence of Vermilituus gregarius inside the anterior section of vetulicolians, combined with the observed patterns of localisation and occasional preferred orientation (Supplementary data file), argues against a chance post-mortem association, or generalist epibiontic habit. In the latter scenarios, the posterior section should also be infested. Furthermore, V. gregarius is absent from any other fossil organism in the Chengjiang biota, suggesting a highly specific relationship. The robust (possibly biomineralised) and curved tubes of V. gregarius are consistent with a sessile, attached ecology, but not with a motile scavenger that might have fed on vetulicolians after death. The size range of Vermilituus on each specimen (Supplementary data file) suggests animals growing in situ for some time, rather than colonising carrion. In addition, the lack of evidence for decay and disarticulation of infested vetulicolians combined with their preservation in event beds supports an in vivo association. In this light, the observed patterns in size, number and distribution of V. gregarius tubes also shed light on vetulicolian biology and the ecological relationship between the taxa. More

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Field experiment
Estimation of turtle catch per unit effort
We conducted our field experiment in February–April 2018 at two wetland complexes near Murray Bridge, South Australia, selecting two study sites at each complex (Supplementary Fig. S3). At each site, we estimated turtle population density using catch-per-unit-effort (CPUE; Supplementary Table S1). We conducted three 3-day rounds of turtle trapping using a combination of fyke and cathedral traps, baited with offal. Up to eight traps were deployed at a time. We calculated turtle CPUE by dividing the total number of turtles caught (regardless of species) by the total trap-hours. The number of trap-hours was similar across all four sites (average 1685 ± 7.6 SE total trap-hours).
Carp carcass decomposition
After the first and the second trapping rounds, we deployed whole carp carcasses at each site to measure carp decomposition rates depending on turtle accessibility. We placed each carp in a pre-weighed plastic box (340 × 230 × 120 mm), securing it with cable ties. Carp were made non-accessible to turtles in half of the deployments by covering the plastic boxes with 25 × 25 mm mesh (Supplementary Fig. S4). The mesh prevented turtle access to the carp, but was large enough to allow scavenging by crayfish (Cherax destructor) and other freshwater invertebrates. We tied each box to a brick and submerged the boxes around the four study sites ≥ 30 m away from each other, sunk at an average depth of 436 mm (± 13 SE). We used a total of 38 accessible and 40 non-accessible carp, split between our four study sites over two rounds (Supplementary Table S9). Every day, starting from day 2, the box and carp were weighed together with a digital scale. In all measurements, we calculated the wet mass of the carp by subtracting the box weight from the total weight. Carp carcasses were left in the wetlands for up to 10 days, or until they were fully consumed. All work was performed in accordance with DEWNR Permit M26663-1, PIRSA permits MP0085 and ME9902980, and The University of Sydney Animal Ethics Committee approval (project number 2017/1208), observing all relevant guidelines and regulations.
Statistical analysis
We analysed our data using RStudio 1.1.45633 (packages: “lme4” 1.1-2134, “MuMIn” 1.42.135). To assess whether turtles were important scavengers of our carcasses, we computed a linear mixed model testing whether turtle CPUE and carp access (yes/no) affected the rate of mass loss of the carp carcasses. The turtle CPUE values used were the average CPUE in the trapping round before and after each carp was deployed. We used the rate of mass loss per day as a dependent variable. We included the carp mass before deployment as an independent variable to account for initial mass variation, and we included study site as a random variable. We log-transformed all data before analysis. We assessed model fit by examining predicted versus residual and Q–Q plots, and testing the normality of residuals.
Mesocosm experiment
Turtle trapping and experiment procedure
We caught 20 adult male E. macquarii with fyke nets baited with offal at Hawkesview Lagoon, Albury, NSW, in November 2018. The E. macquarii captured at this site belong to the same genetic population as the E. macquarii trapped in South Australia36, therefore we expect behaviours to be similar between the two populations. We focussed on E. macquarii as this is the most common species in the Murray–Darling Basin, and fish carrion is an important part of its diet19,37. The turtles were transported by car to the Experimental Wetlands facility at Western Sydney University, in Richmond, NSW (Supplementary Fig. S5). This facility is comprised of 10 circular mesocosms (0.42 m depth × 2.1 m diameter) filled with 1,450 L of tap water. Each is an independent flow-through system where the water flow is regulated, and was maintained at 1998.6 ml/min (± 149.5 SE) throughout the experiment. Each mesocosm had two cement blocks for the turtles to bask on, and two plastic tunnels for shelter. The experiment was conducted for 40 days, therefore it is a short-term study (Supplementary Fig. S6). Upon arrival at the facility, we placed four adult male E. macquarii turtles in each of five random mesocosms, which means the experimental replication was 5. The remaining five mesocosms were controls and had no turtles. The four turtles comprised an average 5,376.6 g total biomass per pond, each being 3.46 m2. This would result in a biomass of 11,560 individuals/ha or 15,537 kg/ha on average. Kinosternon integrum has been estimated reaching densities of 20,000 individuals/ha in Sonora, Mexico, while Podocnemis vogli may reach 10,300 individuals/ha or 15,450 kg/ha in Venezuela, likely in temporary aggregations38. Emydura macquarii tend to congregate around food sources, therefore we considered four turtles per carp carrion as a realistic density. After 7 days of acclimation, we introduced one carp carcass to all mesocosms, and a second 6 days later. We used one ~ 1 kg carp at a time to simulate a density close to 3,144 kg carp/ha31. The turtles had continual access to the carp, which was their main food source throughout the experiment. The day all carp carcasses were fully eaten in all turtle mesocosms, we removed turtles from their mesocosms and released them at the point of capture. On the same day (day 10), we ended the data collection in their mesocosms, because any further change in water quality here would not have been related to carp decomposition. We continued the daily water quality measurements in the five control mesocosms until all carp were fully decomposed (day 32). This experimental design allowed us to collect water quality data without the need to add turtle food to the mesocosms, which would have biased our measurements once carp were removed from the turtle mesocosms.
We measured water temperature, dissolved oxygen, conductivity, turbidity, phosphate, and ammonia concentration in all mesocosms every morning from the day before the first carp introduction (see Supplementary Materials for equipment used). We also photographed the carcasses daily to estimate their decomposition rate based on a scale (Supplementary Table S10) designed after the decomposition stages described by Benninger et al.39 Due to the short transit time of fish matter in E. macquarii’s gut37, the effects of the turtles’ metabolic wastes on water quality are included in our experiment for carp 1. All work was performed in accordance with OEH Permit SL100401, DPI permit P09/0070-3.0, and Western Sydney University Animal Ethics Committee Animal Research Authority approval A12390, observing all relevant guidelines and regulations.
Statistical analysis
To assess whether the presence of turtles affected the decomposition of carp we computed a mixed linear model using the repeated measures PROC MIXED procedure using SAS (3.8 University Edition, SAS Institute Inc., Cary, NC, USA). For this model, days to total decomposition/removal was a dependent variable, turtle presence/absence was a fixed effect, and carp number (first or second) was a repeated fixed effect.
We used DO, conductivity, turbidity, phosphate, and ammonia to carry out a principal component analysis (PCA) using PROC PRINCOMP. We conducted a PCA because the parameters are a multivariate response and have potential to covary with each other, which would not be detected in univariate analyses. We considered a parameter loaded onto a PC when the absolute value of its eigenvector was > 0.300. If the same parameter loaded onto more than one PC, we considered it only on the PC where its eigenvector had a higher absolute value.
To test the effect of turtles scavenging on water quality, we computed general linear mixed models (GLMMs), using PCs as response variables, in PROC MIXED. We used a PC as response variable if its eigenvalue was greater than one (Kaiser criterion40). For each of these GLMMs, we included turtle presence (yes/no) and day number after the first carp introduction as fixed effects, water temperature and flow as covariates, and mesocosm ID as a random effect. We computed a model with full interactions first, and then, in absence of four- or three-way interactions, simplified the model to focus on main effects.
Finally, to test the effect of turtle scavenging on each water quality parameter, a GLMM was computed for each (logged) parameter that loaded onto a PC with eigenvalue > 1, i.e. dissolved oxygen, ammonia, turbidity, conductivity, phosphate. For these GLMMs, turtle presence and day number were fixed effects, water temperature and flow were covariates, and mesocosm ID was a random effect. More